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Graña, D., T. Gardella, and M. M. Susskind. "The effects of mutations in the ant promoter of phage P22 depend on context." Genetics 120, no. 2 (1988): 319–27. http://dx.doi.org/10.1093/genetics/120.2.319.
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Abstract Recombination was used to construct 22 two- or three-way combinations of down- and up-mutations in Pant, a strong, near-consensus promoter of phage P22. The relative strengths of these promoters in vivo were assayed by fusing them to an ant/lacZ gene fusion and measuring beta-galactosidase levels produced by lysogens carrying the fusions on single-copy prophages. The results of these assays show that the magnitude of the effect of a promoter mutation can vary considerably when its context is changed by the presence of another mutation. In addition, as Pant approaches conformity with the consensus promoter sequence, the up-mutations decrease promoter strength, even though the same mutations increase promoter strength in the presence of a down-mutation. These context effects imply that individual consensus base pairs cannot be considered to contribute to promoter strength independently.
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Parikh, Purvish M., J. Wadhwa, S. Minhas, et al. "Practical consensus recommendation on when to do BRCA testing." South Asian Journal of Cancer 07, no. 02 (2018): 106. http://dx.doi.org/10.4103/sajc.sajc_112_18.
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Abstract BRCA-mutation associated breast cancer and to future cancer risks and sensitivity to systemic therapies. Now that rapid genetic testing for BRCA1 and BRCA2 mutations is available, BRCA mutation status can be considered when making treatment and prevention decisions for BRCA testing, BRCA mutation carriers with breast cancer. Expert group used data from published literature, practical experience, and opinion of a large group of academic oncologists, to arrive at practical consensus recommendations for use by the community oncologists.
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Dong, Baijun, Bin Yang, Yonghong Li, et al. "Insights into Chinese prostate cancer germline gene mutation profile: HOXB13 G84E mutation is unsuitable for genetic testing." Journal of Clinical Oncology 38, no. 15_suppl (2020): e17515-e17515. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e17515.
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e17515 Background: Philadelphia Prostate Cancer Consensus Conference 2017 developed an expert consensus-driven working framework for comprehensive genetic evaluation of inherited PCA. However, the consensus was mainly based on data from Caucasian populations. Genetic differences in the PC molecular landscape between Asian and Caucasian men have been established. Whether Caucasian-based genetic information can be used to guide clinical practice in Chinese population needs further evidence. Methods: 1123 patients with confirmed prostate cancer admitted from March 2018 to August 2019 from 18 Chinese centers were included in this retrospective study. We sequenced the association of 50 gene with prostate cancer risk, clinical treatment implications and predisposition, focusing on DNA repair gene and genetic susceptibility genes pathogenic mutations in Philadelphia Prostate Cancer Consensus Conference. Only protein-truncating alterations (nonsense/stop-gains, frameshift insertions and deletions, and donor and acceptor splice-site mutations) were coded as pathogenic or likely pathogenic protein-truncating alterations. Results: Among all cases, DNA repair gene pathogenic mutations were found in 133 men (11.84%), including BRCA2 (62 [5.5%]), ATM (15 [1.3%]), PALB2 (11 [0.97%]), GEN1 (7 [0.62%]), BRCA1 (6 [0.53%]), MLH3 (4 [0.35%]), MUTYH (4 [0.35%]), PMS1 (4 [0.35%]), RAD50 (4 [0.35%]), ATR (3 [0.27%]), CHEK2 (3 [0.27%]), FANCD2 (3 [0.27%]) etc. Similar germline DRG mutation frequencies were observed between our cohort and Caucasian men. Noticeably, G84E mutation in HOXB13, a rare but recurrent missense mutation associated with a significantly increased risk of hereditary prostate cancer was not found in our cohort of patients. Furthermore, the frequency of HSD3B1 (1245C) allele in the Chinese patients is much lower than that in the Caucasian populations (11.7% vs 63%). Conclusions: Our study retrospectively analyzed germline mutation profile of prostate cancer in Chinese population. The frequency of HSD3B1 (1245C) allele varies across ethnic populations in spite of the similar DNA repair gene mutations rates. Considering the gene list should be tested based on clinical/familial scenarios from the Philadelphia Prostate Cancer Consensus Conference, a prevalence of certain mutations, G84E mutation in HOXB13 was unnecessary for genetic testing in Chinese population.
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Bergeron, Julie, Jose-Mario Capo-Chichi, Hubert Tsui, et al. "The Clinical Utility of FLT3 Mutation Testing in Acute Leukemia: A Canadian Consensus." Current Oncology 30, no. 12 (2023): 10410–36. http://dx.doi.org/10.3390/curroncol30120759.
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FMS-like tyrosine kinase 3 (FLT3) mutations are detected in approximately 20–30% of patients with acute myeloid leukemia (AML), with the presence of a FLT3 internal tandem duplication (FLT3-ITD) mutation being associated with an inferior outcome. Assessment of FLT3 mutational status is now essential to define optimal upfront treatment in both newly diagnosed and relapsed AML, to support post-induction allogeneic hematopoietic stem cell transplantation (alloSCT) decision-making, and to evaluate treatment response via measurable (minimal) residual disease (MRD) evaluation. In view of its importance in AML diagnosis and management, the Canadian Leukemia Study Group/Groupe canadien d’étude sur la leucémie (CLSG/GCEL) undertook the development of a consensus statement on the clinical utility of FLT3 mutation testing, as members reported considerable inter-center variability across Canada with respect to testing availability and timing of use, methodology, and interpretation. The CLSG/GCEL panel identified key clinical and hematopathological questions, including: (1) which patients should be tested for FLT3 mutations, and when?; (2) which is the preferred method for FLT3 mutation testing?; (3) what is the clinical relevance of FLT3-ITD size, insertion site, and number of distinct FLT3-ITDs?; (4) is there a role for FLT3 analysis in MRD assessment?; (5) what is the clinical relevance of the FLT3-ITD allelic burden?; and (6) how should results of FLT3 mutation testing be reported? The panel followed an evidence-based approach, taken together with Canadian clinical and laboratory experience and expertise, to create a consensus document to facilitate a more uniform approach to AML diagnosis and treatment across Canada.
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Amar, Laurence, Karel Pacak, Olivier Steichen, et al. "International consensus on initial screening and follow-up of asymptomatic SDHx mutation carriers." Nature Reviews Endocrinology 17, no. 7 (2021): 435–44. http://dx.doi.org/10.1038/s41574-021-00492-3.
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AbstractApproximately 20% of patients diagnosed with a phaeochromocytoma or paraganglioma carry a germline mutation in one of the succinate dehydrogenase (SDHx) genes (SDHA, SDHB, SDHC and SDHD), which encode the four subunits of the SDH enzyme. When a pathogenic SDHx mutation is identified in an affected patient, genetic counselling is proposed for first-degree relatives. Optimal initial evaluation and follow-up of people who are asymptomatic but might carry SDHx mutations have not yet been agreed. Thus, we established an international consensus algorithm of clinical, biochemical and imaging screening at diagnosis and during surveillance for both adults and children. An international panel of 29 experts from 12 countries was assembled, and the Delphi method was used to reach a consensus on 41 statements. This Consensus Statement covers a range of topics, including age of first genetic testing, appropriate biochemical and imaging tests for initial tumour screening and follow-up, screening for rare SDHx-related tumours and management of elderly people who have an SDHx mutation. This Consensus Statement focuses on the management of asymptomatic SDHx mutation carriers and provides clinicians with much-needed guidance. The standardization of practice will enable prospective studies in the near future.
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Kipling, D., and S. E. Kearsey. "Reversion of autonomously replicating sequence mutations in Saccharomyces cerevisiae: creation of a eucaryotic replication origin within procaryotic vector DNA." Molecular and Cellular Biology 10, no. 1 (1990): 265–72. http://dx.doi.org/10.1128/mcb.10.1.265-272.1990.
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To investigate how a defective replicon might acquire replication competence, we have studied the reversion of autonomously replicating sequence (ARS) mutations. By mutagenesis of a Saccharomyces cerevisiae plasmid lacking a functional origin of replication, we have obtained a series of cis-acting mutations which confer ARS activity on the plasmid. The original plasmid contained an ARS element inactivated by point mutation, but surprisingly only 1 of the 10 independent Ars+ revertants obtained shows a back mutation in this element. In the remainder of the revertants, sequence changes in the M13 vector DNA generate new ARSs. In two cases, a single nucleotide change results in an improved match to the ARS consensus, while six other cases show small duplications of vector sequence creating additional matches to the ARS consensus. These results suggest that changes in replication origin distribution may arise de novo by point mutation rather than by transposition of preexisting origin sequences.
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Kipling, D., and S. E. Kearsey. "Reversion of autonomously replicating sequence mutations in Saccharomyces cerevisiae: creation of a eucaryotic replication origin within procaryotic vector DNA." Molecular and Cellular Biology 10, no. 1 (1990): 265–72. http://dx.doi.org/10.1128/mcb.10.1.265.
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To investigate how a defective replicon might acquire replication competence, we have studied the reversion of autonomously replicating sequence (ARS) mutations. By mutagenesis of a Saccharomyces cerevisiae plasmid lacking a functional origin of replication, we have obtained a series of cis-acting mutations which confer ARS activity on the plasmid. The original plasmid contained an ARS element inactivated by point mutation, but surprisingly only 1 of the 10 independent Ars+ revertants obtained shows a back mutation in this element. In the remainder of the revertants, sequence changes in the M13 vector DNA generate new ARSs. In two cases, a single nucleotide change results in an improved match to the ARS consensus, while six other cases show small duplications of vector sequence creating additional matches to the ARS consensus. These results suggest that changes in replication origin distribution may arise de novo by point mutation rather than by transposition of preexisting origin sequences.
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Baer, Constance Regina, Niroshan Nadarajah, Claudia Haferlach, Wolfgang Kern, and Torsten Haferlach. "The Use of Unique Molecular Identifiers (UMIs) Strongly Improves Sequencing Detection Limits Allowing Earlier Detection of Small TP53 Mutated Clones in Leukemias." Blood 128, no. 22 (2016): 2027. http://dx.doi.org/10.1182/blood.v128.22.2027.2027.
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Abstract Background: TP53 mutations arise in a broad set of hematologic diseases and are associated with poor prognosis and therapy failure. Even small TP53 mutated clones were demonstrated to be of clinical relevance and therefore their early detection is mandatory. Mutations can occur throughout the entire gene (mainly exons 4-10) and include base exchanges, deletions and insertions. Next generation sequencing (NGS) generally detects mutations, which are present in at least 3% of sequences. The detection of mutations at burdens below 3% is still hampered by polymerase and sequencing errors. Especially true mutations caused by single base exchanges (missense-, nonsense- and splice site mutations) are difficult to distinguish from non-specific background. To overcome this limitation, individual molecules can be tagged by unique molecular identifiers (UMIs). UMIs are small random sequences added to each individual molecule before amplification. Building a consensus sequence out of all amplified products derived from one original DNA template, allows reconstructing the sequence of the initial molecule and thereby eliminates amplification errors in silico. Aim: 1) To evaluate reduction of non-specific background in NGS assays after using UMIs to build consensus sequences. 2) To use consensus sequencing to identify early subclones by backtracking of known TP53 mutations in CLL patients. Methods: We added eight random nucleotides as UMI to all reverse primers (design adapted from Peng, et al. 2015) and performed an initial primer extension step. In a subsequent PCR, regions of interest including UMIs were amplified and adapters were added for MiSeq sequencing (Illumina, San Diego, CA). We performed 119 sequencing assays, and analyzed results with a 1% detection limit. Consensus sequences were built using SeqNext 4.3 (JSI Medical Systems, Kippenheim, Germany). A median number of 6 (range: 2-115) reads/consensus read was obtained. Samples contained 66 previously identified mutations (47 single base exchanges; 14 small deletions; 5 small insertions), of which 29 had a burden of 3% or lower. These had been confirmed to be specific by independently repeated sequencing analysis or known in patients at multiple time points during follow-up. Results: We evaluated background signal at each position before consensus read building. On average 97.5% of bases had low-level non-specific background. At each individual position, 0.01-0.87% of reads deviated from the reference sequence (Figure A). Building consensus reads by combining all sequences derived from one original DNA molecule reduced the number of bases with low-level non-specific signal to an average of 18% (Figure B). We performed 119 sequencing analysis with a 1% detection limit, aiming to identify 66 known mutations and no non-specific deviations from the reference sequence. With both approaches, 63/66 mutations were detected and correlation of mutation burdens was high (R2=0.99; P<0.001, calculated by linear regression). Two mutations (1% and 2%) only reached the detection cutoff without consensus read building and one mutation only after consensus read building. Importantly, without using UMIs for consensus reads, in sum 88 non-specific deviations from the reference sequence (likely artifacts) were detectable with the 1% cutoff, while only two likely artifacts remained after consensus sequences building. Thus, the reduction of sequencing artifacts should allow using a 1% cutoff for mutation detection in future routine settings. Therefore, we conducted a backtracking using 31 of the above identified TP53 mutations detected in 15 CLL patients. Samples covered a median timeframe of 26 (range: 2-68) months. Using the previous 3% cutoff for mutation burden, we identified 8/31 (26%) mutations 2-55 months earlier (median: 4 months). Even more, using the adjusted 1% cutoff with UMIs allowed detecting 18/31 (58%) TP53 mutations earlier (2-55 months; median: 18 months). Conclusion: Including UMIs and building consensus sequences, 1) reduced background signal in silico and 2) allowed improving NGS detection limits. This is crucial for the identification of low burden mutations in TP53 and other genes, where small subclones can rapidly expand and have been shown to require early treatment intervention. Disclosures Baer: MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Yuryev, Anton, and Jeffry L. Corden. "Suppression Analysis Reveals a Functional Difference Between the Serines in Positions Two and Five in the Consensus Sequence of the C-Terminal Domain of Yeast RNA Polymerase II." Genetics 143, no. 2 (1996): 661–71. http://dx.doi.org/10.1093/genetics/143.2.661.
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Abstract The largest subunit of RNA polymerase II contains a repetitive C-terminal domain (CTD) consisting of tandem repeats of the consensus sequence TyrlSer2Pro3Thr4Ser5Pro6Ser7. Substitution of nonphosphe rylatable amino acids at positions two or five of the Saccharomyces cerevisiae CTD is lethal. We developed a selection ssytem for isolating suppressors of this lethal phenotype and cloned a gene, SCA1 (suppressor of CTD alanine), which complements recessive suppressors of lethal multiple-substitution mutations. A partial deletion of SCA1 (sca1Δ::hisG) suppresses alanine or glutamate substitutions at position two of the consensus CTD sequence, and a lethal CTD truncation mutation, but SCA1 deletion does not suppress alanine or glutamate substitutions at position five. SCA1 is identical to SRB9, a suppressor of a cold-sensitive CTD truncation mutation. Strains carrying dominant SRB mutations have the same suppression properties as a sca1Δ::hisG strain. These results reveal a functional difference between positions two and five of the consensus CTD heptapeptide repeat. The ability of SCA1 and SRB mutant alleles to suppress CTD truncation mutations suggest that substitutions at position two, but not at position five, cause a defect in RNA polymerase II function similar to that introduced by CTD truncation.
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Ahn, Eun Hyun, and Seung Hyuk Lee. "Detection of Low-Frequency Mutations and Identification of Heat-Induced Artifactual Mutations Using Duplex Sequencing." International Journal of Molecular Sciences 20, no. 1 (2019): 199. http://dx.doi.org/10.3390/ijms20010199.
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We present a genome-wide comparative and comprehensive analysis of three different sequencing methods (conventional next generation sequencing (NGS), tag-based single strand sequencing (e.g., SSCS), and Duplex Sequencing for investigating mitochondrial mutations in human breast epithelial cells. Duplex Sequencing produces a single strand consensus sequence (SSCS) and a duplex consensus sequence (DCS) analysis, respectively. Our study validates that although high-frequency mutations are detectable by all the three sequencing methods with the similar accuracy and reproducibility, rare (low-frequency) mutations are not accurately detectable by NGS and SSCS. Even with conservative bioinformatical modification to overcome the high error rate of NGS, the NGS frequency of rare mutations is 7.0 × 10−4. The frequency is reduced to 1.3 × 10−4 with SSCS and is further reduced to 1.0 × 10−5 using DCS. Rare mutation context spectra obtained from NGS significantly vary across independent experiments, and it is not possible to identify a dominant mutation context. In contrast, rare mutation context spectra are consistently similar in all independent DCS experiments. We have systematically identified heat-induced artifactual variants and corrected the artifacts using Duplex Sequencing. Specific sequence contexts were analyzed to examine the effects of neighboring bases on the accumulation of heat-induced artifactual variants. All of these artifacts are stochastically occurring rare mutations. C > A/G > T, a signature of oxidative damage, is the most increased (170-fold) heat-induced artifactual mutation type. Our results strongly support the claim that Duplex Sequencing accurately detects low-frequency mutations and identifies and corrects artifactual mutations introduced by heating during DNA preparation.
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Jaravine, Victor, James Balmford, Patrick Metzger, Melanie Boerries, Harald Binder, and Martin Boeker. "Annotation of Human Exome Gene Variants with Consensus Pathogenicity." Genes 11, no. 9 (2020): 1076. http://dx.doi.org/10.3390/genes11091076.
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A novel approach is developed to address the challenge of annotating with phenotypic effects those exome variants for which relevant empirical data are lacking or minimal. The predictive annotation method is implemented as a stacked ensemble of supervised base-learners, including distributed random forest and gradient boosting machines. Ensemble models were trained and cross-validated on evidence-based categorical variant effect annotations from the ClinVar database, and were applied to 84 million non-synonymous single nucleotide variants (SNVs). The consensus model combined 39 functional mutation impacts, cross-species conservation score, and gene indispensability score. The indispensability score, accounting for differences in variant pathogenicities including in essential and mutation-tolerant genes, considerably improved the predictions. The consensus combination is consistent with as many input scores as possible while minimizing false predictions. The input scores are ranked based on their ability to predict effects. The score rankings and categorical phenotypic variant effect predictions are aimed for direct use in clinical and biological applications to prioritize human exome variants and mutations.
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Wong, C., SE Antonarakis, SC Goff, et al. "Beta-thalassemia due to two novel nucleotide substitutions in consensus acceptor splice sequences of the beta-globin gene." Blood 73, no. 4 (1989): 914–18. http://dx.doi.org/10.1182/blood.v73.4.914.914.
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Abstract We have identified two novel RNA-splicing mutations affecting a critical nucleotide (nt) in the acceptor consensus sequences at both the IVS-1/exon 2 and IVS-2/exon 3 junctions of the human beta-globin gene. Both mutations are single nt substitutions, T to G and C to A, at position -3 adjacent to the invariant AG dinucleotide. For the IVS- 2/exon 3 mutation abnormal splicing into the cryptic splice site at IVS- 2 nt 579 is documented. Identification of these two mutations provides further support for the importance of the location of specific nucleotides within the consensus sequences in splice site selection and RNA processing.
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Wong, C., SE Antonarakis, SC Goff, et al. "Beta-thalassemia due to two novel nucleotide substitutions in consensus acceptor splice sequences of the beta-globin gene." Blood 73, no. 4 (1989): 914–18. http://dx.doi.org/10.1182/blood.v73.4.914.bloodjournal734914.
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We have identified two novel RNA-splicing mutations affecting a critical nucleotide (nt) in the acceptor consensus sequences at both the IVS-1/exon 2 and IVS-2/exon 3 junctions of the human beta-globin gene. Both mutations are single nt substitutions, T to G and C to A, at position -3 adjacent to the invariant AG dinucleotide. For the IVS- 2/exon 3 mutation abnormal splicing into the cryptic splice site at IVS- 2 nt 579 is documented. Identification of these two mutations provides further support for the importance of the location of specific nucleotides within the consensus sequences in splice site selection and RNA processing.
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Zhao, Linjie, Tanlin Sun, Jianfeng Pei, and Qi Ouyang. "Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis." Proceedings of the National Academy of Sciences 112, no. 30 (2015): E4046—E4054. http://dx.doi.org/10.1073/pnas.1502126112.
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It has been a consensus in cancer research that cancer is a disease caused primarily by genomic alterations, especially somatic mutations. However, the mechanism of mutation-induced oncogenesis is not fully understood. Here, we used the mitochondrial apoptotic pathway as a case study and performed a systematic analysis of integrating pathway dynamics with protein interaction kinetics to quantitatively investigate the causal molecular mechanism of mutation-induced oncogenesis. A mathematical model of the regulatory network was constructed to establish the functional role of dynamic bifurcation in the apoptotic process. The oncogenic mutation enrichment of each of the protein functional domains involved was found strongly correlated with the parameter sensitivity of the bifurcation point. We further dissected the causal mechanism underlying this correlation by evaluating the mutational influence on protein interaction kinetics using molecular dynamics simulation. We analyzed 29 matched mutant–wild-type and 16 matched SNP—wild-type protein systems. We found that the binding kinetics changes reflected by the changes of free energy changes induced by protein interaction mutations, which induce variations in the sensitive parameters of the bifurcation point, were a major cause of apoptosis pathway dysfunction, and mutations involved in sensitive interaction domains show high oncogenic potential. Our analysis provided a molecular basis for connecting protein mutations, protein interaction kinetics, network dynamics properties, and physiological function of a regulatory network. These insights provide a framework for coupling mutation genotype to tumorigenesis phenotype and help elucidate the logic of cancer initiation.
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Rogozin, Igor, Abiel Roche-Lima, Artem Lada, et al. "Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes." Cancers 11, no. 2 (2019): 211. http://dx.doi.org/10.3390/cancers11020211.
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Cancer genomes accumulate nucleotide sequence variations that number in the tens of thousands per genome. A prominent fraction of these mutations is thought to arise as a consequence of the off-target activity of DNA/RNA editing cytosine deaminases. These enzymes, collectively called activation induced deaminase (AID)/APOBECs, deaminate cytosines located within defined DNA sequence contexts. The resulting changes of the original C:G pair in these contexts (mutational signatures) provide indirect evidence for the participation of specific cytosine deaminases in a given cancer type. The conventional method used for the analysis of mutable motifs is the consensus approach. Here, for the first time, we have adopted the frequently used weight matrix (sequence profile) approach for the analysis of mutagenesis and provide evidence for this method being a more precise descriptor of mutations than the sequence consensus approach. We confirm that while mutational footprints of APOBEC1, APOBEC3A, APOBEC3B, and APOBEC3G are prominent in many cancers, mutable motifs characteristic of the action of the humoral immune response somatic hypermutation enzyme, AID, are the most widespread feature of somatic mutation spectra attributable to deaminases in cancer genomes. Overall, the weight matrix approach reveals that somatic mutations are significantly associated with at least one AID/APOBEC mutable motif in all studied cancers.
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Scherer, Florian, Cristina Bertinetti-Lapatki, Marcus Duehren-von Minden, Joachim Boehm, and Hendrik J. Veelken. "Quantitative Analysis of AID Expression and Somatic Hypermutation Identifies Isotype-Switched and Non-Switched Follicular Lymphomas As Distinct Biological Subgroups,." Blood 118, no. 21 (2011): 3666. http://dx.doi.org/10.1182/blood.v118.21.3666.3666.
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Abstract Abstract 3666 Introduction: Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation (SHM) and class switch recombination (CSR) in B cells. Deamination of cytosine residues by AID leads to double-strand breaks and point mutations in immunoglobulin (Ig) genes by subsequent mechanisms. Physiological AID expression is tightly regulated and restricted to germinal center (GC) B cells. AID acts not exclusively on Ig loci but effects aberrant SHM (ASHM) throughout the genome (Liu et al., 2008). High-fidelity mutation repair mechanisms protect most non-Ig AID target genes against mutation accumulation. Some genes including BCL6, the most highly mutated non-Ig gene, also undergo error-prone repair and consequently accumulate aberrant somatic mutations (Liu et al., 2009). In contrast to normal B cells, AID is constitutively expressed in follicular lymphoma (FL) and diffuse large B cell lymphoma (DLBCL) (Greeve et al., 2003; Lossos et al., 2004). These lymphoma entities are derived from GC B cells and continue to accumulate somatic mutations in the immunoglobulin heavy variable region (IGHV) through ongoing SHM (Kosmas et al., 1998). In FL, the 5` noncoding region of BCL6 is altered by aberrant somatic mutations. Histological transformation of FL to DLBCL is associated with ASHM of this gene segment (Pasqualucci et al., 2001; Lossos et al., 2000). To further elucidate the role of AID in FL pathogenesis, we performed precise quantitative correlations between AID expression, frequency of ongoing SHM of IGHV and ASHM of BCL6 in 16 isotype-switched (IgG-expressing) and 23 non-switched (IgM-expressing) FL. Methods: AID expression was measured by quantitative real-time PCR. SHM of IGHV and ASHM of the 5` noncoding region of BCL6 were determined by PCR-based cloning and sequencing, followed by alignment with their consensus and germ-line sequences, respectively. Detected mutations were further categorized into consensus mutations, defined by their presence in the majority of clones, and sporadic mutations, defined by their presence in the minority of clones. Consensus and sporadic mutations are taken to represent previous and current AID activity, respectively. Results: All FL had readily detectable AID transcripts, albeit at highly variable levels. Overall, AID expression levels did not differ between isotype-switched and non-switched FL (p=0.99). Sporadic IGHV mutations were slightly more prevalent in switched FL (p=0.026). Consensus IGHV mutations (p=0.99) and both sporadic and consensus mutations in BCL6 did not differ between the FL subgroups (p=0.91 and p=0.77, respectively). In non-switched FL, AID expression levels were positively correlated with sporadic (r=0.44, p=0.041) and consensus IGHV mutations (r=0.42, p=0.049) and sporadic BCL6 mutations (r=0.51, p=0.016). Consensus mutations in BCL6 were independent of AID levels (r=0.23, p=0.30). In switched FL, AID expression was inversely correlated with consensus IGHV mutations (r= -0.71, p=0.004). There was no correlation between AID expression and sporadic IGHV mutations (r= -0.055, p=0.85), nor with sporadic or consensus BCL6 mutations (r=0.056, p=0.84 and r= -0.058, p=0.82, respectively). Conclusions: Only in non-switched FL, AID expression levels determine its enzymatic activity with respect to expected mutations in its physiological and unphysiological target genes IGHV and BCL6 in a manner that appears to be quantitatively independent from AID cofactors or repair mechanisms. In contrast, the rates of ongoing IGHV mutations and of ASHM in isotype-switched FL are not directly dependent on AID expression levels. The unexpected inverse correlation to consensus IGHV mutations points to efficient high-fidelity mutation repair or alternative mechanisms that suppress AID activity in isotype-switched FL. Therefore, our data demonstrate hitherto unrecognized biological differences between isotype-switched and non-switched FL. These results predict that the combination of IgM isotype with high AID expression define an FL subgroup that is genetically less stable over time than their IgG-expressing or AID low-expressing counterparts. As a consequence, we postulate that continuous AID activity and the resulting ASHM of BCL6 and perhaps other proto-oncogenes cause a more aggressive clinical behaviour and an inferior prognosis in this FL subgroup, including a predisposition to histological transformation. Disclosures: No relevant conflicts of interest to declare.
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Thunnissen, Erik, Judith V. M. G. Bovée, Hans Bruinsma, et al. "EGFR and KRAS quality assurance schemes in pathology: generating normative data for molecular predictive marker analysis in targeted therapy." Journal of Clinical Pathology 64, no. 10 (2011): 884–92. http://dx.doi.org/10.1136/jclinpath-2011-200163.
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IntroductionThe aim of this study was to compare the reproducibility of epidermal growth factor receptor (EGFR) immunohistochemistry (IHC), EGFR gene amplification analysis, and EGFR and KRAS mutation analysis among different laboratories performing routine diagnostic analyses in pathology in The Netherlands, and to generate normative data.MethodsIn 2008, IHC, in-situ hybridisation (ISH) for EGFR, and mutation analysis for EGFR and KRAS were tested. Tissue microarray sections were distributed for IHC and ISH, and tissue sections and isolated DNA with known mutations were distributed for mutation analysis. In 2009, ISH and mutation analysis were evaluated. False-negative and false-positive results were defined as different from the consensus, and sensitivity and specificity were estimated.ResultsIn 2008, eight laboratories participated in the IHC ring study. In only 4/17 cases (23%) a consensus score of ≥75% was reached, indicating that this analysis was not sufficiently reliable to be applied in clinical practice. For EGFR ISH, and EGFR and KRAS mutation analysis, an interpretable result (success rate) was obtained in ≥97% of the cases, with mean sensitivity ≥96% and specificity ≥95%. For small sample proficiency testing, a norm was established defining outlier laboratories with unsatisfactory performance.ConclusionsThe result of EGFR IHC is not a suitable criterion for reliably selecting patients for anti-EGFR treatment. In contrast, molecular diagnostic methods for EGFR and KRAS mutation detection and EGFR ISH may be reliably performed with high accuracy, allowing treatment decisions for lung cancer.
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Gandy, Lisa M., Jordan Gumm, Amanda L. Blackford, Elana J. Fertig, and Luis A. Diaz. "A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation." Cancer Informatics 16 (January 1, 2017): 117693511771194. http://dx.doi.org/10.1177/1176935117711940.
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ClinicalTrials.org is a popular portal which physicians use to find clinical trials for their patients. However, the current setup of ClinicalTrials.org makes it difficult for oncologists to locate clinical trials for patients based on mutational status. We present CTMine, a system that mines ClinicalTrials.org for clinical trials per cancer mutation and displays the trials in a user-friendly Web application. The system currently lists clinical trials for 6 common genes (ALK, BRAF, ERBB2, EGFR, KIT, and KRAS). The current machine learning model used to identify relevant clinical trials focusing on the above gene mutations had an average 88% precision/recall. As part of this analysis, we compared human versus machine and found that oncologists were unable to reach a consensus on whether a clinical trial mined by CTMine was “relevant” per gene mutation, a finding that highlights an important topic which deems future exploration.
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Palladino, F., and H. L. Klein. "Analysis of mitotic and meiotic defects in Saccharomyces cerevisiae SRS2 DNA helicase mutants." Genetics 132, no. 1 (1992): 23–37. http://dx.doi.org/10.1093/genetics/132.1.23.
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Abstract The hyper-gene conversion srs2-101 mutation of the SRS2 DNA helicase gene of Saccharomyces cerevisiae has been reported to suppress the UV sensitivity of rad18 mutants. New alleles of SRS2 were recovered using this suppressor phenotype. The alleles have been characterized with respect to suppression of rad18 UV sensitivity, hyperrecombination, reduction of meiotic viability, and definition of the mutational change within the SRS2 gene. Variability in the degree of rad18 suppression and hyperrecombination were found. The alleles that showed the severest effects were found to be missense mutations within the consensus domains of the DNA helicase family of proteins. The effect of mutations in domains I (ATP-binding) and V (proposed DNA binding) are reported. Some alleles of SRS2 reduce spore viability to 50% of wild-type levels. This phenotype is not bypassed by spo13 mutation. Although the srs2 homozygous diploids strains undergo normal commitment to meiotic recombination, this event is delayed by several hours in the mutant strains and the strains appear to stall in the progression from meiosis I to meiosis II.
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Rozen, F., J. Pelletier, H. Trachsel, and N. Sonenberg. "A lysine substitution in the ATP-binding site of eucaryotic initiation factor 4A abrogates nucleotide-binding activity." Molecular and Cellular Biology 9, no. 9 (1989): 4061–63. http://dx.doi.org/10.1128/mcb.9.9.4061-4063.1989.
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Eucaryotic initiation factor 4A (eIF-4A) is a member of a family of proteins believed to be involved in the ATP-dependent melting of RNA secondary structure. These proteins contain a derivative of the consensus ATP-binding site AXXGXGKT. To assess the importance of the consensus amino acid sequence in eIF-4A for ATP binding, we mutated the consensus amino-proximal glycine and lysine to isoleucine and asparagine, respectively. The effect of the mutations was examined by UV-induced cross-linking of [alpha-32P]dATP to eIF-4A. Mutation of the lysine residue (but not of the glycine residue) resulted in the loss of [alpha-32P]dATP cross-linking to eIF-4A, suggesting that the lysine is an important determinant in ATP binding to eIF-4A.
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Rozen, F., J. Pelletier, H. Trachsel, and N. Sonenberg. "A lysine substitution in the ATP-binding site of eucaryotic initiation factor 4A abrogates nucleotide-binding activity." Molecular and Cellular Biology 9, no. 9 (1989): 4061–63. http://dx.doi.org/10.1128/mcb.9.9.4061.
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Eucaryotic initiation factor 4A (eIF-4A) is a member of a family of proteins believed to be involved in the ATP-dependent melting of RNA secondary structure. These proteins contain a derivative of the consensus ATP-binding site AXXGXGKT. To assess the importance of the consensus amino acid sequence in eIF-4A for ATP binding, we mutated the consensus amino-proximal glycine and lysine to isoleucine and asparagine, respectively. The effect of the mutations was examined by UV-induced cross-linking of [alpha-32P]dATP to eIF-4A. Mutation of the lysine residue (but not of the glycine residue) resulted in the loss of [alpha-32P]dATP cross-linking to eIF-4A, suggesting that the lysine is an important determinant in ATP binding to eIF-4A.
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Yaung, Stephanie J., Jian Li, Adeline Pek, Lili Niu, John F. Palma, and Maximilian Schmid. "Evaluation of a regularly updated knowledge base for curation of somatic mutations detected in whole exomes of melanoma and lung, colorectal, and breast cancers." Journal of Clinical Oncology 38, no. 15_suppl (2020): e14072-e14072. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e14072.
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e14072 Background: Evolving medical guidelines and complex multi-variant data from next-generation sequencing (NGS) testing of cancer samples make routine clinical interpretation of somatic variants challenging. We assessed the ability of NAVIFY(R) Mutation Profiler*, a CE-IVD somatic variant interpretation tool, to yield accurate time- and geography-specific clinical content on 2511 samples from The Cancer Genome Atlas (TCGA) across six solid tumor types. Methods: Whole exomes from lung adenocarcinoma (n = 469), lung squamous cell carcinoma (n = 325), colon adenocarcinoma (n = 368), rectum adenocarcinoma (n = 149), breast invasive carcinoma (n = 806), and skin cutaneous melanoma (n = 394) cases were analyzed. We utilized TCGA data from the Multi-Center Mutation Calling in Multiple Cancers (MC3) project to obtain consensus calling results of single nucleotide variants and indels. The open-access Mutation Annotation Format (MAF) file (v0.2.8) that stores variant calls was lifted to human reference genome GRCh38 and converted to individual Variant Call Format (VCF) files per case. VCF files were uploaded to NAVIFY Mutation Profiler to interpret actionable mutations according to a highly curated and up-to-date knowledge base (Roche Content v2.13.0 released December 6, 2019). We further assessed the accuracy of interpreting co-occurrences of actionable mutations. Results: Over 1.24 million somatic mutations across 20,590 genes were assessed with NAVIFY Mutation Profiler, which reported tier classifications of variants based on consensus recommendations from AMP, ASCO, CAP, and ACMG. 86% of cases had variants of strong (Tier I-A or I-B) or potential (Tier II-C or II-D) clinical significance; 56% of these cases had Tier I classifications, supported by robust clinical evidence. Potentially actionable variant-variant interactions were found in 14% of cases. The tool also identified appropriate tier classifications by geographic region in accordance with local medical guidelines. Conclusions: To benchmark against other tools, we utilized available exome data from TCGA MC3 to assess NAVIFY Mutation Profiler. While this study likely underestimates the fraction of cases with actionable mutations, given that copy number alterations or rearrangements are also present in TCGA samples, we found a higher yield of potentially actionable annotation than other published methods. * This product has not been evaluated by the Food and Drug Administration and is not commercially available in the United States.
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Anna, Abramowicz, and Gos Monika. "Splicing mutations in human genetic disorders: examples, detection, and confirmation." Journal of Applied Genetics 59, no. 3 (2018): 253–68. http://dx.doi.org/10.1007/s13353-018-0444-7.
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Abstract Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus “cis” sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones. Usually such mutations result in errors during the splicing process and may lead to improper intron removal and thus cause alterations of the open reading frame. Recent research has underlined the abundance and importance of splicing mutations in the etiology of inherited diseases. The application of modern techniques allowed to identify synonymous and nonsynonymous variants as well as deep intronic mutations that affected pre-mRNA splicing. The bioinformatic algorithms can be applied as a tool to assess the possible effect of the identified changes. However, it should be underlined that the results of such tests are only predictive, and the exact effect of the specific mutation should be verified in functional studies. This article summarizes the current knowledge about the “splicing mutations” and methods that help to identify such changes in clinical diagnosis.
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McGowan, Francis. "Services de base et libéralisation : un consensus en mutation." L Economie politique 24, no. 4 (2004): 59. http://dx.doi.org/10.3917/leco.024.0059.
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Hamza, Noha M., Daryl L. Essam, and Ruhul A. Sarker. "Constraint Consensus Mutation-Based Differential Evolution for Constrained Optimization." IEEE Transactions on Evolutionary Computation 20, no. 3 (2016): 447–59. http://dx.doi.org/10.1109/tevc.2015.2477402.
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Goode, David L., Sally M. Hunter, Maria A. Doyle, et al. "A simple consensus approach improves somatic mutation prediction accuracy." Genome Medicine 5, no. 9 (2013): 90. http://dx.doi.org/10.1186/gm494.
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Budczies, Jan, Eva Romanovsky, Klaus Kluck, et al. "Abstract 2607: Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis." Cancer Research 83, no. 7_Supplement (2023): 2607. http://dx.doi.org/10.1158/1538-7445.am2023-2607.
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Abstract TP53 mutations are the most common single gene alteration in human cancer with diagnostic and prognostic implications in some cancer types. While no TP53-targeting therapeutics have been approved in the USA or Europe yet, drugs tailored to specific TP53 mutations, restoring the functionality of mutated TP53 (TP53mut), and protecting TP53 from negative regulation are being explored in preclinical studies and clinical trials. We performed a comprehensive mRNA expression analysis in 24 cancer types of the TCGA to extract (i) a consensus expression signature shared across TP53 mutation types and cancer types, (ii) differential gene expression patterns between different TP53 mutation types such as LOF, GOF, as well as dominant-negative mutations, and (iii) cancer types specific gene expression patterns. Mutational hotspots showed a similar pattern across cancer types, but at the same time prevalence was significantly different between cancer types for about half of the most prevalent hotspots. Both can be explained in part by the mutational processes operational for example the clock-like process behind SBS1 that is operational across cancer types and aflatoxin exposure assocated with SBS24 that ist operational in liver hepatocellular carcinoma. Virtually no genes were differential between tumors harboring different types of TP53 mutations in none of the cancer types, while hundreds of genes were over- and underexpressed in TP53mut compared to TP53wt tumors. A consensus gene list of 178 common over- and 32 common underexpressed genes was shared between at least two-thirds of the 24 cancer types. Analysis of the immune tumor microenvironment revealed exclusively decreased immune cell populations in the TP53mut tumors in six, a mixed pattern in four, exclusively increased immune cell populations in two, and no significant alterations in 20 cancer subtypes. The analysis of a large cohort of human tumors complements results from experimental studies and support the development of novel strategies for therapeutic targeting of TP53mut. Citation Format: Jan Budczies, Eva Romanovsky, Klaus Kluck, Iordanis Ourailidis, Michael Menzel, Susanne Beck, Markus Ball, Daniel Kazdal, Petros Christopoulos, Peter Schirmacher, Thorsten Stiewe, Albrecht Stenzinger. Homogenous TP53mut-associated tumor biology across mutation and cancer types revealed by comprehensive mRNA expression analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2607.
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Kara, Osman, and Tayfun Elibol. "Two cases of Chronic Neutrophilic Leukemia were successfully treated with Allogeneic Stem Cell Transplantation." Medical Science and Discovery 9, no. 6 (2022): 375–77. http://dx.doi.org/10.36472/msd.v9i6.750.
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Objective: Chronic Neutrophilic Leukemia (CNL) is a rarely seen myeloproliferative neoplasia (MPN) in which the BCR-ABL1 gene mutation is negative, and is characterized by persistent neutrophilic proliferation in the bloodstream and granulocytic hyperplasia in the bone marrow. CNL is usually diagnosed incidentally in asymptomatic individuals with persistent neutrophilic leukocytosis. When genetically examined, BCR-ABL1 fusion gene, JAK-2 V617F, and exon12 mutations, CALR mutations, PDGFRA-B, FGRF1 mutations are all not detected, while CSF3R mutation is observed in most of the cases. The WHO-2016 classification determined the presence of CSF3R T618I and other activating CSF3R mutations as diagnostic criteria. While the prognosis is poor in CNL cases with the CSF3R T618I mutation, it is more moderate in the presence of other CSF3R mutations. The average life expectancy is 21-30 months, and 5-year survival rates are around 28%. Although no treatment modality provides an average survival advantage other than hematopoietic stem cell transplantation (HSCT), there is no accepted 'standard of care' consensus. HSCT procedures performed in CNL cases are limited in the literature. Case: In this study, we presented two cases of CNL who were successfully treated with allogeneic stem cell transplantation and cured.
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Nakahara, Yoshifumi, Hajime Tsuji, Katsumi Nakagawa, et al. "Genetic Analysis in Japanese Kindreds of Congenital Type I Antithrombin Deficiency Causing Thrombosis." Thrombosis and Haemostasis 77, no. 04 (1997): 616–19. http://dx.doi.org/10.1055/s-0038-1656021.
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SummaryWe have identified two novel minor deletions (case 1; -TA or -AT at nucleotide 9831-3 in exon 5 and case 2; -A at nucleotide 7640-1 in exon 4), one novel nonsense mutation (case 3; TAT to TAA at nucleotide 7491 in exon 4), and one recurrent nonsense mutation (case 4; CGA to TGA at nucleotide 5381 in exon 3A) in Japanease kindreds with congenital type I antithrombin deficiency. The deletion detected in case 1 represented a symmetric element (CTCTGTCTC) and possessed a direct repeat (CTCTATGTCTC). The deletion in case 2 was recognized in a consensus sequence (TGAAT) and possessed a direct repeat (GATGAA). The nonsense mutation in case 3 formed a palindrome (CCGTTAACGG) and that in case 4 was caused hy a CpG dinucleotide mutation. These results confirm that the mutations of congenital type I antithrombin deficiency are not random events but are influenced strongly by DNA sequences.
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Moss, Tyler J., Yuan Qi, Liu Xi, et al. "Comprehensive genomic characterization of upper tract urothelial carcinoma (UTUC)." Journal of Clinical Oncology 35, no. 6_suppl (2017): 375. http://dx.doi.org/10.1200/jco.2017.35.6_suppl.375.
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375 Background: Integrated analysis of UTUC was performed to characterize the genomic landscape of UTUC and provide insights into biology. Methods: 31 untreated samples underwent WES, RNAseq, and RPPA. Consensus mutation calls from independent pipelines of 2 centers identified gene expression clusters using unsupervised consensus hierarchical clustering (UCHC). Results: Clinical data are shown in the Table. WES identified mutations in FGFR3 (74.1%; 92% low grade, 60% high grade), KMT2D (44.4%), PIK3CA (25.9%), TP53 (22.2%). APOBEC and CpG signatures were identified. Expressed marker genes from bladder TCGA were not associated with molecular subtypes in this study. UCHC of RNAseq segregated samples into 4 molecular subtypes. Cluster 1: no PIK3CA mutations; enriched for nonsmokers, high grade non-muscle invasive tumors, high recurrence rates and favorable survival. Cluster 2: 100% FGFR3 mutations; enriched for low grade, noninvasive disease, no bladder recurrences. Cluster 3: 100% FGFR3 mutations, 71% PIK3CA, no TP53 mutations; high tobacco use and bladder recurrence (62.5%); tumors all non-muscle invasive. Cluster 4: KMT2D (62.5%), FGFR3 (50%), TP53 (50%) mutations, no PIK3CA mutations; enriched for high grade, muscle-invasive disease, tobacco use, CIS, reduced survival; novel fusion of SH3KBP1-CNTNAP5 was identified, with high expression levels in the sample. Conclusions: We show mutations in UTUC occurring at differing frequencies and subtypes than bladder cancer. Novel fusion SH3KBP1 regulates RTK signaling and acts to recycle TGFβ receptors. Further studies are needed to validate the described subtypes, explore their responses to therapy, and better define the novel fusion mutation. [Table: see text]
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Wang, Tao-Yeuan, and Chi-Kuan Chen. "Identification of real-time PCR-negative EGFR mutations by direct sequencing test." Journal of Clinical Oncology 31, no. 15_suppl (2013): e22118-e22118. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e22118.
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e22118 Background: High percentage of patients with non-small cell lung cancer (NSCLC) has EGFR activating mutations in Taiwan and responses to EGFR inhibitors such as Tarceva (1, 2, 3). Timely molecular diagnosis is critical and molecular testing should be performed before treatment for the individual patient. It is important to develop an effective molecular diagnostic method for accurately detecting mutations and preventing false positive results. Therefore, we used a universal genetic detecting method (FemtoPath) to increase sensitivity of gene mutation detection and improve the sensitivity limitation (0.1%). Our previous reports indicated that FemtoPath/direct sequencing test is more sensitive, accurate and inexpensive than Cobas KRAS real- time PCR mutation test. Methods: In this study, we compared two molecular testing methods for the detection of EGFR mutation; the direct sequencing and the real-time PCR. Results: FemtoPath EGFR direct sequencing test identified mutations in 57 of the 73 tumors (77.03%) and Cobas EGFR mutation test identifies mutations in 53 of the 73 tumors (72.97%). Six negative results obtained by Real-Time PCR test were re-confirmed to be positive by direct sequencing test. From the results above, FemtoPath/direct sequencing test not only accurately detected all of the mutations, but also identified mutations adjacent toexons 18, 19, 20 and 21 of the EGFR gene. In 52 consensus cases of EGFR mutation obtained from both methods, there were 10 major discrepancies including two S768, four Exon 19 deletion, one L858, five T790, and one exon 20 insertion in this experiment. Conclusions: FemtoPath/direct sequencing test has lower invalid rate than Real-Time PCR test while fewer sample amount was required with increased detection efficiency of unknown mutation site.
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CAPRIOLI, JESSICA, PAOLA BETTINAGLIO, PETER F. ZIPFEL, et al. "The Molecular Basis of Familial Hemolytic Uremic Syndrome: Mutation Analysis of Factor H Gene Reveals a Hot Spot in Short Consensus Repeat 20." Journal of the American Society of Nephrology 12, no. 2 (2001): 297–307. http://dx.doi.org/10.1681/asn.v122297.
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Abstract. The aim of the present study was to clarify whether factor H mutations were involved in genetic predisposition to hemolytic uremic syndrome, by performing linkage and mutation studies in a large number of patients from those referred to the Italian Registry for Recurrent and Familial HUS/TTP. PCR and Western blot analyses were conducted to characterize the biochemical consequences of the mutations. Five mutations in the factor H gene were identified. Three, identified in two families and in a sporadic case, are heterozygous point mutations within the most C-terminal short consensus repeat 20 (SCR20) of factor H, resulting in single amino acid substitutions. The other two mutations introduce premature stop codons that interrupt the translation of factor H. A heterozygous nonsense mutation was identified in SCR8 in one family, and a homozygous 24-bp deletion within SCR20 was identified in a Bedouin family with a recessive mode of inheritance. Reverse transcription-PCR analysis of cDNA from peripheral blood leukocytes from the Bedouin family showed that the deletion lowered factor H mRNA levels. Although heterozygous mutations were associated with normal factor H levels and incomplete penetrance of the disease, the homozygous mutation in the Bedouin family resulted in severe reduction of factor H levels accompanied by very early disease onset. These data provide compelling molecular evidence that genetically determined deficiencies in factor H are involved in both autosomal-dominant and autosomal-recessive hemolytic uremic syndrome and identify SCR20 as a hot spot for mutations in the disease. The mutations identified here give an important hint to the relevance of the C-terminus of factor H in the control of the alternative complement activation pathway.
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Malhotra, Hemant, Pradnya Kowtal, Nikita Mehra, et al. "Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology." JCO Global Oncology, no. 6 (September 2020): 991–1008. http://dx.doi.org/10.1200/jgo.19.00381.
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PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Press, Richard D., Stephanie G. Willis, Jennifer Laudadio, Michael J. Mauro, and Michael W. N. Deininger. "Determining the rise in BCR-ABL RNA that optimally predicts a kinase domain mutation in patients with chronic myeloid leukemia on imatinib." Blood 114, no. 13 (2009): 2598–605. http://dx.doi.org/10.1182/blood-2008-08-173674.
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AbstractIn imatinib-treated chronic myeloid leukemia (CML), secondary drug resistance is often caused by mutations in the BCR-ABL kinase domain (KD). As alternative therapies are available for imatinib resistance, early identification of mutations may prevent disease progression. Because most patients are routinely monitored by BCR-ABL quantitative polymerase chain reaction (PCR), it is important to define the optimal increase in BCR-ABL that should trigger mutation testing. Expert panels have provisionally recommended a 10-fold BCR-ABL increase as the trigger for mutation screening, acknowledging the lack of consensus. To address this question, we monitored 150 CML patients by quantitative PCR and DNA sequencing. Thirty-five different mutations were identified in 53 patients, and, during 22.5 months (median) of follow-up after sequencing, mutations were significantly predictive of shorter progression-free survival. An unbiased receiver operating characteristic analysis identified a 2.6-fold increase in BCR-ABL RNA as the optimal cutoff for predicting a concomitant KD mutation, with a sensitivity of 77% (94% if including subsequent samples). The 2.6-fold threshold approximated the analytic precision limit of our PCR assay. In contrast, transcript rise cutoffs of 5-fold or greater had poor diagnostic sensitivity and no significant association with mutations. We conclude that the currently recommended 10-fold threshold to trigger mutation screening is insensitive and not universally applicable.
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Xu, Chunwei, Bin Lian, Juanjuan Ou, et al. "Expert Consensus on the Diagnosis and Treatment of FGFR Gene-Altered Solid Tumors." Global Medical Genetics 11, no. 04 (2024): 330–43. http://dx.doi.org/10.1055/s-0044-1790230.
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AbstractThe fibroblast growth factor receptor (FGFR) is a crucial receptor tyrosine kinase involved in essential biological processes, including growth, development, and tissue repair. However, FGFR gene mutations, including amplification, fusion, and mutation, can disrupt epigenetics, transcriptional regulation, and tumor microenvironment interactions, leading to cancer development. Targeting these kinase mutations with small molecule drugs or antibodies has shown clinical benefits. For example, erdafitinib is approved for treating locally advanced or metastatic urothelial cancer patients with FGFR2/FGFR3 mutations, and pemigatinib is approved for treating cholangiocarcinoma with FGFR2 fusion/rearrangement. Effective screening of FGFR variant patients is crucial for the clinical application of FGFR inhibitors. Various detection methods, such as polymerase chain reaction, next-generation sequencing, fluorescence in situ hybridization, and immunohistochemistry, are available, and their selection should be based on diagnostic and treatment decision-making needs. Our developed expert consensus aims to standardize the diagnosis and treatment process for FGFR gene mutations and facilitate the practical application of FGFR inhibitors in clinical practice.
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McGlennen, Ronald C., and Nigel S. Key. "Clinical and Laboratory Management of the Prothrombin G20210A Mutation." Archives of Pathology & Laboratory Medicine 126, no. 11 (2002): 1319–25. http://dx.doi.org/10.5858/2002-126-1319-calmot.
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Abstract Objective.—To make recommendations regarding the appropriate evaluation for the prothrombin G20210A mutation, as reflected by published evidence and the consensus opinion of recognized experts in the field. Data Sources.—Review of the medical literature, primarily since 1996. Data Extraction and Synthesis.—After an initial assessment of the literature, key points defining the condition, and review of the clinical study design, a draft manuscript was prepared and circulated to every participant in the College of American Pathologists Conference on Diagnostic Issues in Thrombophilia before the meeting. Each of the key points and associated recommendations were then presented for discussion at the conference. Recommendations were accepted if a consensus of 70% of experts attending the conference was reached. The results of the discussion were used to revise the manuscript into its final form. Conclusions.—Consensus was reached on several recommendations concerning the criteria for testing for the prothrombin G20210A mutation and for the method of testing. First, a major point of consensus was that the prothrombin G20210A mutation is a significant risk factor for venous thromboembolism (VTE) and that testing should be considered in the initial evaluation of suspected inherited thrombophilia. Second, although several analytic methods are commonly used for genetic testing for the prothrombin mutation, all are generally robust and reliable. The recommendations for testing for the prothrombin mutation parallel those for the factor V Leiden mutation and include patients with a history of recurrent VTE, a first episode of VTE before the age of 50 years, a history of an unprovoked VTE at any age, thromboses in unusual anatomic sites, or an affected first-degree relative with VTE. A history of VTE related to pregnancy or estrogen use and unexplained pregnancy loss during the second or third trimesters were also considered to be indications for testing. Other scenarios remain controversial or not recommended, including general population screening.
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Prashantha Karunakar, Padmini Arunkumar, Kumar Sankaran, and Shivangi Naik. "Predicting Pathogenic Missense Mutations in the Human c-MET Oncogene Using a Nucleotide Scoring Functio." International Journal of Fundamental and Applied Sciences (IJFAS) 7, no. 4 (2018): 73–76. http://dx.doi.org/10.59415/ijfas.v7i4.127.
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Background: Many nucleotide variations in the human genome remain uncharacterized even more than ten years after the first draft was published. Objective: A three-parameter nucleotide-based scoring function was designed to predict the possible pathogenicity of 163 uncharacterized but validated missense mutations of the c-MET oncogene. Methodology: The parameters used by the scoring function were: surrounding consensus regions in a multiple sequence alignment of the human c-MET oncogene and five orthologous variants, inter-species allele frequency of each human missense mutation, and the nature of the mutation. Results: Out of 163 variants of unknown significance, 99 and 52 mutations were characterized as likely pathogenic and pathogenic respectively. An analysis of nine variants of known significance revealed that this scoring function could classify six out of nine (66.67%) variants with a reasonable accuracy.
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Schaffner, Claudia, Stephan Stilgenbauer, Gudrun A. Rappold, Hartmut Döhner, and Peter Lichter. "Somatic ATM Mutations Indicate a Pathogenic Role of ATM in B-Cell Chronic Lymphocytic Leukemia." Blood 94, no. 2 (1999): 748–53. http://dx.doi.org/10.1182/blood.v94.2.748.
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Abstract Deletion in chromosome bands 11q22-q23 is one of the most common chromosome aberrations in B-cell chronic lymphocytic leukemia (B-CLL). It is associated with extensive lymph node involvement and poor survival. The minimal consensus deletion comprises a segment, which contains the ATM gene presenting an interesting candidate gene, as mutations in ATM predispose A-T patients to lymphoid malignancies. To investigate a potential pathogenic role of ATM in B-cell tumorigenesis, we performed mutation analysis of ATM in 29 malignant lymphomas of B-cell origin (B-CLL = 27; mantle cell lymphoma, [MCL] = 2). Twenty-three of these carried an 11q22-q23 deletion. In five B-CLLs and one MCL with deletion of one ATMallele, a point mutation in the remaining allele was detected, which resulted in aberrant transcript splicing, alteration, or truncation of the protein. In addition, mutation analysis identified point mutations in three cases without 11q deletion: two B-CLLs with one altered allele and one MCL with both alleles mutated. In four cases analyzed, theATM alterations were not present in the germ line indicating a somatic origin of the mutations. Our study demonstrates somatic disruption of both alleles of the ATM gene by deletion or point mutation and thus its pathogenic role in sporadic B-cell lineage tumors.
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Schaffner, Claudia, Stephan Stilgenbauer, Gudrun A. Rappold, Hartmut Döhner, and Peter Lichter. "Somatic ATM Mutations Indicate a Pathogenic Role of ATM in B-Cell Chronic Lymphocytic Leukemia." Blood 94, no. 2 (1999): 748–53. http://dx.doi.org/10.1182/blood.v94.2.748.414k02_748_753.
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Deletion in chromosome bands 11q22-q23 is one of the most common chromosome aberrations in B-cell chronic lymphocytic leukemia (B-CLL). It is associated with extensive lymph node involvement and poor survival. The minimal consensus deletion comprises a segment, which contains the ATM gene presenting an interesting candidate gene, as mutations in ATM predispose A-T patients to lymphoid malignancies. To investigate a potential pathogenic role of ATM in B-cell tumorigenesis, we performed mutation analysis of ATM in 29 malignant lymphomas of B-cell origin (B-CLL = 27; mantle cell lymphoma, [MCL] = 2). Twenty-three of these carried an 11q22-q23 deletion. In five B-CLLs and one MCL with deletion of one ATMallele, a point mutation in the remaining allele was detected, which resulted in aberrant transcript splicing, alteration, or truncation of the protein. In addition, mutation analysis identified point mutations in three cases without 11q deletion: two B-CLLs with one altered allele and one MCL with both alleles mutated. In four cases analyzed, theATM alterations were not present in the germ line indicating a somatic origin of the mutations. Our study demonstrates somatic disruption of both alleles of the ATM gene by deletion or point mutation and thus its pathogenic role in sporadic B-cell lineage tumors.
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Kwong, Ava, Cecilia Yuen Sze Ho, Chun Hang Au, Sze Keong Tey, and Edmond Shiu Kwan Ma. "Germline RAD51C and RAD51D Mutations in High-Risk Chinese Breast and/or Ovarian Cancer Patients and Families." Journal of Personalized Medicine 14, no. 8 (2024): 866. http://dx.doi.org/10.3390/jpm14080866.
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Background: RAD51C and RAD51D are crucial in homologous recombination (HR) DNA repair. The prevalence of the RAD51C and RAD51D mutations in breast cancer varies across ethnic groups. Associations of RAD51C and RAD51D germline pathogenic variants (GPVs) with breast and ovarian cancer predisposition have been recently reported and are of interest. Methods: We performed multi-gene panel sequencing to study the prevalence of RAD51C and RAD51D germline mutations among 3728 patients with hereditary breast and/or ovarian cancer (HBOC). Results: We identified 18 pathogenic RAD51C and RAD51D mutation carriers, with a mutation frequency of 0.13% (5/3728) and 0.35% (13/3728), respectively. The most common recurrent mutation was RAD51D c.270_271dupTA; p.(Lys91Ilefs*13), with a mutation frequency of 0.30% (11/3728), which was also commonly identified in Asians. Only four out of six cases (66.7%) of this common mutation tested positive for homologous recombination deficiency (HRD). Conclusions: Taking the family studies in our registry and tumor molecular pathology together, we concluded that this relatively common RAD51D variant showed incomplete penetrance in our local Chinese community. Personalized genetic counseling emphasizing family history for families with this variant, as suggested at the UK Cancer Genetics Group (UKCGG) Consensus meeting, would also be appropriate in Chinese families.
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Wang, Weicheng, Rui Wang, Xiao Han, Wei Zhang, Lijun Zhu, and Yanhong Gu. "Epidemiological and clinicopathological features of KRAS, NRAS, BRAF mutations and MSI in Chinese patients with stage I–III colorectal cancer." Medicine 103, no. 14 (2024): e37693. http://dx.doi.org/10.1097/md.0000000000037693.
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The selection of appropriate treatment modalities based on the presence or absence of mutations in KRAS, NRAS, BRAF, and the microsatellite instability (MSI) status has become a crucial consensus in colorectal cancer (CRC) therapy. However, the distribution pattern of these genetic mutations and the prevalence of MSI status in Chinese stage I–III CRCs remain unclear. We retrospectively analyzed clinicopathological features, mutations in the KRAS, NRAS, and BRAF genes, as well as MSI status of 411 patients with stage I–III CRC who underwent surgery from June 2020 to December 2022 in the First Affiliated Hospital of Nanjing Medical University. The mutation rates of KRAS, NRAS, and BRAF were 48.9%, 2.2%, and 3.2%, respectively, and the microsatellite instability-high rate was 9.5%. KRAS mutation was independently associated with mucinous adenocarcinoma. Multivariate analysis suggested that tumor location and mucinous adenocarcinoma were independently associated with BRAF mutation. Only T stage was associated with NRAS mutations in the univariate analysis. Multivariate analysis revealed that factors such as larger tumor size, tumor location, younger age, and poor differentiation were independently associated with microsatellite instability-high status. The results illustrate the mutation frequencies of KRAS, NRAS, BRAF genes and MSI status in stage I–III CRC from the eastern region of China. These findings further validate the associations between these genes status and various clinicopathological characteristics.
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Carothers, A. M., G. Urlaub, D. Grunberger, and L. A. Chasin. "Splicing mutants and their second-site suppressors at the dihydrofolate reductase locus in Chinese hamster ovary cells." Molecular and Cellular Biology 13, no. 8 (1993): 5085–98. http://dx.doi.org/10.1128/mcb.13.8.5085-5098.1993.
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Point mutants induced with a variety of mutagens at the dihydrofolate reductase (dhfr) locus in Chinese hamster ovary (CHO) cells were screened for aberrantly spliced dhfr mRNA by RNase protection and/or reverse transcriptase coupled with cDNA amplification by the polymerase chain reaction (PCR). Of 115 mutants screened, 28 were found to be affected in splicing. All exhibited less than 1% correct splicing, probably because the selection procedure was stringent. All 26 unique mutations were located within the consensus splice sequences; changes were found at 9 of 10 possible sites in this 25-kb six-exon gene. Mutations at the sites flanking the first and last exons resulted in the efficient recruitment of a cryptic site within each exon. In contrast, mutations bordering internal exons caused predominantly exon skipping. In many cases, multiple exons were skipped, suggesting the clustering of adjacent exons prior to actual splicing. Six mutations fell outside the well-conserved GU and AG dinucleotides. All but one were donor site single-base substitutions that decreased the agreement with the consensus and resulted in little or no correct splicing. Starting with five of these donor site mutants, we isolated 31 DHFR+ revertants. Most revertants carried a single-base substitution at a site other than that of the original mutation, and most had only partially regained the ability to splice correctly. The second-site suppression occurred through a variety of mechanisms: (i) a second change within the consensus sequence that produced a better agreement with the consensus; (ii) a change close to but beyond the consensus boundaries, as far as 8 bases upstream in the exon or 28 bases downstream in the intron; (iii) mutations in an apparent pseudo 5' site in the intron, 84 and 88 bases downstream of a donor site; and (iv) mutations that improved the upstream acceptor site of the affected exon. Taken together, these second-site suppressor mutations extend the definition of a splice site beyond the consensus sequence.
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Carothers, A. M., G. Urlaub, D. Grunberger, and L. A. Chasin. "Splicing mutants and their second-site suppressors at the dihydrofolate reductase locus in Chinese hamster ovary cells." Molecular and Cellular Biology 13, no. 8 (1993): 5085–98. http://dx.doi.org/10.1128/mcb.13.8.5085.
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Point mutants induced with a variety of mutagens at the dihydrofolate reductase (dhfr) locus in Chinese hamster ovary (CHO) cells were screened for aberrantly spliced dhfr mRNA by RNase protection and/or reverse transcriptase coupled with cDNA amplification by the polymerase chain reaction (PCR). Of 115 mutants screened, 28 were found to be affected in splicing. All exhibited less than 1% correct splicing, probably because the selection procedure was stringent. All 26 unique mutations were located within the consensus splice sequences; changes were found at 9 of 10 possible sites in this 25-kb six-exon gene. Mutations at the sites flanking the first and last exons resulted in the efficient recruitment of a cryptic site within each exon. In contrast, mutations bordering internal exons caused predominantly exon skipping. In many cases, multiple exons were skipped, suggesting the clustering of adjacent exons prior to actual splicing. Six mutations fell outside the well-conserved GU and AG dinucleotides. All but one were donor site single-base substitutions that decreased the agreement with the consensus and resulted in little or no correct splicing. Starting with five of these donor site mutants, we isolated 31 DHFR+ revertants. Most revertants carried a single-base substitution at a site other than that of the original mutation, and most had only partially regained the ability to splice correctly. The second-site suppression occurred through a variety of mechanisms: (i) a second change within the consensus sequence that produced a better agreement with the consensus; (ii) a change close to but beyond the consensus boundaries, as far as 8 bases upstream in the exon or 28 bases downstream in the intron; (iii) mutations in an apparent pseudo 5' site in the intron, 84 and 88 bases downstream of a donor site; and (iv) mutations that improved the upstream acceptor site of the affected exon. Taken together, these second-site suppressor mutations extend the definition of a splice site beyond the consensus sequence.
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Rohlfs, Elizabeth M., William G. Learning, Kenneth J. Friedman, Fergus J. Couch, Barbara L. Weber, and Lawrence M. Silverman. "Direct detection of mutations in the breast and ovarian cancer susceptibility gene BRCA1 by PCR-mediated site-directed mutagenesis." Clinical Chemistry 43, no. 1 (1997): 24–29. http://dx.doi.org/10.1093/clinchem/43.1.24.
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Abstract The tumor suppressor genes BRCA1 and BRCA2, which confer increased susceptibility to breast and (or) ovarian cancer, were recently identified. Mutation analysis of BRCA1 has demonstrated significant allelic heterogeneity; however, some distinct mutations have been detected in unrelated individuals. The most notable is the 185delAG mutation, which occurs at an estimated frequency of ∼1% in individuals of Ashkenazi Jewish descent [1]. Although consensus has not been reached regarding clinical testing for mutations in BRCA1, a tiered strategy may be appropriate, in which direct testing for the more common mutations is one component. Specific alleles can be detected by using PCR-mediated site-directed mutagenesis (PSM), which alters the PCR products derived from either the wild-type or mutant allele to create or destroy a restriction endonuclease recognition site. Recognition sites are introduced by a base substitution in one of the primers. The alleles are then resolved by electrophoresis of the digested PCR products. We have applied this technique to the detection of four BRCA1 mutations: 185delAG, 5382insC, E1250X, and R1443X. Another mutation, 1294del40, can be resolved from the wild-type allele by high-resolution gel electrophoresis alone. The PSM technique is sensitive, does not require radioactivity, and is specific for individual mutations.
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Armstrong, Kimberly L., Tun-Hou Lee, and M. Essex. "Replicative Fitness Costs of Nonnucleoside Reverse Transcriptase Inhibitor Drug Resistance Mutations on HIV Subtype C." Antimicrobial Agents and Chemotherapy 55, no. 5 (2011): 2146–53. http://dx.doi.org/10.1128/aac.01505-10.
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ABSTRACTSingle-dose nevirapine (NVP) is quite effective in preventing transmission of the human immunodeficiency virus (HIV) from mother to child; however, many women develop resistance to NVP in this setting. Comparing outcomes of clinical studies reveals an increased amount of resistance in subtype C relative to that in other subtypes. This study investigates how nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations of subtype C affect replication capacity. The 103N, 106A, 106M, 181C, 188C, 188L, and 190A drug resistance mutations were placed in a reverse transcriptase (RT) that matches the consensus subtype C sequence as well as the HXB2 RT, as a subtype B reference. The replicative fitness of each mutant was compared with that of the wild type in a head-to-head competition assay. The 106A mutant of subtype C would not grow in the competition assay, making it the weakest virus tested. The effect of the 106M mutation was weaker than those of the 181C and 188C mutations in the consensus C RT, but in subtype B, this difference was not seen. To see if the 106A mutation in a different subtype C background would have a different replicative profile, the same NNRTI resistance mutations were added to the MJ4 RT, a reference subtype C molecular clone. In the context of MJ4 RT, the 106A mutant was not the only mutant that showed poor replicative fitness; the 106M, 188C, and 190A mutants also failed to replicate. These results suggest that NNRTIs may be a cost-effective alternative for salvage therapy if deleterious mutations are present in a subtype C setting.
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Weinberg, Olga K., Frank Kuo, and Katherine R. Calvo. "Germline Predisposition to Hematolymphoid Neoplasia." American Journal of Clinical Pathology 152, no. 3 (2019): 258–76. http://dx.doi.org/10.1093/ajcp/aqz067.
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Abstract Objectives The 2017 Workshop of the Society for Hematopathology/European Association for Haematopathology aimed to review clinical cases with germline predisposition to hematolymphoid neoplasms. Methods The Workshop Panel reviewed 51 cases with germline mutations and rendered consensus diagnoses. Of these, six cases were presented at the meeting by the submitting pathologists. Results The cases submitted to the session covering germline predisposition included 16 cases with germline GATA2 mutations, 10 cases with germline RUNX1 mutations, two cases with germline CEBPA mutations, two germline TP53 mutations, and one case of germline DDX41 mutation. The most common diagnoses were acute myeloid leukemia (15 cases) and myelodysplastic syndrome (MDS, 14 cases). Conclusions The majority of the submitted neoplasms occurring in patients with germline predisposition were myeloid neoplasms with germline mutations in GATA2 and RUNX1. The presence of a germline predisposition mutation is not sufficient for a diagnosis of a neoplasm until the appearance of standard diagnostic features of a hematolymphoid malignancy manifest: in general, the diagnostic criteria for neoplasms associated with germline predisposition disorders are the same as those for sporadic cases.
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Berends, Maran J. W., Ying Wu, Rolf H. Sijmons, et al. "Toward New Strategies to Select Young Endometrial Cancer Patients for Mismatch Repair Gene Mutation Analysis." Journal of Clinical Oncology 21, no. 23 (2003): 4364–70. http://dx.doi.org/10.1200/jco.2003.04.094.
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Purpose: To determine the frequency of mismatch repair (MMR) gene germline mutations in endometrial cancer patients who were diagnosed at less than 50 years of age; to relate the presence of mutations to family history, histopathologic data, presence of tumor microsatellite instability (MSI), and immunostaining; and to formulate criteria for genetic testing in these patients. Patients and Methods: Endometrial cancer patients (N = 58), who were diagnosed at less than 50 years of age, were included and questioned about their family history. Mutation analysis of the MLH1, MSH2, and MSH6 genes was performed (denaturing gradient gel electrophoresis and sequence analysis to detect small mutations and multiplex ligation-dependent probe amplification to detect large deletions or duplications). For MSI analysis, five consensus markers were used, and immunostaining of the three MMR proteins was performed. Results: In five of 22 patients with a positive first-degree family history for hereditary nonpolyposis colorectal cancer (HNPCC)-related cancers, pathogenic germline mutations were found (one MLH1, three MSH2, and one MSH6). Four mutation carriers belonged to families fulfilling the revised Amsterdam criteria. No mutations were found in the 35 patients without such family history (P = .006). MSI was detected in 20 of 57 cancers, among which four were from mutation carriers. In 23 of 51 cancers, one or more MMR protein was absent; in all five mutation carriers, immunostaining indicated the involved MMR gene. Conclusion: In 23% of the young endometrial cancer patients with at least one first-degree relative with an HNPCC-related cancer, an MMR gene mutation was detected. Therefore, presence of an HNPCC-related cancer in a first-degree relative seems to be an important selection criterion for mutation analysis. Subsequent immunostaining of MMR proteins will point to the gene(s) that should be analyzed.
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Susanna, Kim A., Aleksandra M. Mironczuk, Wiep Klaas Smits, Leendert W. Hamoen, and Oscar P. Kuipers. "A Single, Specific Thymine Mutation in the ComK-Binding Site Severely Decreases Binding and Transcription Activation by the Competence Transcription Factor ComK of Bacillus subtilis." Journal of Bacteriology 189, no. 13 (2007): 4718–28. http://dx.doi.org/10.1128/jb.00281-07.
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ABSTRACT The competence transcription factor ComK plays a central role in competence development in Bacillus subtilis by activating the transcription of the K regulon. ComK-activated genes are characterized by the presence of a specific sequence to which ComK binds, a K-box, in their upstream DNA region. Each K-box consists of two AT-boxes with the consensus sequence AAAA-(N)5-TTTT, which are separated by a flexible spacer resulting in either two, three, or four helical turns between the starting nucleotides of the repeating AT-box units. In this study, the effects of potential determinants of ComK regulation in K-boxes were investigated by testing ComK's transcription activation and DNA-binding affinity on altered K-boxes with mutations either in the spacer between the AT-boxes or in the consensus sequence of the AT-boxes. The most striking result demonstrates the importance of the second thymine base in the AT-boxes. Mutation of this T into a guanine resulted in a threefold reduction in transcription activation and DNA binding by ComK. Transcription activation, as well as DNA binding, was almost completely abolished when both AT-boxes contained a T2-to-G mutation. This result was corroborated by in silico analyses demonstrating that a combination of mutations at the T2 positions of both AT-boxes is not found among any ComK-activated K-boxes, indicating that at least one consensus T2 position is required to maintain a functional K-box. The results suggest an important structural role for T2 in ComK binding, probably by its specific position in the minor groove of the DNA.
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Edworthy, Nicole L., and Andrew J. Easton. "Mutational analysis of the avian pneumovirus conserved transcriptional gene start sequence identifying critical residues." Journal of General Virology 86, no. 12 (2005): 3343–47. http://dx.doi.org/10.1099/vir.0.81352-0.
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Seven of the eight genes in the avian pneumovirus (APV) genome contain a conserved 9 nt transcriptional start sequence with the virus large (L) polymerase gene differing from the consensus at three positions. The sequence requirements of the APV transcriptional gene start sequence were investigated by generating a series of mutations in which each of the nine conserved bases was mutated to each of the other three possible nucleotides in a minigenome containing two reporter genes. The effect of each mutation was assessed by measuring the relative levels of expression from the altered and unaltered gene start sequences. Mutations at positions 2, 7 and 9 significantly reduced transcription levels while alterations to position 5 had little effect. The L gene start sequence directed transcription at levels approximately 50 % below that of the consensus gene start sequence. These data suggest that there are common features in pneumovirus transcriptional control sequences.
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Smeby, Jørgen, Anita Sveen, Christian H. Bergsland, et al. "Exploratory analyses of consensus molecular subtype-dependent associations of TP53 mutations with immunomodulation and prognosis in colorectal cancer." ESMO Open 4, no. 3 (2019): e000523. http://dx.doi.org/10.1136/esmoopen-2019-000523.
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BackgroundAccumulating evidence suggests immunomodulatory and context-dependent effects of TP53 mutations in cancer. We performed an exploratory analysis of the transcriptional, immunobiological and prognostic associations of TP53 mutations within the gene expression-based consensus molecular subtypes (CMSs) of colorectal cancer (CRC).Materials and methodsIn a single-hospital series of 401 stage I–IV primary CRCs, we sequenced the whole coding region of TP53 and analysed CMS-dependent transcriptional consequences of the mutations by gene expression profiling. Immunomodulatory associations were validated by multiplex, fluorescence-based immunohistochemistry of immune cell markers. Prognostic associations of TP53 mutations were analysed in an aggregated series of 635 patients classified according to CMS, including publicly available data from a French multicentre cohort (GSE39582).ResultsTP53 mutations were found in 60% of the CRCs. However, gene set enrichment analyses indicated that their transcriptional consequences varied among the CMSs and were most pronounced in CMS1-immune and CMS4-mesenchymal. Subtype specificity was primarily seen as an upregulation of gene sets reflecting cell cycle progression in CMS4 and a downregulation of T cell activity in CMS1. The subtype-dependent immunomodulatory associations were reinforced by significant depletion of several immune cell populations in mutated tumours compared with wild-type (wt) tumours exclusively in CMS1, including cytotoxic lymphocytes (adjusted p value in CMS1=0.002 and CMS2−4>0.9, Microenvironment Cell Populations (MCP)-counter algorithm). This was validated by immunohistochemistry-based quantification of tumour infiltrating CD8+ cells. Within CMS1, the immunomodulatory association of TP53 mutations was strongest among microsatellite stable (MSS) tumours, and this translated into a propensity for metastatic disease and poor prognostic value of the mutations specifically in the CMS1/MSS subtype (both series overall survival: TP53 mutation vs wt: HR 5.52, p=0.028).ConclusionsIntegration of TP53 mutation status with the CMS framework in primary CRC suggested subtype-dependent immunobiological associations with prognostic and potentially immunotherapeutic implications, warranting independent validation.