Assessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis.

Functional analyses are the main method to classify mismatch repair (MMR) gene variants of uncertain significance (VUSs). However, the pathogenicity remains unclear for many variants because of conflicting results between clinical, molecular, and functional data. In this study, we evaluated whether whole exome sequencing (WES) could add another layer of evidence to elucidate the pathogenicity of MMR variants with conflicting interpretations.

DNA mismatch repair controls the mutagenicity of Polymerase ζ-dependent translesion synthesis at methylated guanines.

By replicating damaged nucleotides, error-prone DNA translesion synthesis (TLS) enables the completion of replication, albeit at the expense of fidelity. TLS of helix-distorting DNA lesions, that usually have reduced capacity of basepairing, comprises insertion opposite the lesion followed by extension, the latter in particular by polymerase ζ (Pol ζ). However, little is known about involvement of Pol ζ in TLS of non- or poorly-distorting, but miscoding, lesions such as O-methyldeoxyguanosine (O-medG).

Out-of-equilibrium charge redistribution in a copper-oxide based superconductor by time-resolved X-ray photoelectron spectroscopy.

Charge-transfer excitations are of paramount importance for understanding the electronic structure of copper-oxide based high-temperature superconductors. In this study, we investigate the response of a Bi Sr CaCu O crystal to the charge redistribution induced by an infrared ultrashort pulse. Element-selective time-resolved core-level photoelectron spectroscopy with a high energy resolution allows disentangling the dynamics of oxygen ions with different coordination and bonds thanks to their different chemical shifts.

Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO.

Altermagnets are an emerging elementary class of collinear magnets. Unlike ferromagnets, their distinct crystal symmetries inhibit magnetization while, unlike antiferromagnets, they promote strong spin polarization in the band structure. The corresponding unconventional mechanism of time-reversal symmetry breaking without magnetization in the electronic spectra has been regarded as a primary signature of altermagnetism but has not been experimentally visualized to date.

Real-time observation of non-equilibrium phonon-electron energy and angular momentum flow in laser-heated nickel.

Identifying the microscopic nature of non-equilibrium energy transfer mechanisms among electronic, spin, and lattice degrees of freedom is central to understanding ultrafast phenomena such as manipulating magnetism on the femtosecond timescale. Here, we use time- and angle-resolved photoemission spectroscopy to go beyond the often-used ensemble-averaged view of non-equilibrium dynamics in terms of quasiparticle temperature evolutions. We show for ferromagnetic Ni that the non-equilibrium electron and spin dynamics display pronounced variations with electron momentum, whereas the magnetic exchange interaction remains isotropic.

Discordant Staining Patterns and Microsatellite Results in Tumors of MSH6 Pathogenic Variant Carriers.

Diagnosis of Lynch syndrome (LS) caused by a pathogenic germline MSH6 variant may be complicated by discordant immunohistochemistry (IHC) and/or by a microsatellite stable (MSS) phenotype. This study aimed to identify the various causes of the discordant phenotypes of colorectal cancer (CRC) and endometrial cancer (EC) in MSH6-associated LS. Data were collected from Dutch family cancer clinics.

Circular dichroism in hard X-ray photoelectron diffraction observed by time-of-flight momentum microscopy.

X-ray photoelectron diffraction (XPD) is a powerful technique that yields detailed structural information of solids and thin films that complements electronic structure measurements. Among the strongholds of XPD we can identify dopant sites, track structural phase transitions, and perform holographic reconstruction. High-resolution imaging of k-distributions (momentum microscopy) presents a new approach to core-level photoemission.

Unexpected moves: a conformational change in MutSα enables high-affinity DNA mismatch binding.

The DNA mismatch repair protein MutSα recognizes wrongly incorporated DNA bases and initiates their correction during DNA replication. Dysfunctions in mismatch repair lead to a predisposition to cancer. Here, we study the homozygous mutation V63E in MSH2 that was found in the germline of a patient with suspected constitutional mismatch repair deficiency syndrome who developed colorectal cancer before the age of 30.

Multispectral time-resolved energy-momentum microscopy using high-harmonic extreme ultraviolet radiation.

A 790-nm-driven high-harmonic generation source with a repetition rate of 6 kHz is combined with a toroidal-grating monochromator and a high-detection-efficiency photoelectron time-of-flight momentum microscope to enable time- and momentum-resolved photoemission spectroscopy over a spectral range of 23.6-45.5 eV with sub-100 fs time resolution.

CNOT6: A Novel Regulator of DNA Mismatch Repair.

DNA mismatch repair (MMR) is a highly conserved pathway that corrects both base-base mispairs and insertion-deletion loops (IDLs) generated during DNA replication. Defects in MMR have been linked to carcinogenesis and drug resistance. However, the regulation of MMR is poorly understood.

Rev1 deficiency induces replication stress to cause metabolic dysfunction differently in males and females.

DNA damage responses compete for cellular resources with metabolic pathways, but little is known about the metabolic consequences of impaired DNA replication, a process called replication stress. Here we characterized the metabolic consequences of DNA replication stress at endogenous DNA lesions by using mice with a disruption of Rev1, a translesion DNA polymerase specialized in the mutagenic replication of damaged DNA. Male and female Rev1 knockout (KO) mice were compared with wild-type (WT) mice and followed over time to study the natural course of body weight gain and glucose tolerance.

Induction of mismatch repair deficiency, compromised DNA damage signaling and compound hypermutagenesis by a dietary mutagen in a cell-based model for Lynch syndrome.

The prevalent cancer predisposition Lynch syndrome (LS, OMIM #120435) is caused by an inherited heterozygous defect in any of the four core DNA mismatch repair (MMR) genes MSH2, MSH6, MLH1 or PMS2. MMR repairs errors by the replicative DNA polymerases in all proliferating tissues. Its deficiency, following somatic loss of the wild-type copy, results in a spontaneous mutator phenotype that underlies the rapid development of, predominantly, colorectal cancer (CRC) in LS.

Suppression of the vacuum space-charge effect in fs-photoemission by a retarding electrostatic front lens.

The performance of time-resolved photoemission experiments at fs-pulsed photon sources is ultimately limited by the e-e Coulomb interaction, downgrading energy and momentum resolution. Here, we present an approach to effectively suppress space-charge artifacts in momentum microscopes and photoemission microscopes. A retarding electrostatic field generated by a special objective lens repels slow electrons, retaining the k-image of the fast photoelectrons.

DNA mismatch repair-dependent DNA damage responses and cancer.

Canonical DNA mismatch repair (MMR) excises base-base mismatches to increase the fidelity of DNA replication. Thus, loss of MMR leads to increased spontaneous mutagenesis. MMR genes also are involved in the suppression of mutagenic, and the induction of protective, responses to various types of DNA damage.

Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation.

Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in , , and , including 12 missense variants that were also assessed using a cell-free MMR activity (CIMRA) assay.

Digenic inheritance of MSH6 and MUTYH variants in familial colorectal cancer.

We describe a family severely affected by colorectal cancer (CRC) where whole-exome sequencing identified the coinheritance of the germline variants encoding MSH6 p.Thr1100Met and MUTYH p.Tyr179Cys in, at least, three CRC patients diagnosed before 60 years of age.

Two integrated and highly predictive functional analysis-based procedures for the classification of MSH6 variants in Lynch syndrome.

Purpose: Variants in the DNA mismatch repair (MMR) gene MSH6, identified in individuals suspected of Lynch syndrome, are difficult to classify owing to the low cancer penetrance of defects in that gene. This not only obfuscates personalized health care but also the development of a rapid and reliable classification procedure that does not require clinical data.

Methods: The complete in vitro MMR activity (CIMRA) assay was calibrated against clinically classified MSH6 variants and, employing Bayes' rule, integrated with computational predictions of pathogenicity.

Effect of sequence context on Polζ-dependent error-prone extension past (6-4) photoproducts.

The (6-4) pyrimidine-pyrimidone photoproduct [(6-4)PP] is a major DNA lesion induced by ultraviolet radiation. (6-4)PP induces complex mutations opposite its downstream bases, in addition to opposite 3' or 5' base, as has been observed through a site-specific translesion DNA synthesis (TLS) assay. The mechanism by which these mutations occur is not well understood.

A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome.

Purpose: To enhance classification of variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes in the cancer predisposition Lynch syndrome, we developed the cell-free in vitro MMR activity (CIMRA) assay. Here, we calibrate and validate the assay, enabling its integration with in silico and clinical data.

Methods: Two sets of previously classified MLH1 and MSH2 variants were selected from a curated MMR gene database, and their biochemical activity determined by the CIMRA assay.

Adjuvant Treatment for Proofreading Domain-Mutant Cancers: Sensitivity to Radiotherapy, Chemotherapy, and Nucleoside Analogues.

Pathogenic proofreading domain mutations are found in many malignancies where they are associated with ultramutation and favorable prognosis. The extent to which this prognosis depends on their sensitivity to adjuvant treatment is unknown, as is the optimal therapy for advanced-staged or recurrent -mutant cancers. We examined the recurrence-free survival of women with -mutant and wild-type endometrial cancers (EC) in the observation arm of the randomized PORTEC-1 endometrial cancer trial ( = 245 patients with stage I endometrial cancer for analysis).

Author Correction: Rev1 contributes to proper mitochondrial function via the PARP-NAD-SIRT1-PGC1α axis.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Rev1 contributes to proper mitochondrial function via the PARP-NAD-SIRT1-PGC1α axis.

Nucleic acids, which constitute the genetic material of all organisms, are continuously exposed to endogenous and exogenous damaging agents, representing a significant challenge to genome stability and genome integrity over the life of a cell or organism. Unrepaired DNA lesions, such as single- and double-stranded DNA breaks (SSBs and DSBs), and single-stranded gaps can block progression of the DNA replication fork, causing replicative stress and/or cell cycle arrest. However, translesion synthesis (TLS) DNA polymerases, such as Rev1, have the ability to bypass some DNA lesions, which can circumvent the process leading to replication fork arrest and minimize replicative stress.