Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics.

Intrinsically disordered proteins participate in many biological processes by folding upon binding to other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main questions is whether folding occurs prior to or after binding. Here we use a novel, unbiased, high-throughput adaptive sampling approach to reconstruct the binding and folding between the disordered transactivation domain of c-Myb and the KIX domain of the CREB-binding protein. The reconstructed long-term dynamical process highlights the binding of a short stretch of amino acids on c-Myb as a folded α-helix. Leucine residues, especially Leu298-Leu302, establish initial native contacts that prime the binding and folding of the rest of the peptide, with a mixture of conformational selection on the N-terminal region with an induced fit of the C-terminal.

Intersections between syndemic conditions and stages along the continuum of overdose risk among women who inject drugs in Mexicali, Mexico.

BACKGROUND: Research on women who inject drugs is scarce in low- and middle-income countries. Women experience unique harms such as sexism and sexual violence which translate into negative health outcomes. The present work aims to provide insight into the experiences of women who inject drugs at the US-Mexico border to identify social and health-related risk factors for overdose to guide harm reduction interventions across the Global South. METHODS: We recruited 25 women ≥ 18 years of age accessing harm reduction and sexual health services at a non-governmental harm reduction organization, "Verter", in Mexicali, Mexico. We employed purposeful sampling to recruit women who inject drugs who met eligibility criteria. We collected quantitative survey data and in-depth interview data. Analyses of both data sources involved the examination of descriptive statistics and thematic analysis, respectively, and were guided by the syndemic and continuum of overdose risk frameworks. RESULTS: Survey data demonstrated reports of initiating injection drug use at a young age, experiencing homelessness, engaging in sex work, being rejected by family members, experiencing physical violence, injecting in public spaces, and experiencing repeated overdose events. Interview data provided evidence of stigma and discrimination toward women, a lack of safe spaces and support systems, risk of overdose-related harms, sexual violence, and the overall need for harm reduction services. CONCLUSION: Women who inject drugs in Mexicali describe experiences of violence, overdose, and public injecting. Women are particularly vulnerable in the Mexicali context, as this area faces a noticeable lack of health and social services. Evidenced-based harm reduction strategies such as safe consumption sites and overdose prevention strategies (e.g., naloxone distribution and training) may benefit this population. Evidence from local organizations could help close the gap in service provision in low-resource settings like Mexico, where government action is almost nonexistent.

EvAM-Tools: tools for evolutionary accumulation and cancer progression models.

SUMMARY: EvAM-Tools is an R package and web application that provides a unified interface to state-of-the-art cancer progression models and, more generally, evolutionary models of event accumulation. The output includes, in addition to the fitted models, the transition (and transition rate) matrices between genotypes and the probabilities of evolutionary paths. Generation of random cancer progression models is also available. Using the GUI in the web application, users can easily construct models (modifying directed acyclic graphs of restrictions, matrices of mutual hazards or specifying genotype composition), generate data from them (with user-specified observational/genotyping error) and analyze the data. AVAILABILITY AND IMPLEMENTATION: Implemented in R and C; open source code available under the GNU Affero General Public License v3.0 at https://github.com/rdiaz02/EvAM-Tools. Docker images freely available from https://hub.docker.com/u/rdiaz02. Web app freely accessible at https://iib.uam.es/evamtools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Behavior change after fentanyl testing at a safe consumption space for women in Northern Mexico: A pilot study.

BACKGROUND: Fentanyl has led to an increased number of overdose deaths in North America. Testing substances for fentanyl may be a harm reduction strategy to prevent overdose. Little is known about behavior change after fentanyl testing and the attitudes around fentanyl knowledge and testing along the US-Mexico border in the context of a safe consumption site. METHODS: This was a pilot quantitative and qualitative study with 30 women who use drugs at an unsanctioned safe consumption site in Mexicali, Mexico. Women participated in a quantitative survey, a semi-structured interview, and fentanyl testing of substances. Injection behavior was observed after fentanyl testing results were provided. Qualitative data were collected to explore the meanings participants attributed to fentanyl and fentanyl testing. RESULTS: Half of the substances tested positive for fentanyl (n=15, 50%), and all of them were in samples of black tar heroin. Among those participants who tested positive for fentanyl, 7 (47%) subsequently used less of the intended substance, 1 did not use the intended substance, and 7 (47%) did not change their behavior (i.e., used as originally intended). In qualitative interviews, a predominant theme was a description of fentanyl as dangerous and deadly and fentanyl testing as being helpful for modifying drug use behaviors. However, participants recognized that there could be no change in behavior following a positive fentanyl test in the context of not being able to find substances free of fentanyl. CONCLUSION: We observed mixed results related to behavior change after women's intended substance for use tested positive for fentanyl. Fentanyl testing was acceptable to women, but behavior change was hampered by the inability to find substances free of fentanyl. Further research is needed to maximize the potential of fentanyl testing as a harm reduction tool especially in the context of a changing drug supply.

Cost-minimisation analysis of chronic lymphocytic leukemia in Spain in the era of oral targeted therapies.

OBJECTIVE: Chronic lymphocytic leukaemia places a considerable economic burden on the Spanish National Health System. This study estimated the direct costs of chronic lymphocytic leukaemia oral targeted therapies from 2011 to 2025, inclusive, in a scenario with fixed  treatment oral targeted therapies and in a scenario without them. Method: The clinical course of adult chronic lymphocytic leukaemia patients  was represented by a Markov model with four health states: watchful waiting,  first-line treatment, relapse, and death. The treatment pattern was defined  according to patient type by disease status or situation, age, presence or  absence of deletion in the short arm of chromosome 17, immunoglobulin heavy  chain mutation status, and year of treatment. The treatment algorithm  was simulated from 2011 to 2025, and included therapies funded by the  Spanish National Health System and their use in routine clinical practice,  validated by leading experts. A single treatment option was assumed for each  type of patient and time period (the most widely option used at each time  point). Direct costs were included: pharmacological, administration, tests  performed, routine visits, hospitalizations, and adverse events. Results: From 2011 to 2025, there would be a mean annual chronic  ymphocytic leukaemia prevalence of 16,436 patients in the scenario without  fixed treatment oral targeted therapies and 16,413 in the scenario  with  in the scenario without fixed treatment oral targeted therapies would be €4,676.7 million and in the scenario with fixed treatment oral targeted therapies they would be €4,111.8 million. Thus, the introduction of fixed treatment oral targeted therapies would entail a saving of €564.9 million (12.1% of the total cost of care of chronic lymphocytic leukaemia patients during the period assessed). In this period, the total cost per patient would decrease from €266,019 in the scenario without fixed treatment oral targeted therapies to €236,852 in the scenario with fixed treatment oral targeted therapies, representing a saving of €29,167 per patient. CONCLUSIONS: This study estimates that, between 2011 and 2025, the introduction of fixed treatment oral targeted therapies for the treatment of chronic lymphocytic leukaemia would entail €564.9 million cost savings for  the Spanish National Health System (12.1% of the total cost of care of chronic  lymphocytic leukaemia patients during the period assessed).

OBJETIVO: La leucemia linfocítica crónica supone una carga económica considerable para el Sistema Nacional de Salud español. Este  estudio estimó los costes directos de las terapias orales dirigidas para leucemia linfocítica crónica desde 2011 a 2025, inclusive, en un escenario con terapias orales de duración fija y en un escenario sin ellas.Método: Se representó el curso clínico de pacientes adultos con leucemia linfocítica crónica mediante un modelo de Markov con cuatro estados de salud: vigilancia activa, tratamiento de primera línea, recaída y  muerte. Patrón de tratamiento definido por tipo de paciente: estado o situación  de la enfermedad, edad, presencia o no de deleción en el brazo corto  del cromosoma 17, estado mutacional de la cadena pesada de  inmunoglobulinas y año de tratamiento. Algoritmo de tratamiento simulado  desde 2011 a 2025, incluyendo terapias financiadas por el Sistema Nacional de Salud español y su uso en práctica clínica habitual, validado por expertos de  referencia. Se asumió una opción de tratamiento por tipo de  paciente y periodo de tiempo (la más ampliamente utilizada en cada  momento). Se incluyeron costes directos: farmacológicos, administración,  pruebas realizadas, visitas rutinarias, hospitalizaciones y acontecimientos  adversos. RESULTADOS: Se estimó una prevalencia media anual de leucemia linfocítica crónica desde 2011 a 2025 de 16.436 pacientes en el escenario sin  terapias orales de duración fija y 16.413 en el escenario con terapias  orales de  duración fija. Los costes totales desde 2011 a 2025 en el escenario sin  terapias orales de duración fija ascendieron a 4.676,7 millones de € y a  4.111,8 millones de € en el escenario con terapias orales de duración fija. Así,  la introducción de las terapias orales de duración fija supondría un ahorro de  564,9 millones de € (12,1% del total del coste de atención de los pacientes con  leucemia linfocítica crónica durante el periodo evaluado). El coste total por  paciente en este periodo de tiempo pasaba de 266.019 € en el escenario  sin terapias orales de duración fija a 236.852 € en el escenario con terapias  rales de duración fija, suponiendo un ahorro de 29.167 € por paciente. CONCLUSIONES: Este estudio estima que la introducción de las terapias orales  de duración fija para el tratamiento de la leucemia linfocítica crónica entre  2011 y 2025 supone un ahorro para el Sistema Nacional de Salud español de  564,9 millones de € (12,1% del total del coste de atención de los pacientes con  leucemia linfocítica crónica durante el periodo evaluado).

Transcriptome diversity is a systematic source of variation in RNA-sequencing data.

RNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to interpret and remove artifactual signals. Several biological and technical factors such as sex, age, batches, and sequencing technology have been found to bias these estimates. Probabilistic estimation of expression residuals (PEER), which infers broad variance components in gene expression measurements, has been used to account for some systematic effects, but it has remained challenging to interpret these PEER factors. Here we show that transcriptome diversity-a simple metric based on Shannon entropy-explains a large portion of variability in gene expression and is the strongest known factor encoded in PEER factors. We then show that transcriptome diversity has significant associations with multiple technical and biological variables across diverse organisms and datasets. In sum, transcriptome diversity provides a simple explanation for a major source of variation in both gene expression estimates and PEER covariates.

Análisis de minimización de costes de la leucemia linfocítica crónica en España en la era de las terapias orales dirigidas / Cost-minimisation analysis of chronic lymphocytic leukemia in Spain in the era of oral targeted therapies

Objetivo: La leucemia linfocítica crónica supone una carga económica considerable para el Sistema Nacional de Salud español. Este estudioestimó los costes directos de las terapias orales dirigidas para leucemia linfocítica crónica desde 2011 a 2025, inclusive, en un escenario conterapias orales de duración fija y en un escenario sin ellas.Método: Se representó el curso clínico de pacientes adultos con leucemia linfocítica crónica mediante un modelo de Markov con cuatro estados de salud: vigilancia activa, tratamiento de primera línea, recaída y muerte. Patrón de tratamiento definido por tipo de paciente: estado o situación dela enfermedad, edad, presencia o no de deleción en el brazo corto del cromosoma 17, estado mutacional de la cadena pesada de inmunoglobulinasy año de tratamiento. Algoritmo de tratamiento simulado desde 2011a 2025, incluyendo terapias financiadas por el Sistema Nacional deSalud español y su uso en práctica clínica habitual, validado por expertosde referencia. Se asumió una opción de tratamiento por tipo de pacientey periodo de tiempo (la más ampliamente utilizada en cada momento).Se incluyeron costes directos: farmacológicos, administración, pruebasrealizadas, visitas rutinarias, hospitalizaciones y acontecimientos adversos.Resultados: Se estimó una prevalencia media anual de leucemia linfocíticacrónica desde 2011 a 2025 de 16.436 pacientes en el escenariosin terapias orales de duración fija y 16.413 en el escenario con terapias orales de duración fija. Los costes totales desde 2011 a 2025 en el escenariosin terapias orales de duración fija ascendieron a 4.676,7 millonesde € y a 4.111,8 millones de € en el escenario con terapias orales deduración fija. Así, la introducción de las terapias orales de duración fijasupondría un ahorro de 564,9 millones de € (12,1% del total del costede atención de los pacientes con leucemia linfocítica crónica durante elperiodo evaluado).

Objective: Chronic lymphocytic leukaemia places a considerable economicburden on the Spanish National Health System. This study estimatedthe direct costs of chronic lymphocytic leukaemia oral targetedtherapies from 2011 to 2025, inclusive, in a scenario with fixed treatmentoral targeted therapies and in a scenario without them.Method: The clinical course of adult chronic lymphocytic leukaemiapatients was represented by a Markov model with four health states: watchfulwaiting, first-line treatment, relapse, and death. The treatment patternwas defined according to patient type by disease status or situation, age,presence or absence of deletion in the short arm of chromosome 17,immunoglobulin heavy chain mutation status, and year of treatment. Thetreatment algorithm was simulated from 2011 to 2025, and includedtherapiesfunded by the Spanish National Health System and their use inroutine clinical practice, validated by leading experts. A single treatmentoption was assumed for each type of patient and time period (the mostwidely option used at each time point). Direct costs were included: pharmacological,administration, tests performed, routine visits, hospitalizations,and adverse events.Results: From 2011 to 2025, there would be a mean annual chronic lymphocyticleukaemia prevalence of 16,436 patients in the scenario withoutfixed treatment oral targeted therapies and 16,413 in the scenario with fixed treatment oral targeted therapies. In the same period, the total costsin the scenario without fixed treatment oral targeted therapies would be€4,676.7 million and in the scenario with fixed treatment oral targetedtherapies they would be €4,111.8 million. Thus, the introduction of fixedtreatment oral targeted therapies would entail a saving of €564.9 million(12.1% of the total cost of care of chronic lymphocytic leukaemia patientsduring the period assessed).

Impact of an overdose reversal program in the context of a safe consumption site in Northern Mexico.

Background: Drug overdoses are prevalent in low- and middle-income countries but are scarcely reported in the literature. We report on an opioid overdose reversal and naloxone distribution program that was instituted at the first safe consumption site in Latin America. Methods: A cross-sectional analysis of witnessed drug overdoses and naloxone distribution between 1 June 2019 and 31 May 2021 in Mexicali, Mexico. Case report forms were entered in an electronic database. Trends in overdose and naloxone distribution were described. Comparisons were made before and after the COVID-19 pandemic was declared in the city. Maps were created to represent the geographic distribution of overdose in the city. Results: During the study period 1,534 doses of naloxone were distributed throughout the community. In addition, there were 464 overdoses reported during this period, of which 4 were fatal. There was a 30% increase in reported overdoses from the period before the COVID-19 pandemic to the period after the pandemic was declared (p = 0.03). Most common substance reported included heroin (93%), sedatives (21%), methamphetamine (16%) and fentanyl (14%). Naloxone was given in 96% of cases (median 1 dose, IQR 1-2 doses) and emergency services were called in 20% of cases. Conclusions: An opioid overdose reversal program in Mexicali, Mexico was able to distribute naloxone and register drug overdoses between 2019 and 2021 as a harm reduction strategy. This adds to the growing body of literature on the impact of community-based programs on preventing fatal overdoses and the potential for implementation in low-resource settings.

Genome-wide profiles of UV lesion susceptibility, repair, and mutagenic potential in melanoma.

Exposure to the ultraviolet (UV) radiation in sunlight creates DNA lesions, which if left unrepaired can induce mutations and contribute to skin cancer. The two most common UV-induced DNA lesions are the cis-syn cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), both of which can initiate mutations. Interestingly, mutation frequency across the genomes of many cancers is heterogenous with significant increases in heterochromatin. Corresponding increases in UV lesion susceptibility and decreases in repair are observed in heterochromatin versus euchromatin. However, the individual contributions of CPDs and 6-4PPs to mutagenesis have not been systematically examined in specific genomic and epigenomic contexts. In this study, we compared genome-wide maps of 6-4PP and CPD lesion abundances in primary cells and conducted comprehensive analyses to determine the genetic and epigenetic features associated with susceptibility. Overall, we found a high degree of similarity between 6-4PP and CPD formation, with an enrichment of both in heterochromatin regions. However, when examining the relative levels of the two UV lesions, we found that bivalent and Polycomb-repressed chromatin states were uniquely more susceptible to 6-4PPs. Interestingly, when comparing UV susceptibility and repair with melanoma mutation frequency in these regions, disparate patterns were observed in that susceptibility was not always inversely associated with repair and mutation frequency. Functional enrichment analysis hint at mechanisms of negative selection for these regions that are essential for cell viability, immune function and induce cell death when mutated. Ultimately, these results reveal both the similarities and differences between UV-induced lesions that contribute to melanoma.

Author Correction: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations.

The extreme dynamic behavior of intrinsically disordered proteins hinders the development of drug-like compounds capable of modulating them. There are several examples of small molecules that specifically interact with disordered peptides. However, their mechanisms of action are still not well understood. Here, we use extensive molecular dynamics simulations combined with adaptive sampling algorithms to perform free ligand binding studies in the context of intrinsically disordered proteins. We tested this approach in the system composed by the D2 sub-domain of the disordered protein p27 and the small molecule SJ403. The results show several protein-ligand bound states characterized by the establishment of a loosely oriented interaction mediated by a limited number of contacts between the ligand and critical residues of p27. Finally, protein conformations in the bound state are likely to be explored by the isolated protein too, therefore supporting a model where the addition of the small molecule restricts the available conformational space.

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations.

The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for [Formula: see text] 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel [Formula: see text]-sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations.

Sampling from the equilibrium distribution has always been a major problem in molecular simulations due to the very high dimensionality of the conformational space. Over several decades, many approaches have been used to overcome the problem. In particular, we focus on unbiased simulation methods such as parallel and adaptive sampling. Here, we recast adaptive sampling schemes on the basis of multi-armed bandits and develop a novel adaptive sampling algorithm under this framework, AdaptiveBandit. We test it on multiple simplified potentials and in a protein folding scenario. We find that this framework performs similarly to or better than previous methods in every type of test potential. Furthermore, it provides a novel framework to develop new sampling algorithms with better asymptotic characteristics.

The somatic mutation landscape of the human body.

BACKGROUND: Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet they remain largely uncharacterized. RESULTS: To gain a better understanding of the genome-wide distribution and functional impact of somatic mutations, we leverage the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, reveals a wide diversity of tissue-specific mutation profiles associated with gene expression levels and chromatin states. For example, lung samples with low expression of the mismatch-repair gene MLH1 show a mutation signature of deficient mismatch repair. In addition, we find pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which are under positive selection and are highly enriched in many healthy tissues. CONCLUSIONS: These findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis.

Effect of alkali ions on optical properties of flavins: vibronic spectra of cryogenic M+lumiflavin complexes (M = Li-Cs).

Flavin compounds are frequently used by nature in photochemical processes because of their unique optical properties which can be strongly modulated by the surrounding environment such as solvation or coordination with metal ions. Herein, we employ vibronic photodissociation spectroscopy of cryogenic M+LF complexes composed of lumiflavin (LF, C13H12N4O2), the parent molecule of the flavin family, and alkali ions (M = Li-Cs) to characterize the strong impact of metalation on the electronic properties of the LF chromophore. With the aid of time-dependent density functional theory calculations (PBE0/cc-pVDZ) coupled to multidimensional Franck-Condon simulations, the visible photodissociation (VISPD) spectra of M+LF ions recorded in the 500-570 nm range are assigned to the S1 ← S0 (ππ*) transitions into the first optically bright S1 state of the lowest-energy M+LF(O4+) isomers. In this O4+ structure, M+ binds in a bent chelate to the lone pairs of both the O4 and the N5 atom of LF. Charge reorganization induced by S1 excitation strongly enhances the interaction between M+ and LF at this binding site, leading to substantial red shifts in the S1 absorption of the order of 10-20% (e.g., from 465 nm in LF to 567 nm in Li+LF). This strong change in M+LF interaction strength in M+LF(O4+) upon ππ* excitation can be rationalized by the orbitals involved in the S1 ← S0 transition and causes strong vibrational activity. In particular, progressions in the intermolecular bending and stretching modes provide an accurate measure of the strength of the M+LF bond. In contrast to the experimentally identified O4+ ions, the predicted S1 origins of other low-energy M+LF isomers, O2+ and O2, are slightly blue-shifted from the S1 of LF, demonstrating that the electronic properties of metalated LF not only drastically change with the size of the metal ion but also with its binding site.

Effect of alkali ions on optical properties of flavins: vibronic spectra of cryogenic M+lumichrome ions (M = Li-Cs) in the gas phase.

The photochemical properties of flavins depend sensitively on their environment and are strongly modified by coordination with metal ions. Herein, the electronic spectra of cold complexes of the smallest flavin molecule (lumichrome, LC, C12N4O2H10) with alkali ions (M+LC, M = Li-Cs) are measured by photodissociation in the visible range (VISPD) in a cryogenic ion trap coupled to a tandem mass spectrometer and an electrospray ionization source. The observed vibronic spectra of all ions are assigned to the optically bright S1 ← S0 (ππ*) transition of the most stable O4 isomer of M+LC by comparison with quantum chemical calculations at the PBE0/cc-pVDZ level coupled to multidimensional Franck-Condon simulations. The rich vibronic spectra indicate substantial geometry changes upon S1 excitation. Large red shifts of the S1 origins upon metal complexation and progressions in the intermolecular in-plane metal stretch and bend modes demonstrate that the strength of the metal-flavin interaction in M+LC(O4) strongly increases by S1 excitation. The stronger M+LC bond in the S1 state of M+LC(O4) is rationalized by the charge reorganization upon ππ* excitation of the LC chromophore. The computations confirm that the optical properties of LC can be strongly modulated by metalation via both the type and binding site of the metal ion.

Optical spectroscopy of isolated flavins: photodissociation of protonated lumichrome.

The optical properties of flavins strongly depend on the charge and oxidation states as well as the environment. Herein, the electronic spectrum of cold protonated lumichrome, the smallest flavin molecule, is recorded by means of photodissociation in the visible range (VISPD) in a cryogenic ion trap tandem mass spectrometer coupled to an electrospray ionization source. The vibronic spectrum is assigned to the S1 ← S0 (ππ*) transition of the most stable N5-protonated isomer by comparison with quantum chemical calculations at the PBE0/cc-pVDZ level in combination with multidimensional Franck-Condon simulations. Analysis of the geometric and electronic structures of neutral and protonated lumichrome explains the large red shift of the band origin upon protonation (ΔS1 ∼ -6000 cm-1), which corresponds to the increase in proton affinity upon S1 excitation as a result of charge transfer. N5 protonation greatly modifies the structure of the central pyrazine ring of the chromophore. The orbitals involved in S1 ← S0 excitation include an important fraction of the probability at the central ring and they are, hence, largely influenced by the positive charge of the attached proton. The rich vibronic spectrum indicates the large geometry change upon S1 excitation. This combined experimental and computational approach is shown to be suitable to determine the optical properties of flavins as a function of oxidation, protonation, metalation, and microsolvation state.

The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation.

Chromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators in Saccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis. In particular, mitochondrial maintenance is disrupted in ies6 mutants. INO80 is also needed to communicate TORC1-mediated signaling to chromatin, as ino80 mutants exhibit defective transcriptional profiles and altered histone acetylation of TORC1-responsive genes. Furthermore, comparative analysis reveals subunits of INO80 and mTORC1 have high co-occurrence of alterations in human cancers. Collectively, these results demonstrate that the INO80 complex is a central component of metabolic homeostasis that influences histone acetylation and may contribute to disease when disrupted.

Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis.

The development of many sporadic cancers is directly initiated by carcinogen exposure. Carcinogens induce malignancies by creating DNA lesions (i.e., adducts) that can result in mutations if left unrepaired. Despite this knowledge, there has been remarkably little investigation into the regulation of susceptibility to acquire DNA lesions. In this study, we present the first quantitative human genome-wide map of DNA lesions induced by ultraviolet (UV) radiation, the ubiquitous carcinogen in sunlight that causes skin cancer. Remarkably, the pattern of carcinogen susceptibility across the genome of primary cells significantly reflects mutation frequency in malignant melanoma. Surprisingly, DNase-accessible euchromatin is protected from UV, while lamina-associated heterochromatin at the nuclear periphery is vulnerable. Many cancer driver genes have an intrinsic increase in carcinogen susceptibility, including the BRAF oncogene that has the highest mutation frequency in melanoma. These findings provide a genome-wide snapshot of DNA injuries at the earliest stage of carcinogenesis. Furthermore, they identify carcinogen susceptibility as an origin of genome instability that is regulated by nuclear architecture and mirrors mutagenesis in cancer.

IRMPD Spectroscopy of Metalated Flavins: Structure and Bonding of Lumiflavin Complexes with Alkali and Coinage Metal Ions.

Flavins are a fundamental class of biomolecules, whose photochemical properties strongly depend on their environment and their redox and metalation state. Infrared multiphoton dissociation (IRMPD) spectra of mass-selected isolated metal-lumiflavin ionic complexes (M+LF) are analyzed in the fingerprint range (800-1830 cm-1) to determine the bonding of lumiflavin with alkali (M = Li, Na, K, Cs) and coinage (M = Cu, Ag) metal ions. The complexes are generated in an electrospray ionization source coupled to an ion cyclotron resonance mass spectrometer and the IR free electron laser FELIX. Vibrational and isomer assignments of the IRMPD spectra are accomplished by comparison to quantum chemical calculations at the B3LYP/cc-pVDZ level, yielding structure, binding energy, bonding mechanism, and spectral properties of the complexes. The most stable binding sites identified in the experiments involve metal bonding to the oxygen atoms of the two available CO groups of LF. Hence, CO stretching frequencies are a sensitive indicator of both the metal binding site and the metal bond strength. More than one isomer is observed for M = Li, Na, and K, and the preferred CO binding site changes with the size of the alkali ion. For Cs+LF, only one isomer is identified, although the energies of the two most stable structures differ by less than 7 kJ/mol. While the M+-LF bonds for alkali ions are mainly based on electrostatic forces, substantial covalent contributions lead to stronger bonds for the coinage metal ions. Comparison between lumiflavin and lumichrome reveals substantial differences in the metal binding motifs and interactions due to the different flavin structures.