Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)

Cytosine methylation in CpG dinucleotides is believed to be important in gene regulation, and is generally associated with reduced levels of transcription. Methylation-mediated gene silencing involves a series of DNA-protein and protein-protein interactions that begins with the binding of methyl-CpG binding proteins (MBPs) followed by the recruitment of histone-modifying enzymes that together promote chromatin condensation and inactivation. It is widely known that alterations in methylation patterns, and associated gene activities, are often found in human tumors. However, the mechanisms by which methylation patterns are altered are not currently understood. In this paper, we investigate the impact of oxidative damage to a methyl-CpG site on MBP binding by the selective placement of 8-oxoguanine (8-oxoG) and 5-hydroxymethylcytosine (HmC) in a MBP recognition sequence. Duplexes containing these specific modifications were assayed for binding to the methyl-CpG binding domain (MBD) of one member of the MBP family, methyl-CpG binding protein 2 (MeCP2). Our results reveal that oxidation of either a single guanine to 8-oxoG or of a single 5mC to HmC, significantly inhibits binding of the MBD to the oligonucleotide duplex, reducing the binding affinity by at least an order of magnitude. Oxidative damage to DNA could therefore result in heritable, epigenetic changes in chromatin organization.

Chemical decomposition of 5-aza-2'-deoxycytidine (Decitabine): kinetic analyses and identification of products by NMR, HPLC, and mass spectrometry

The nucleoside analogue 5-aza-2'-deoxycytidine (Decitabine, DAC) is one of several drugs in clinical use that inhibit DNA methyltransferases, leading to a decrease of 5-methylcytosine in newly replicated DNA and subsequent transcriptional activation of genes silenced by cytosine methylation. In addition to methyltransferase inhibition, DAC has demonstrated toxicity and potential mutagenicity, and can induce a DNA-repair response. The mechanisms accounting for these events are not well understood. DAC is chemically unstable in aqueous solutions, but there is little consensus between previous reports as to its half-life and corresponding products of decomposition at physiological temperature and pH, potentially confounding studies on its mechanism of action and long-term use in humans. Here, we have employed a battery of analytical methods to estimate kinetic rates and to characterize DAC decomposition products under conditions of physiological temperature and pH. Our results indicate that DAC decomposes into a plethora of products, formed by hydrolytic opening and deformylation of the triazine ring, in addition to anomerization and possibly other changes in the sugar ring structure. We also discuss the advantages and problems associated with each analytical method used. The results reported here will facilitate ongoing studies and clinical trials aimed at understanding the mechanisms of action, toxicity, and possible mutagenicity of DAC and related analogues.

5-Formyluracil-induced perturbations of DNA function

Oxidation of the thymine methyl group can generate 5-formyluracil (FoU), which is known to be both mutagenic and chemically unstable in DNA. Synthetic oligonucleotides containing FoU at defined sites have been prepared to investigate potential mechanisms by which FoU might perturb DNA function. The half-life of the glycosidic bond of an FoU residue in single-stranded DNA under physiological conditions of temperature and pH is estimated to be approximately 148 days, orders of magnitude shorter than the parent pyrimidine, thymine. This reduced stability of FoU residues in DNA is attributed to the inductive properties of the 5-formyl substituent. Oxidative modification of the thymine methyl group could also inhibit association with sequence-specific DNA-binding proteins. Alternatively, the 5-formyl substituent of FoU could cross-link nonspecifically with protein amino groups. Transcription factor AP-1 is known to make specific contacts with thymine methyl groups of DNA in its recognition sequence. Substitution of T by FoU is shown to inhibit AP-1 (c-Jun homodimer) binding with a DeltaDeltaG of approximately 0.6 kcal/mol. No evidence of cross-link formation is observed with either AP-1 or polylysine. Molecular modeling studies on the FoU-containing oligonucleotide sequence corresponding to the duplex used in the experimental studies demonstrate that the 5-formyl substituent of an FoU residue paired with adenine lies in the plane of the pyrimidine base and is well protected from solvent on one face and only partially accessible on the other. The results of this study suggest that although FoU residues in DNA are considerably more labile than thymine, they are likely to be present long enough to miscode as well as interfere with DNA-protein interactions.

Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylase

hSMUG1 (human single-stranded selective monofunctional uracil-DNA glyscosylase) is one of three glycosylases encoded within a small region of human chromosome 12. Those three glycosylases, UNG (uracil-DNA glycosylase), TDG (thymine-DNA glyscosylase), and hSMUG1, have in common the capacity to remove uracil from DNA. However, these glycosylases also repair other lesions and have distinct substrate preferences, indicating that they have potentially redundant but not overlapping physiological roles. The mechanisms by which these glycosylases locate and selectively remove target lesions are not well understood. In addition to uracil, hSMUG1 has been shown to remove some oxidized pyrimidines, suggesting a role in the repair of DNA oxidation damage. In this paper, we describe experiments in which a series of oligonucleotides containing purine and pyrimidine analogs have been used to probe mechanisms by which hSMUG1 distinguishes potential substrates. Our results indicate that the preference of hSMUG1 for mispaired uracil over uracil paired with adenine is best explained by the reduced stability of a duplex containing a mispair, consistent with previous reports with Escherichia coli mispaired uracil-DNA glycosylase. We have also extended the substrate range of hSMUG1 to include 5-carboxyuracil, the last in the series of damage products from thymine methyl group oxidation. The properties used by hSMUG1 to select damaged pyrimidines include the size and free energy of solvation of the 5-substituent but not electronic inductive properties. The observed distinct mechanisms of base selection demonstrated for members of the uracil glycosylase family help explain how considerable diversity in chemical lesion repair can be achieved.

Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The DNA of all organisms is persistently damaged by endogenous reactive molecules. Most of the single-base endogenous damage is repaired through the base excision repair (BER) pathway that is initiated by members of the DNA glycosylase family. Although the BER pathway is often considered to proceed through a common abasic site intermediate, emerging evidence indicates that there are likely distinct branches reflected by the multitude of chemically different 3' and 5' ends generated at the repair site. In this study, we have applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the analysis of model DNA substrates acted on by recombinant glycosylases. We examine the chemical identity of several possible abasic site and nicked intermediates generated by monofunctional and bifunctional glycosylases. Our results suggest that the intermediate from endoIII/Nth might not be a simple beta-elimination product as described previously. On the basis of (18)O incorporation experiments, we propose a new mechanism for the endoIII/Nth family of glycosylases that may resolve several of the previous controversies. We further demonstrate that the use of an array of lesion-containing oligonucleotides can be used to rapidly examine the substrate preferences of a given glycosylase. Some of the lesions examined here can be acted on by more than one glycosylase, resulting in a spectrum of damaged intermediates for each lesion, suggesting that the sequence and coordination of repair activities that act on these lesions may influence the biological outcome of damage repair.

Endogenous DNA lesions can inhibit the binding of the AP-1 (c-Jun) transcription factor

The repair of DNA damage, caused by both endogenous and exogenous sources, is necessary to remove lesions that either miscode or block DNA or RNA polymerases. We propose that damage also must be repaired to maintain sequence-specific DNA-protein interactions. In this paper, we have systematically studied two lesions that interfere with one important DNA landmark, the thymine methyl group. Oxidation of the thymine methyl group in DNA generates 5-hydroxymethyluracil (HmU) whereas the misincorporation of dUMP into DNA generates uracil (U), replacing the methyl group with a hydrogen. Both substitutions are shown to inhibit binding of the AP-1 (c-Jun) transcription factor. The energy cost of the perturbation, approximately 0.4 kcal/mol, is similar in magnitude for both U and HmU substitutions and is additive when multiple substitutions are present. A third lesion, substitution of the central C:G base pair of the AP-1 DNA binding domain with the pro-mutagenic U:G mispair, unexpectedly increases AP-1 binding, allowing the transcription factor to interfere with uracil DNA glycosylase activity. Our results support the hypothesis that an additional role for DNA repair systems is to maintain the integrity of sequence-specific DNA-protein interactions, a role of particular importance in long-lived organisms.

Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair

Inflammation-mediated reactive molecules can damage DNA by oxidation and chlorination. The biological consequences of this damage are as yet incompletely understood. In this paper, we have constructed oligonucleotides containing 5-chlorouracil (ClU), one of the known inflammation damage products. The thermodynamic stability, base pairing configuration, and duplex conformation of oligonucleotides containing ClU paired opposite adenine have been examined. NMR spectra reveal that the ClU-A base pair adopts a geometry similar to that of the T-A base pair, and the ClU-A base pair-containing duplex adopts a normal B-form conformation. The line width of the imino proton of the ClU residue is substantially greater than that of the corresponding T imino proton; however, this difference is not attributed to a reduced thermal or thermodynamic stability or to an increased level of proton exchange with solvent. While the NMR studies reveal an increased level of chemical exchange for the ClU imino proton of the ClU-A base pair, the ClU residue is not a target for removal by the Escherichia coli mispaired uracil glycosylase, which senses damage-related helix instability. The results of this study are consistent with previous reports indicating that the DNA of replicating cells can tolerate substantial substitution with ClU. The fraudulent, pseudo-Watson-Crick ClU-A base pair is sufficiently stable to avoid glycosylase removal and, therefore, might constitute a persistent form of cellular DNA damage.

Enzymatic methylation of DNA in cultured human cells studied by stable isotope incorporation and mass spectrometry

Enzymatic methylation of cytosine residues in DNA, in conjunction with covalent histone modifications, establishes an epigenetic code essential for the proper control of gene expression in higher organisms. Once established during cellular differentiation, the epigenetic code must be faithfully transmitted to progeny cells. However, epigenetic perturbations can be found in most if not all cancer cells, and the mechanisms leading to these changes are not well understood. In this paper, we describe a series of experiments aimed at understanding the dynamic process of DNA methylation that follows DNA replication. Cells in culture can be propagated in the presence of (15)N-enriched uridine, which labels the pyrimidine precursor pool as well as newly replicated DNA. Simultaneous culture in the presence of (2)H-enriched methionine results in labeling of newly methylated cytosine residues. An ensemble of 5-methylcytosine residues differing in the degree of isotopic enrichment is generated, which can be examined by mass spectrometry. Using this method, we demonstrate that the kinetics of both DNA replication and methylation of newly replicated DNA are indistinguishable. The majority of methylation following DNA replication is shown to occur on the newly synthesized DNA. The method reported here does, however, suggest an unexpected methylation of parental DNA during DNA replication, which might indicate a previously undescribed chromatin remodeling process. The method presented here will be useful in monitoring the dynamic process of DNA methylation and will allow a more detailed understanding of the mechanisms of clinically used methylation inhibitors and environmental toxicants.

Asthma Care in the Elderly: Practical Guidance and Challenges for Clinical Management - A Framework of 5 "Ps"

Uncontrolled asthma in the elderly is a public health issue recognized in developed countries such as the United States and among the European Union, both from patient safety and economic perspectives. Variations in the cutoff, which defines elderly age, contribute to epidemiological study difficulties. Nonetheless, the relevance of elderly asthma from a socioeconomic perspective is inarguable. The projected growth of the enlarging geriatric population in the United States portends an impending national health burden that may or may not be preventable with pharmacologic and non-pharmacologic treatments. Asthma in the elderly might be a consequence of uncontrolled disease that is carried throughout a lifetime. Or elderly asthmatics could suffer from uncontrolled asthma, which overlaps with other ailments common with advancing ages that merit consideration, eg, COPD, heart disease, OSA, diabetes mellitus, and other comorbidities. Because of the heterogeneity of asthma phenotypes and other conditions that could mimic the symptoms of elderly asthma, further cohort studies are needed to elucidate the elderly asthmatic pathophysiology and management. More studies to characterize elderly asthma can help address these patients' unmet need for evidence-based guidelines. We introduce the 5 "Ps" (phenotypes, partnership, pharmacology, practice in acute exacerbations, and problems or barriers for the elderly asthmatics) that establish a framework approach for clinical practice.

Measurement of the incorporation and repair of exogenous 5-hydroxymethyl-2'-deoxyuridine in human cells in culture using gas chromatography-negative chemical ionization-mass spectrometry

The DNA of all organisms is constantly damaged by oxidation. Among the array of damage products is 5-hydroxymethyluracil, derived from oxidation of the thymine methyl group. Previous studies have established that HmU can be a sensitive and valuable marker of DNA damage. More recently, the corresponding deoxynucleoside, 5-hydroxymethyl-2'-deoxyuridine (HmdU), has proven to be valuable for the introduction of controlled amounts of a single type of damage lesion into the DNA of replicating cells, which is subsequently repaired by the base excision repair pathway. Complicating the study of HmU formation and repair, however, is the known chemical reactivity of the hydroxymethyl group of HmU under conditions used to hydrolyze DNA. In the work reported here, this chemical property has been exploited by creating conditions that convert HmU to the corresponding methoxymethyluracil (MmU) derivative that can be further derivatized to the 3,5-bis-(trifluoromethyl)benzyl analogue. This derivatized compound can be detected by gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) with good sensitivity. Using isotopically enriched exogenous HmdU and human osteosarcoma cells (U2OS) in culture, we demonstrate that this method allows for the measurement of HmU in DNA formed from the incorporation of exogenous HmdU. We further demonstrate that the addition of isotopically enriched uridine to the culture medium allows for the simultaneous measurement of DNA replication and repair kinetics. This sensitive and facile method should prove valuable for studies on DNA oxidation damage and repair in living cells.

Fatal recurrent disseminated Lomentospora prolificans infection during autologous hematopoietic stem cell transplantation: A case report and review, and discussion on the importance of prolonged neutropenia

Infections with Scedosporium and Lomentospora species, in particular Lomentospora (previously Scedosporium) prolificans, are nearly universally fatal and rapidly-progressive in the transplant population. We report a case of a patient with diffuse large B-cell lymphoma undergoing myelosuppressive chemotherapy who developed disseminated L. prolificans infection which afterward persisted in his knee joint. The infection was treated with early empiric triple antifungal therapy tailored to synergy studies, growth factors to quickly resolve neutropenia, and aggressive debridement (where possible) of infection sites, including amputation. He achieved an 11-month remission until undergoing autologous hematopoietic stem cell transplantation with deep myelosuppression, wherein recrudescent L. prolificans infection occurred, causing death. We highlight the importance of early treatment, synergy studies, and especially recovery of neutropenia in treating this devastating condition.

Evaluating a novel team learning approach for integrating drugs in sports education in preclinical medical training

Use of performance-enhancing drugs and supplements continues to be pervasive in sports. Medical practitioners are key because they are well positioned to prevent doping among athletes as they are a trusted resource for the patients whom they serve. At Loma Linda University School of Medicine, we are seeking to provide medical students with education on the topic of drugs in sports so that they can better serve their patients. This study evaluated the implementation of a novel Case-Based Team Learning session on drugs in sports for preclinical first year (MS1) and second year (MS2) medical students. The session aimed to introduce fundamental concepts of performance-enhancing drugs, anti-doping regulations, and patient communication strategies within the context of sports medicine. Post instructional survey data on the learning environment and qualitative feedback responses were collected from 189 MS1 and 170 MS2 students. Results of the quantitative data showed that MS1 students rated the session more positively than MS2 students. Qualitative data was collected through open-ended questions, allowing for more detailed and nuanced responses. AI models were used to identify common themes and patterns in the qualitative feedback responses. These responses provided valuable insights for future curriculum refinement and development of the newly implemented drugs in sports education program. Both cohorts appreciated the interactive nature of the session and real-life applications but identified areas for improvement, including better alignment with curriculum objectives and exam preparation. Key challenges included balancing content relevance with broader medical education goals and integrating communication skills training within a large group setting. Faculty reflection highlighted the need for restructuring the session to better match instructional block content and USMLE Step 1 exam preparation. Future iterations will focus on emphasizing drug pharmacology, mechanisms of action, and physiological effects for MS1 students, while providing opportunities for more comprehensive knowledge integration through the case studies for MS2 students. This evaluation of the learning session underscores the importance of iterative curriculum development in medical education, particularly when introducing novel topics like drugs in sports.

AIDS-Associated BK Virus Nephropathy in Native Kidneys: A Case Report and Review of the Literature

BK virus (BKV) is a small DNA virus, a member of the polyomavirus family, that causes an opportunistic infection in immunocompromised patients, especially kidney transplant patients. This virus establishes a lifelong infection in most of the population, and once it reactivates in an immunocompromised state, leads to BKV nephropathy. This review seeks to assess the correlation between severe immunosuppression, evident by low CD4 cell counts in HIV-positive patients, and the reactivation of BKV, causing nephropathy. A literature review was conducted, extracting, and analyzing case reports of HIV-positive patients showing correlations between their degree of immunosuppression, as evidenced by their CD4 counts, and the degree of BKV infectivity, confirmed by kidney biopsy. A total of 12 cases of BKV nephropathy in HIV-infected patients were reviewed. A common finding was the presence of profound immunosuppression, with most patients having CD4 counts ≤50 cells/ mm3. A substantial number also had comorbid malignancies, with some undergoing chemotherapy, potentially increasing the risk of BKV reactivation. In addition to the HIV status and malignancies, other risk factors for BKV reactivation included older age, male gender, diabetes mellitus, Caucasian race, and ureteral stent placement. BKV nephropathy in HIV patients with native kidneys is closely correlated with severe immunosuppression. Although therapeutic strategies exist for post-transplant patients, aside from the treatment of HIV with highly active anti-retroviral therapy (HAART), which potentially helps with clearing BKV by increasing CD4 count, there is no definitive treatment for a native kidney BKV nephropathy in patients with AIDS. The complexity of the cases and severity of comorbidities indicate the need for further research to develop therapeutic strategies tailored to this population.

Utility of multimodal sampling and testing during advanced bronchoscopy for diagnosing atypical respiratory infections in a Coccidioides-endemic region

Background

The role of advanced diagnostic bronchoscopy (ADB) for assessing atypical respiratory infections is unclear. The purpose of this study was to ascertain: (I) the diagnostic utility of ADB-tissue sampling in patients with focal thoracic lesions due to atypical respiratory infections; (II) how multimodal bronchoscopic sampling and testing enhance diagnosis in a Coccidioides-endemic region.

Methods

A retrospective observational cohort study analyzing all ADBs performed over a 10-year period in patients with focal thoracic lesions diagnosed with a non-malignant disorder. Only cases which procured lower respiratory tract secretion and tissue samples by ADB, and had both cytohistology and culture results available were included.

Results

Among 403 subjects with non-malignant disease, 136 (33.7%) were diagnosed with atypical respiratory infections, with ADB contributing a diagnosis in 119 (87.5%) of these. Coccidioidal disease was independently associated with a cytohistologic diagnosis [odds ratio =7.64, 95% confidence interval (CI): 2.51-23.26; P<0.001]. Mycobacteria were more effectively identified by culture (overall yield of 8.4%, vs. 2.7% by cytohistology; P<0.001). Among subjects for which both respiratory secretion and tissue sampling were dual-tested with culture and cytology/cytohistology, adding ADB-guided transbronchial needle aspiration and/or forceps biopsy (TBNA/TBFB) to bronchoalveolar lavage and/or bronchial washings (BAL/BW) more than doubled the yield for dimorphic fungi, from 7.1% to 15.1% (increase of 8.0%, 95% CI: 5.2-11.9%). For lung lesions, adding tissue culture to dual TBNA/TBFB cytohistology-tested lung samples doubled the proportion diagnosed with atypical infection over using TBNA-cytohistology alone (increase of 15.8%, 95% CI: 10.4-23.1%). Adding lymph node to lung sampling increased the proportion diagnosed with coccidioidomycosis by 8.8% (95% CI: 4.8-15%). Among subjects with atypical respiratory infections, major ADB-related complications occurred in 1.5%.

Conclusions

ADB is useful for diagnosing atypical respiratory infections manifesting as focal thoracic lesions. A multimodal approach to both sampling and testing enhances yield, while maintaining a favorable procedure safety profile. Cytohistology testing and nodal sampling are beneficial for pulmonary coccidioidomycosis, and culture for mycobacterial disease. The approach to ADB-sampling should be adjusted according to clinical context and regional infection patterns.

Cryptogenic HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella) CNS Abscess in an Otherwise Healthy Patient With a Patent Foramen Ovale

Actinomyces and HACEK (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella) organisms are part of the oral microbiome and rarely affect the central nervous system (CNS). CNS infections with these agents can be caused by contiguous or hematogenous spread. We present a case of a 25-year-old immunocompetent male who presented with a one-week history of progressively worsening generalized headaches, photophobia, nausea, and vomiting. Despite a normal physical exam and the absence of leukocytosis, head imaging showed a right frontal lobe abscess. The patient was started empirically on vancomycin, ceftriaxone, and metronidazole, and surgery was performed. Surgical cultures grew organisms from the HACEK spectrum (Aggregatibacter, Eikenella), Gemella morbillorum, Streptococcus constellatus, and Actinomyces georgiae. Serial imaging studies showed a rapid increase in the size of the residual abscess, and the patient needed repeat intervention within five days. He was discharged five days after the repeat surgery on IV therapy prior to the transition to oral antibiotics. While the patient was found to have a small patent foramen ovale, there was no evidence of bacteremia or valvular vegetation, and no evidence of dental or sinus disease was seen on imaging. This case suggests that even in the absence of any clear sources of infection, cryptogenic brain abscesses can still occur sporadically in young, healthy patients.