Using Chemical Epigenetics to Target Cancer.

Transcription is epigenetically regulated by the orchestrated function of chromatin-binding proteins that tightly control the expression of master transcription factors, effectors, and supportive housekeeping genes required for establishing and propagating the normal and malignant cell state. Rapid advances in chemical biology and functional genomics have facilitated exploration of targeting epigenetic proteins, yielding effective strategies to target transcription while reducing toxicities to untransformed cells. Here, we review recent developments in conventional active site and allosteric inhibitors, peptidomimetics, and novel proteolysis-targeted chimera (PROTAC) technology that have deepened our understanding of transcriptional processes and led to promising preclinical compounds for therapeutic translation, particularly in cancer.

Deliberate foreign body ingestion in patients with underlying mental illness: A retrospective multicentre study.

OBJECTIVE: Deliberate foreign body ingestion (DFBI) is characterised by recurrent presentations among patients with mental health conditions, intellectual disabilities and in prisoners. We aimed to profile the characteristics and evaluate the care of such patients in this study. METHODS: Adult patients with an endoscopic record of attempted foreign body retrieval between January 2013 and September 2020 were identified at three Australian hospitals. Those with a documented mental health diagnosis were included and their standard medical records reviewed. Presentation history, demographics, comorbidities and endoscopic findings were recorded and described. RESULTS: A total of 166 admissions were accounted for by 35 patients, 2/3 of which had borderline personality disorder (BPD). Repetitive presentations occurred in more than half of the cohort. There was an increased trend of hospital admissions throughout the years. At least half of the cohort had a documented mental health review during their admission. An average of 3.3 (2.9) foreign bodies were ingested per single episode. Endoscopic intervention was performed in 76.5% of incidents. The combined Length of stay for all patients was 680 days. CONCLUSION: Deliberate foreign body ingestion in mental health patients is a common, recurring and challenging problem that is increasing in frequency and requires collaborative research to further guide holistic management.

1,4-Dihydropyridinebutyrolactone-derived ring-opened ester and amide analogs targeting BET bromodomains.

Based on a previously reported 1,4-dihydropyridinebutyrolactone virtual screening hit, nine lactone ring-opened ester and seven amide analogs were prepared. The analogs were designed to provide interactions with residues at the entrance of the ZA loop of the testis-specific bromodomain (ZA) channel to enhance the affinity and selectivity for the bromodomain and extra-terminal (BET) subfamily of bromodomains. Compound testing by AlphaScreen showed that neither the affinity nor the selectivity of the ester and lactam analogs was improved for BRD4-1 and the first bromodomain of the testis-specific bromodomain (BRDT-1). The esters retained affinity comparable to the parent compound, whereas the affinity for the amide analogs was reduced 10-fold. A representative benzyl ester analog was found to retain high selectivity for BET bromodomains as shown by a BROMOscan. X-ray analysis of the allyl ester analog in complex with BRD4-1 and BRDT-1 revealed that the ester side chain is located next to the ZA loop and solvent exposed.

Impact of Race and Socioeconomic Status on Psychologic Outcomes in Childhood Cancer Patients and Caregivers.

Complex relationships between race and socioeconomic status have a poorly understood influence on psychologic outcomes in pediatric oncology. The Family Symptom Inventory was used to assess symptoms of depression and anxiety in pediatric patients with cancer and their caregivers. Separate hierarchical linear regression models examined the relationship between demographic variables, cancer characteristics, socioeconomic status, and access to care and patient or caregiver depression/anxiety. Participants included 196 pediatric patients with cancer (mean age, 11.21 y; 49% African American) and their caregivers. On average, caregivers reported low levels of depression/anxiety. Symptoms of depression and anxiety in patients were correlated with poorer mental health in caregivers (r=0.62; P<0.01). Self-reported financial difficulty (ß=0.49; P<0.001) and brain cancer diagnosis for their child (ß=0.42; P=0.008) were significantly associated with depression and anxiety in caregivers. Analysis did not reveal significant associations between race, household income, or access to care and patient or caregiver depression/anxiety. Perception of financial hardship can adversely impact mental health in caregivers of children with cancer. Psychosocial assessment and interventions may be especially important for caregivers of patients with brain tumors and caregivers who report feeling financial difficulty.

Screening Positive for Cognitive Impairment: Impact on Healthcare Utilization and Provider Action in Primary and Specialty Care Practices.

BACKGROUND: Alzheimer's disease, the most common cause of dementia, goes unrecognized in half of patients presenting to healthcare providers and is associated with increased acute care utilization. Routine cognitive screening of older adults in healthcare settings could improve rates of dementia diagnosis and patterns of healthcare utilization. OBJECTIVE: To evaluate the impact of screening positive for cognitive impairment on provider action in primary and specialty care practices and patient healthcare utilization. DESIGN: Individuals asymptomatic for cognitive impairment completed cognitive screening with the Mini-Cog (MC). Outcomes included MC screen-positive rates, provider follow-up actions, and healthcare utilization for all participants over a period of 36 months (18 months prior to and following MC screening). Data were extracted from the electronic medical record (EMR). Healthcare provider interventions and healthcare utilization for screen-positive and -negative groups, before and after screening, were compared. PARTICIPANTS: Primary and specialty care patients (n = 787) aged ≥ 65 without history of cognitive impairment seen in HealthPartners, an integrated healthcare system in Minnesota and Western Wisconsin. KEY RESULTS: In primary care and neurology practices combined, over the entire 36-month study window, individuals screening positive showed 32% higher rates of ED visits (p < 0.05) pre and post-screening compared to those screening negative. Screen positive also showed 39% higher rates of hospitalizations pre-screening (p < 0.05) and 58% higher rates post-screening (p < 0.01). While screen-detected cognitive impairment was associated with some relevant provider follow-up action in 32% of individuals, subsequent healthcare utilization did not change between the 18-month pre- and post-screening periods. CONCLUSION: Despite being associated with higher rates of healthcare utilization, screening positive on the MC led to a change in provider action in a minority of cases and did not reduce post-screening healthcare utilization. Screening for cognitive impairment alone is not sufficient to alter patterns of provider practice or patient healthcare utilization.

Effect of Ionic Strength on Solvation Geometries in Aqueous Nitrate Ion Solutions.

Temperature-dependent infrared spectra of aqueous nitrate solutions with a range of concentrations and ionic strengths are used to determine the effect of ionic strength on the relative stabilities of different solvation geometries in aqueous nitrate ion. The asymmetric stretching absorption band from 1250 to 1450 cm-1 changes line shape with temperature, allowing two distinct peaks to be fit for each spectrum. Because each peak is assigned based on electronic structure calculations as a proxy to a different solvation motif, van't Hoff plots provide insight into the thermodynamics of exchange between different solvation geometries. A strong linear trend is seen between increased ionic strength and the magnitude of both the enthalpic and entropic contributions to the solvation geometry stabilities. Electronic structure computations of previously proposed structures in different ionic strengths are performed in the presence of external fields, roughly simulating the impact of ions in solution.

Achieving a Safe Endotracheal Tube Cuff Pressure in the Prehospital Setting: Is It Time to Revise the Standard Cuff Inflation Practice?

Numerous studies have reported unsafe endotracheal tube (ETT) cuff pressures (CP) in the prehospital environment. The purpose of this study was to identify an optimal cuff inflation volume (CIV) to achieve a safe CP (20-30 cmH2O). This observational study utilized 30 recently harvested ovine tracheae, which were warmed from refrigeration in a water bath at 85°F prior to testing. Each trachea was intubated with five different ETT sizes (6.0-8.0 mm), and each size tube was tested with six cuff inflation volumes (5-10 cc). The order of ETT size for each trachea and CIV for each size ETT was randomly pre-assigned. Data were descriptively summarized and categorized before mixed-effects logistic regression was used to determine optimal CIV. Only 113 CP measurements (12.6%, N = 900) were within the optimal range (M = 54.75 cmH2O, SD = 38.52), all of which resulted from a CIV 6 or 7 cc (61% and 39%, respectively). CIVs of 5 cc (n = 150) resulted in underinflation (<20 cmH2O) in all instances, while CIVs of 8, 9, or 10 cc (n = 150 each) resulted in overinflation (>30 cmH2O) in all instances, regardless of ETT size. The odds of achieving a safe CP were greater with CIV of 6 cc for tube sizes 6.0 (OR = 15.9, 95% CI = 3.85-65.58, p < 0.01) and 6.5 mm (OR = 3.16, 95% CI = 1.06-9.39, p = 0.039); however, there was no significant difference in the odds of achieving a safe CP between CIV of 6 and 7 cc for tube sizes 7.0, 7.5, or 8.0 mm. Neither trachea circumference (M = 7.11 cm, SD = 0.40), nor tissue temperature (M = 81.32°F, SD = 0.93) were found to be significant predictors of CP (p = 0.20 and 0.81, respectively). Our study showed a high frequency of CP measurements outside of the desired norms. The CIV range of 6-7 cc resulted in the highest likelihood of achieving the desired cuff pressure range, while cuffs inflated with 8-10 cc resulted in dangerously high CPs in all instances. In the absence of a more ideal solution, the results of this study suggest that narrowing the recommended CIV from 5-10 cc to 6-7 cc might be a reasonable target for any tube size.

Does computed tomographic scan affect diagnosis and management of patients with suspected renal colic?

BACKGROUND: Patients with renal colic commonly present to the emergency department (ED) and are usually treated with analgesics, antiemetics and hydration. Computed tomographic (CT) scan is commonly utilized in evaluating patients with suspected renal colic. OBJECTIVES: We compared diagnosis and treatment plans before and after CT in patients with suspected renal colic with the aim to evaluate how often changes in diagnosis, treatment and disposition are made. METHODS: In this prospective observational study, we enrolled a convenience sample of clinically Stable ED patients older than 17 with suspected renal colic for whom CT was planned. Exclusion criteria were: chronic kidney disease, urinary tract infection, recent CT and history of previous kidney stone. Pre-CT and Post-CT surveys were completed by the treating provider. RESULTS: The discharge diagnosis was renal colic in 62 of 93 enrolled patients (67%). Urinalysis showed blood in 52 of these patients (84%). CT confirmed obstructing kidney or bladder stone in 50 patients. There were five cases of alternative diagnoses noted on CT scan. After CT scan, 7 patients had changes in disposition. Sixteen providers felt that CT would not change management. In these cases, CT offered no alternative diagnosis and didn't change disposition. CONCLUSION: CT scan didn't change management when providers did not expect it would. This indicates that providers who are confident with the diagnosis of renal colic should consider forgoing a CT scan. CT scan did occasionally find important alternative diagnoses and should be utilized when providers are considering other concerning pathology.

Metabolic potential of Nitrososphaera-associated clades.

Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. Seventy-two MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition.

Chemical discovery efforts commonly target individual protein domains. Many proteins, including the EP300/CBP histone acetyltransferases (HATs), contain several targetable domains. EP300/CBP are critical gene-regulatory targets in cancer, with existing high potency inhibitors of either the catalytic HAT domain or protein-binding bromodomain (BRD). A domain-specific inhibitory approach to multidomain-containing proteins may identify exceptional-responding tumor types, thereby expanding a therapeutic index. Here, we discover that targeting EP300/CBP using the domain-specific inhibitors, A485 (HAT) or CCS1477 (BRD) have different effects in select tumor types. Group 3 medulloblastoma (G3MB) cells are especially sensitive to BRD, compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, bromodomain inhibition causes rapid disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB.

Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture.

Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (µ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing µ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of µmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards µmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.

Radiographic Comparison of Heterotopic Ossification After Primary Total Ankle Arthroplasty in Fourth-Generation Implants.

LEVEL OF EVIDENCE: Level III: Retrospective comparative.

Outcomes and Complications of the INFINITY Total Ankle: A Systematic Review.

LEVEL OF EVIDENCE: IV.

Unexpected complexity of the ammonia monooxygenase in archaea.

Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.

SALL4B, not targeted by IMiD, is important for SALL4-mediated tumorigenesis.

Oncofetal transcription factor SALL4 is essential for cancer cell survival. 1-5 Recently, several groups reported that immunomodulatory imide drugs (IMiDs) could degrade SALL4 in a proteasome-dependent manner. 6,7 Intriguingly, we observed that IMiDs had no effect on SALL4-positive cancer cells. Further studies demonstrated that IMiDs could only degrade SALL4A, one of the SALL4 isoforms. This finding raises the possibility that SALL4B, the isoform not affected by IMiDs, may be essential for SALL4-mediated cancer cell survival. SALL4B knockdown led to an increase in apoptosis and inhibition of cancer cell growth. SALL4B gain-of-function alone led to liver tumor formation in mice. Our observation that protein degraders can possess isoform-specific effects exemplifies the importance of delineating drug action and oncogenesis at the isoform level to develop more effective cancer therapeutics.

Template-assisted covalent modification of DCAF16 underlies activity of BRD4 molecular glue degraders.

Small molecules that induce protein-protein interactions to exert proximity-driven pharmacology such as targeted protein degradation are a powerful class of therapeutics1-3. Molecular glues are of particular interest given their favorable size and chemical properties and represent the only clinically approved degrader drugs4-6. The discovery and development of molecular glues for novel targets, however, remains challenging. Covalent strategies could in principle facilitate molecular glue discovery by stabilizing the neo-protein interfaces. Here, we present structural and mechanistic studies that define a trans-labeling covalent molecular glue mechanism, which we term "template-assisted covalent modification". We found that a novel series of BRD4 molecular glue degraders act by recruiting the CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). BRD4BD2, in complex with DCAF16, serves as a structural template to facilitate covalent modification of DCAF16, which stabilizes the BRD4-degrader-DCAF16 ternary complex formation and facilitates BRD4 degradation. A 2.2 Å cryo-electron microscopy structure of the ternary complex demonstrates that DCAF16 and BRD4BD2 have pre-existing structural complementarity which optimally orients the reactive moiety of the degrader for DCAF16Cys58 covalent modification. Systematic mutagenesis of both DCAF16 and BRD4BD2 revealed that the loop conformation around BRD4His437, rather than specific side chains, is critical for stable interaction with DCAF16 and BD2 selectivity. Together our work establishes "template-assisted covalent modification" as a mechanism for covalent molecular glues, which opens a new path to proximity driven pharmacology.

Borrelia burgdorferi cp32 BpaB modulates expression of the prophage NucP nuclease and SsbP single-stranded DNA-binding protein.

The Borrelia burgdorferi BpaB proteins of the spirochete's ubiquitous cp32 prophages are DNA-binding proteins, required both for maintenance of the bacteriophage episomes and for transcriptional regulation of the cp32 erp operons. Through use of DNase I footprinting, we demonstrate that BpaB binds the erp operator initially at the sequence 5'-TTATA-3'. Electrophoretic mobility shift assays indicated that BpaB also binds with high affinity to sites located in the 5' noncoding regions of two additional cp32 genes. Characterization of the proteins encoded by those genes indicated that they are a single-stranded DNA-binding protein and a nuclease, which we named SsbP and NucP, respectively. Chromatin immunoprecipitation indicated that BpaB binds erp, ssbP, and nucP in live B. burgdorferi. A mutant bacterium that overexpressed BpaB produced significantly higher levels of ssbP and nucP transcript than did the wild-type parent.

BpaB and EbfC DNA-binding proteins regulate production of the Lyme disease spirochete's infection-associated Erp surface proteins.

Vector-borne pathogens regulate their protein expression profiles, producing factors during host infection that differ from those produced during vector colonization. The Lyme disease agent, Borrelia burgdorferi, produces Erp surface proteins throughout mammalian infection and represses their synthesis during colonization of vector ticks. Known functions of Erp proteins include binding of host laminin, plasmin(ogen), and regulators of complement activation. A DNA region immediately 5' of erp operons, the erp operator, is required for transcriptional regulation. The B. burgdorferi BpaB and EbfC proteins exhibit high in vitro affinities for erp operator DNA. In the present studies, chromatin immunoprecipitation (ChIP) demonstrated that both proteins bind erp operator DNA in vivo. Additionally, a combination of in vivo and in vitro methods demonstrated that BpaB functions as a repressor of erp transcription, while EbfC functions as an antirepressor.