Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer.

A prominent source of mutation in cancer is single-stranded DNA cytosine deamination by cellular APOBEC3 enzymes, which results in signature C-to-T and C-to-G mutations in TCA and TCT motifs. Although multiple enzymes have been implicated, reports conflict and it is unclear which protein(s) are responsible. Here we report the development of a selectable system to quantify genome mutation and demonstrate its utility by comparing the mutagenic activities of three leading candidates-APOBEC3A, APOBEC3B, and APOBEC3H. The human cell line, HAP1, is engineered to express the thymidine kinase (TK) gene of HSV-1, which confers sensitivity to ganciclovir. Expression of APOBEC3A and APOBEC3B, but not catalytic mutant controls or APOBEC3H, triggers increased frequencies of TK mutation and similar TC-biased cytosine mutation profiles in the selectable TK reporter gene. Whole genome sequences from independent clones enabled an analysis of thousands of single base substitution mutations and extraction of local sequence preferences with APOBEC3A preferring YTCW motifs 70% of the time and APOBEC3B 50% of the time (Y = C/T; W = A/T). Signature comparisons with breast tumor whole genome sequences indicate that most malignancies manifest intermediate percentages of APOBEC3 signature mutations in YTCW motifs, mostly between 50 and 70%, suggesting that both enzymes contribute in a combinatorial manner to the overall mutation landscape. Although the vast majority of APOBEC3A- and APOBEC3B-induced single base substitution mutations occur outside of predicted chromosomal DNA hairpin structures, whole genome sequence analyses and supporting biochemical studies also indicate that both enzymes are capable of deaminating the single-stranded loop regions of DNA hairpins at elevated rates. These studies combine to help resolve a long-standing etiologic debate on the source of APOBEC3 signature mutations in cancer and indicate that future diagnostic and therapeutic efforts should focus on both APOBEC3A and APOBEC3B.

Changing the phospholipid composition of lipid droplets alters localization of select lipid droplet proteins.

Our experiments aim to determine if decreasing the amount of phosphatidylcholine (PC) relative to phosphatidylethanolamine (PE) at the lipid droplet surface changes the localization of specific lipid droplet proteins. We manipulate lipid droplet phospholipids in both a cultured mouse hepatocyte (AML12) cell line and on synthetic lipid droplets. Decreasing the PC:PE ratio increases perilipin 2, decreases DGAT2, and does not change rab18 or lanosterol synthase levels on lipid droplets. These differences may be explained by the distinct structural motifs that mediate the protein-lipid droplet interactions.

APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.

The single-stranded DNA cytosine-to-uracil deaminase APOBEC3B is an antiviral protein implicated in cancer. However, its substrates in cells are not fully delineated. Here APOBEC3B proteomics reveal interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R-loops in cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B and decreases in cells overexpressing APOBEC3B. Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions, as well as binding of APOBEC3B to many of these sites. APOBEC3 mutagenesis impacts genes overexpressed in tumors and splice factor mutant tumors preferentially, and APOBEC3-attributed kataegis are enriched in RTCW motifs consistent with APOBEC3B deamination. Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B regulates R-loops and contributes to R-loop mutagenesis in cancer.

Single-cell analysis of human nasal mucosal IgE antibody secreting cells reveals a newly minted phenotype.

Immunoglobulin (Ig) E is central to the pathogenesis of allergic conditions, including allergic fungal rhinosinusitis. However, little is known about IgE antibody secreting cells (ASCs). We performed single-cell RNA sequencing from cluster of differentiation (CD)19+ and CD19- ASCs of nasal polyps from patients with allergic fungal rhinosinusitis (n = 3). Nasal polyps were highly enriched in CD19+ ASCs. Class-switched IgG and IgA ASCs were dominant (95.8%), whereas IgE ASCs were rare (2%) and found only in the CD19+ compartment. Through Ig gene repertoire analysis, IgE ASCs shared clones with IgD-CD27- "double-negative" B cells, IgD+CD27+ unswitched memory B cells, and IgD-CD27+ switched memory B cells, suggesting ontogeny from both IgD+ and memory B cells. Transcriptionally, mucosal IgE ASCs upregulate pathways related to antigen presentation, chemotaxis, B cell receptor stimulation, and survival compared with non-IgE ASCs. Additionally, IgE ASCs have a higher expression of genes encoding lysosomal-associated protein transmembrane 5 (LAPTM5) and CD23, as well as upregulation of CD74 (receptor for macrophage inhibitory factor), store-operated Calcium entry-associated regulatory factor (SARAF), and B cell activating factor receptor (BAFFR), which resemble an early minted ASC phenotype. Overall, these findings reinforce the paradigm that human ex vivo mucosal IgE ASCs have a more immature plasma cell phenotype than other class-switched mucosal ASCs and suggest unique functional roles for mucosal IgE ASCs in concert with Ig secretion.

A comparison of international treatment guidelines for Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis.

Stevens-Johnson Syndrome (SJS) and Toxic Epidermal Necrolysis (TEN) are rare and life-threatening mucocutaneous diseases that occur almost exclusively as a result of adverse drug reactions, although there are rare cases attributed to infection, immunization, or malignancy.1,2 Given the low incidence of these diseases as well as the high level of morbidity and mortality, randomized controlled clinical trials are difficult to perform, making it difficult to establish a "gold-standard" treatment. To date, there are only five published articles in the literature detailing evidence-based guidelines for the treatment of SJS and TEN, one of which is specifically tailored to pediatric and young adult patients.3-7 These guidelines have significant overlap in regards to the importance of prompt discontinuation of the offending drug and the need for supportive care, but there are differences in regards to the ideal supportive care measures. Additionally, there is still no clear consensus agreement on the pharmacological treatment of SJS and TEN.4-7 Herein, we aim to compare the international treatment guidelines for management of SJS and TEN as well as promote continued discussion and a multidisciplinary approach to establish consensus recommendations for these mucocutaneous emergencies.

Numerous large nodules on scalp.

The patient told us that his father had "cysts" on his body, too. This familial connection provided a clue to the diagnosis.

Delivering personal care for people with advanced dementia.

This is the second article in a six-part series in Nursing Older People exploring the nursing care of people living with advanced dementia. This article considers the complexity of providing personal care, including the need for expert nursing practice to assess and lead the fundamentals of care: washing, dressing, continence care, nutrition and hydration. The contemporary evidence base for effective assessment, care planning, partnership working and evaluation of personal care for people with advanced dementia is presented, supported by sources of further information.

Introduction to living with advanced dementia series.

This is the introductory article in a six-part series in Nursing Older People exploring the nursing care of people living with advanced dementia. It discusses the complex and progressive array of nursing required to meet the needs of individuals, the provision of personal care, learning and leadership, meaningful activity, and palliative and end of life care. A main theme of the series is the exceptional nursing skills and knowledge required to deliver evidence-informed care with compassion and respect for people living with advanced dementia. This introductory article provides background information to contextualise advanced dementia and identify the main challenges facing nurses, nurse educators and nurse leaders.

Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol.

We report an engineered strain of Escherichia coli that catabolizes the carbonaceous component of the extremely toxic chemical warfare agent sarin. Enzymatic decomposition of sarin generates isopropanol waste that, with this engineered strain, is then transformed into acetyl-CoA by enzymatic conversion with a key reaction performed by the acetone carboxylase complex (ACX). We engineered the heterologous expression of the ACX complex from Xanthobacter autotrophicus PY2 to match the naturally occurring subunit stoichiometry and purified the recombinant complex from E. coli for biochemical analysis. Incorporating this ACX complex and enzymes from diverse organisms, we introduced an isopropanol degradation pathway in E. coli, optimized induction conditions, and decoupled enzyme expression to probe pathway bottlenecks. Our engineered E. coli consumed 65% of isopropanol compared to no-cell controls and was able to grow on isopropanol as a sole carbon source. In the process, reconstitution of this large ACX complex (370 kDa) in a system naïve to its structural and mechanistic requirements allowed us to study this otherwise cryptic enzyme in more detail than would have been possible in the less genetically tractable native Xanthobacter system.

Pap smear screening, pap smear abnormalities and psychosocial risk factors among women in a residential alcohol and drug rehabilitation facility.

AIM: To compare rates of late- screening, abnormal Pap smears and prevalence of psychosocial factors for cervical cancer between women in the community and women attending a residential drug and alcohol facility. BACKGROUND: Women with drug and alcohol addiction experience higher rates of abnormal Pap smears, late- or under- screening and psychosocial risk factors including domestic violence and sexual assault. DESIGN: A descriptive cross-sectional study of women attending publically funded women's health clinics in the community or in a live-in residential drug and alcohol rehabilitation facility. METHODS: The study was approved in May 2012. Data were collected between October 2012-December 2013 using standardized women's health questionnaires, domestic violence screening tools and Pap smear tests. RESULTS: Women attending the rehabilitation facility had higher rates of abnormal Pap smears (16·7% vs. 1·6%) and self-reported history of abnormal Pap smears (44·4% vs. 20·6%). They also reported higher rates of smoking (72·2% vs. 29·2%), experience of sexual assault (44·1% vs. 16·9%), experience of domestic violence (65·7% vs. 10·9%) and other psychosocial risk factors, than women living in the general community. Unexpectedly, women in the rehabilitation facility reported similar levels of late screening as women in the community (52·8% vs. 55·4%). CONCLUSION: Women with drug and alcohol addiction have significantly higher incidence of risk factors for cervical cancer and abnormal Pap smears. Provision of opportunistic cervical cancer screening during residential treatment appears to reduce incidence of late-screening. Roles of Women's Health Nurses in providing services to vulnerable women should be explored further.

Improving surgical outcomes for people with dementia.

Surgical intervention in older people with dementia is becoming increasingly common as the population ages and the number of people with dementia continues to rise. People with dementia have unique needs that require sensitive management at all stages of hospitalisation for surgery. This article sets out a suggested pathway for the care of these patients, in the form of a flow chart. It discusses recognition and assessment of dementia and delirium, issues of capacity and consent, interventions required for optimum care of older people with dementia and peri-operative management. It explores the role of family and friends in achieving integrated care.

Genetic and biochemical investigations of the role of MamP in redox control of iron biomineralization in Magnetospirillum magneticum.

Magnetotactic bacteria have evolved complex subcellular machinery to construct linear chains of magnetite nanocrystals that allow the host cell to sense direction. Each mixed-valent iron nanoparticle is mineralized from soluble iron within a membrane-encapsulated vesicle termed the magnetosome, which serves as a specialized compartment that regulates the iron, redox, and pH environment of the growing mineral. To dissect the biological components that control this process, we have carried out a genetic and biochemical study of proteins proposed to function in iron mineralization. In this study, we show that the redox sites of c-type cytochromes of the Magnetospirillum magneticum AMB-1 magnetosome island, MamP and MamT, are essential to their physiological function and that ablation of one or both heme motifs leads to loss of function, suggesting that their ability to carry out redox chemistry in vivo is important. We also develop a method to heterologously express fully heme-loaded MamP from AMB-1 for in vitro biochemical studies, which show that its Fe(III)-Fe(II) redox couple is set at an unusual potential (-89 ± 11 mV) compared with other related cytochromes involved in iron reduction or oxidation. Despite its low reduction potential, it remains competent to oxidize Fe(II) to Fe(III) and mineralize iron to produce mixed-valent iron oxides. Finally, in vitro mineralization experiments suggest that Mms mineral-templating peptides from AMB-1 can modulate the iron redox chemistry of MamP.

Screening for traumatic brain injury: findings and public health implications.

OBJECTIVE: To provide an overview of a series of projects that used a structured self-report screening tool in diverse settings and samples to screen for lifetime history of traumatic brain injury (TBI). SETTING: Diverse community settings. PARTICIPANTS: Homeless persons (n = 111), individuals with HIV seeking vocational rehabilitation (n = 173), youth in the juvenile justice system (n = 271), public schoolchildren (n = 174), substance users (n = 845), intercollegiate athletes (n = 90), and other community-based samples (n = 396). DESIGN: Cross-sectional. MAIN MEASURE: Brain Injury Screening Questionnaire. RESULTS: Screening using the Brain Injury Screening Questionnaire finds that 27% to 54% of those in high-risk populations report a history of TBI with chronic symptoms. Associations between TBI and social, academic, or other problems are evident in several studies. In non-high-risk community samples, 9% to 12% of individuals report TBI with chronic symptoms. CONCLUSION: Systematic TBI screening can be implemented efficiently and inexpensively in a variety of settings. Lifetime TBI history data gathered using a structured self-report instrument can augment existing estimates of the prevalence of TBI, both as an acute event and as a chronic condition. Identification of individuals with TBI can facilitate primary prevention efforts, such as reducing risk for reinjury in high-risk groups, and provide access to appropriate interventions that can reduce the personal and societal costs of TBI (tertiary prevention).

Enriching the care of patients with dementia in acute settings? The Dementia Champions Programme in Scotland.

Admission to hospital has been found to have a negative impact on people with dementia. The Scottish Dementia Champions programme was developed to prepare health and social service Dementia Champions working in acute settings as Change Agents. The programme was initially delivered to a cohort of 100 health professionals via blended learning, and comprised five study days, a half day spent in a local community setting, and e-learning. In order to complete the programme and graduate, participants were required to complete and submit reports relating to three work-based activities. The evaluation of the project adopted a two-pronged approach: Impact on programme participants was assessed by scores derived from the Approaches to Dementia Questionnaire (ADQ) (Lintern, 1996) completed at Study Days 1 and 5, and analysis of qualitative data derived from the three written assignments. Participants were asked to evaluate course materials and input for each of the five study days, as well as satisfaction with delivery. Analysis of data derived from the ADQ and 100 reflective reports of the community experience indicate that participants' perceptions of people with dementia shifted significantly during the Programme. Participants identified a range of issues which should be addressed with a view to improving the experiences of people with dementia in acute settings, and put in place actions to bring about change. The format of the programme provided a cost effective means to prepare NHS and Social Service Dementia Champions as Change Agents for practice within a relatively short period of time, and would be transferrable to other staff groups as well as different organisational structures in other countries.

Defective nuclear IKKα function in patients with ectodermal dysplasia with immune deficiency.

Ectodermal dysplasia with immune deficiency (EDI) is an immunological and developmental disorder caused by alterations in the gene encoding NF-κB essential modulator (NEMO; also known as IκB kinase γ subunit [IKKγ]). Missense mutations in the gene encoding NEMO are associated with reduced signal-induced nuclear translocation of NF-κB proteins, resulting in defective expression of NF-κB target genes. Here, we report 2 unrelated male patients with EDI, both of whom have normal NEMO coding sequences, but exhibit a marked reduction in expression of full-length NEMO protein. TLR4 stimulation of APCs from these patients induced normal cytoplasmic activation and nuclear translocation of NF-κB. However, cells deficient in full-length NEMO were defective in expression of NF-κB-regulated cytokines, such as IL-12, suggesting a downstream defect in chromatin accessibility for NF-κB transcription factors. TLR4-stimulated APCs from the patients were defective in IKKα-dependent H3 histone phosphorylation at the IL-12 promoter and recruitment of NF-κB heterodimers RelA and cRel to the promoter. Expression of a super-active form of IKKα restored IL-12 production in a NEMO knockdown human monocytic cell line following LPS treatment. Our findings suggest that NEMO regulates the nuclear function of IKKα and offer new insights into the mechanisms underlying diminished NF-κB signaling in patients with EDI.

Partial immune reconstitution of X-linked hyper IgM syndrome with recombinant CD40 ligand.

X-linked hyper IgM syndrome (XHM) is a combined immune deficiency disorder caused by genetic alterations in CD40 ligand. The purpose of this study was to investigate the safety and efficacy of recombinant CD40 ligand (rCD40L) in the treatment of the disease. Three children were administered rCD40L subcutaneously 3 times per week at 0.03 mg/kg for 22 weeks, and after a 12-week drug-free interval, the dose was increased to 0.05 mg/kg for an additional 22 weeks of treatment. Although specific antibody responses to T cell-dependent antigens was lacking, administration of rCD40 resulted in acquisition of the capacity to mount cutaneous delayed type hypersensitivity reactions that disappeared during the drug-free interval as well as the postbiologic follow-up period. With rCD40L treatment, patient T cells developed a new capacity to respond to T-cell mitogens with synthesis of IFN-γ and TNF-α. Intracellular cytokine staining studies showed that both CD4(+) and CD8(+) T cells participated in this response. Finally, CD40L therapy was associated with changes in lymph node size and architecture based on comparison of biopsies taken before and after therapy. This clinical study showed that rCD40L is capable of improving T cell-immune function in patients with XHM.

IL-5 receptor α levels in patients with marked eosinophilia or mastocytosis.

BACKGROUND: IL-5 plays a central role in the development and maintenance of eosinophilia (EO) and eosinophil activation in a wide variety of eosinophilic disorders. Although IL-5, IL-3, and GM-CSF can modulate the expression of IL-5 receptor α (IL-5Rα) on eosinophils in vitro, little is known about soluble and surface IL-5Rα levels in vivo. OBJECTIVE: To assess soluble and surface IL-5Rα levels in patients with EO and/or mastocytosis. METHODS: Surface IL-5Rα expression was assessed by flow cytometry in blood and/or bone marrow from subjects with EO (n = 39) and systemic mastocytosis (n = 8) and from normal volunteers (n = 28). Soluble IL-5Rα (sIL-5Rα) level was measured in a cohort of 177 untreated subjects and correlated with EO, eosinophil activation, and serum tryptase and cytokine levels. RESULTS: IL-5Rα expression on eosinophils inversely correlated with EO (r = -0.48; P < .0001), whereas serum levels of sIL-5Rα increased with the eosinophil count (r = 0.56; P < .0001) and serum IL-5 (r = 0.40; P < .0001) and IL-13 (r = 0.29; P = .004) levels. Of interest, sIL-5Rα level was significantly elevated in patients with systemic mastocytosis without EO. Although sIL-5Rα levels correlated with serum tryptase levels in these patients, eosinophil activation, assessed by CD69 expression on eosinophils and serum eosinophil-derived neurotoxin levels, was increased compared with that in normal subjects. CONCLUSIONS: These data are consistent with an in vivo IL-5Rα regulatory pathway in human eosinophils similar to that described in vitro and involving a balance between soluble and surface receptor levels. This may have implications with respect to the use of novel therapeutic agents targeting IL-5 and its receptor in patients with EO and/or mastocytosis.