The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.

Multiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.

Global neurosurgery: Reflections on myelomeningocele in the Zanzibar archipelago (Tanzania).

Objective: Our main goal was to describe the general characteristics and demographic data of myelomeningocele (MMC) patients at Mnazi Mmoja Surgical NED Institute (MMSNI) in Zanzibar and to assess the clinical characteristics and medium-term result-impact of the implemented health care measures. Methods: This is a retrospective study on 41 MMC patients treated at the MMSNI in Zanzibar (Tanzania) from September 2016 to September 2018. Patient demographics, prenatal care, clinical and radiographic characteristics, surgical management and nursing care, and clinical outcomes were abstracted. Results: The mean age of the patients was 6.1 ± 4.6 days, and 53.7% were males. A total of 51.2% came from Zanzibar, 39% to Pemba, and 9.8% from mainland Tanzania. Maternal ultrasound checkups revealed hydrocephalus in 18.7% of the cases. 85.4% of the newborns were operated on. Surgical wound infection was the most frequent complication (28.6%). A significantly higher risk of complications was observed in children from Pemba Island (p = 0.046) and those born by vaginal delivery (p = 0.694), particularly infections. During follow-up, 48.57% of the patients presented with infantile hydrocephalus and in the majority of them, a ventriculoperitoneal shunt was inserted. Conclusions: Proper prenatal care with early diagnosis, together with the neurosurgical and nursing standard of care in a specialized institution, are all essential to increase the chances of successful treatment of newborns harboring MMC and is one of the main goals pursued in the MMSNI, as the only referral public health center with locally trained health personnel in Zanzibar archipelago.

Effect of a novel hygiene intervention on older children's handwashing in a humanitarian setting in Kahda district, Somalia: A cluster-randomised controlled equivalence trial.

INTRODUCTION: Improving handwashing with soap (HWWS) among children in humanitarian emergencies has the potential to reduce the transmission of several important infectious diseases. However, there is limited evidence on which approaches are effective in increasing HWWS among children in humanitarian settings. One recent innovation - the "Surprise Soap" intervention - was shown to be successful in a small-scale efficacy trial in a humanitarian setting in Iraq. This intervention includes soap with embedded toys delivered through a short household session comprising a glitter game, instruction of how and when to wash hands, and HWWS practice. Whilst promising, this approach has not been evaluated at programmatic scale in a complex humanitarian setting. METHODS: We conducted a cluster-randomised controlled equivalence trial of the Surprise Soap intervention in IDP camps in Kahda district, Somalia. Proportionate stratified random sampling was employed to recruit 200 households, with at least one child aged 5-12, across the camps. Eligible households were randomly allocated to receive the Surprise Soap intervention (n = 100) or an active comparator handwashing intervention in which plain soap was delivered in a short household session comprising standard health-based messaging and instruction of how and when to wash hands (n = 100). The primary outcome was the proportion of pre-specified occasions when HWWS was practiced by children aged 5-12 years, measured at baseline, 4-weeks, 12 weeks, and 16 weeks post invention delivery. RESULTS: HWWS increased in both groups (by 48 percentage points in the intervention group and 51 percentage points in the control group, at the 4-week follow up), however, there was no evidence of a difference in HWWS between the groups at the 4-week (adjusted RR (aRR) = 1.0, 95% CI 0.9-1.1), 12-week (aRR = 1.1, 95% CI 0.9-1.3), or 16-week (aRR = 1.0, 95% CI 0.9-1.2) follow-up. CONCLUSIONS: In this complex humanitarian setting, where soap availability and past exposure to handwashing promotion was low, it appears that well-designed, household-level targeted handwashing interventions that include soap provision can increase child HWWS and potentially reduce disease risk, but the Surprise Soap intervention offers no marginal benefit over a standard intervention that would justify the additional costs.

Climate Change Vulnerability Assessment for the Rondo Dwarf Galago in Coastal Forests, Tanzania.

Negative effects of climate change on organisms and their habitats pose significant conservation challenges especially for species already under siege from other threats like habitat loss, pollution and diseases. This study assessed the extent to which the Rondo dwarf galago (Paragalago rondoensis), an endangered primate in the coastal forests in eastern Tanzania is threatened by climate change. Past and projected temperature and precipitation records from Tanzania Meteorological Authority were overlaid with P. rondoensis distribution range to assess the species exposure to climate extremes. Traits predisposing it to climate change were also obtained from published literature and experts on the organism's biology to determine its sensitivity. The P. rondoensis vulnerability to climate change was obtained by feeding exposure and sensitivity data into Natureserve's Climate Change Vulnerability Index (CCVI) software. Results indicated that most of Rondo galago's habitat and distribution range will be exposed to a temperature increase of 1 to 1.3 °C by 2050, which if combined with other threats, is likely to further endanger the species survival. Due to its diet specialization on insects, which are moisture-dependent, any extreme decrease in humidity will reduce its diet availability thereby threatening the species further. Moreover, Rondo galago's limited habitats and distribution range in the East African tropical coastal forests, raises the species threat level. Rondo galago's conservation should be enhanced through creation of corridors to facilitate its possible shifts to conducive and safer habitats in the event of extreme weather. Climate change aspects should also be integrated into the species conservation strategies.

DNA methylation-based classification of sinonasal tumors.

The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent potentially previously misclassified adenoid cystic carcinomas. Our findings can aid in improving the diagnostic classification of sinonasal tumors and could help to change the current perception of SNUCs.

Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma.

The immunomodulatory drugs (IMiDs) lenalidomide and pomalidomide are highly effective treatments for multiple myeloma. However, virtually all patients eventually relapse due to acquired drug resistance with resistance-causing genetic alterations being found only in a small subset of cases. To identify non-genetic mechanisms of drug resistance, we here perform integrated global quantitative tandem mass tag (TMT)-based proteomic and phosphoproteomic analyses and RNA sequencing in five paired pre-treatment and relapse samples from multiple myeloma patients. These analyses reveal a CDK6-governed protein resistance signature that includes myeloma high-risk factors such as TRIP13 and RRM1. Overexpression of CDK6 in multiple myeloma cell lines reduces sensitivity to IMiDs while CDK6 inhibition by palbociclib or CDK6 degradation by proteolysis targeting chimeras (PROTACs) is highly synergistic with IMiDs in vitro and in vivo. This work identifies CDK6 upregulation as a druggable target in IMiD-resistant multiple myeloma and highlights the use of proteomic studies to uncover non-genetic resistance mechanisms in cancer.

A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding.

Protein-protein interactions mediated by intrinsically disordered regions are often based on short linear motifs (SLiMs). SLiMs are implicated in signal transduction and gene regulation yet remain technically laborious and notoriously challenging to study. Here, we present an optimized method for a protein interaction screen on a peptide matrix (PRISMA) in combination with quantitative MS. The protocol was benchmarked with previously described SLiM-based protein-protein interactions using peptides derived from EGFR, SOS1, GLUT1, and CEBPB and extended to map binding partners of kinase activation loops. The detailed protocol provides practical considerations for setting up a PRISMA screen and subsequently implementing PRISMA on a liquid-handling robotic platform as a cost-effective high-throughput method. Optimized PRISMA can be universally applied to systematically study SLiM-based interactions and associated post-translational modifications or mutations to advance our understanding of the largely uncharacterized interactomes of intrinsically disordered protein regions.

Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19.

Neutrophils provide a critical line of defense in immune responses to various pathogens, inflicting self-damage upon transition to a hyperactivated, procoagulant state. Recent work has highlighted proinflammatory neutrophil phenotypes contributing to lung injury and acute respiratory distress syndrome (ARDS) in patients with coronavirus disease 2019 (COVID-19). Here, we use state-of-the art mass spectrometry-based proteomics and transcriptomic and correlative analyses as well as functional in vitro and in vivo studies to dissect how neutrophils contribute to the progression to severe COVID-19. We identify a reinforcing loop of both systemic and neutrophil intrinsic IL-8 (CXCL8/IL-8) dysregulation, which initiates and perpetuates neutrophil-driven immunopathology. This positive feedback loop of systemic and neutrophil autocrine IL-8 production leads to an activated, prothrombotic neutrophil phenotype characterized by degranulation and neutrophil extracellular trap (NET) formation. In severe COVID-19, neutrophils directly initiate the coagulation and complement cascade, highlighting a link to the immunothrombotic state observed in these patients. Targeting the IL-8-CXCR-1/-2 axis interferes with this vicious cycle and attenuates neutrophil activation, degranulation, NETosis, and IL-8 release. Finally, we show that blocking IL-8-like signaling reduces severe acute respiratory distress syndrome of coronavirus 2 (SARS-CoV-2) spike protein-induced, human ACE2-dependent pulmonary microthrombosis in mice. In summary, our data provide comprehensive insights into the activation mechanisms of neutrophils in COVID-19 and uncover a self-sustaining neutrophil-IL-8 axis as a promising therapeutic target in severe SARS-CoV-2 infection.

Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories.

Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.

Medical applicant general practice experience and career aspirations: a questionnaire study.

BACKGROUND: Increasing access to general practice work experience placements for school students is a strategy for improving general practice recruitment, despite limited evidence and concerns surrounding equity of access to general practice experiences. AIMS: To examine the association between undertaking general practice experience and the perceptions of general practice as an appealing future career among prospective medical applicants. To identify socioeconomic factors associated with obtaining general practice experience. DESIGN & SETTING: Cross-sectional questionnaire study in the UK. METHOD: Participants were UK residents aged ≥16 years and seriously considering applying to study medicine in 2019/2020. They were invited to take part via the University Clinical Aptitude Test (UCAT). Questionnaire data were analysed using a linear regression of general practice appeal on general practice experience, adjusting for career motivations and demographics, and a logistic regression of general practice experience on measures of social capital and demographics. RESULTS: Of 6391 responders, 4031 were in their last year of school. General practice experience predicted general practice appeal after adjusting for career motivation and demographics (b = 0.37, standard error [SE] = 0.06, P<0.00001). General practice experience was more common among students at private (odds ratio [OR] = 1.65, 95% confidence interval [CI] = 1.31 to 2.08, P<0.0001) or grammar schools (OR = 1.33, 95% CI = 1.02 to 1.72, P = 0.03) and in the highest socioeconomic group (OR = 1.62, 95% CI = 1.28 to 2.05, P<0.0001), and less likely among students of 'other' ethnicity (OR = 0.37, 95% CI = 0.20 to 0.67, P = 0.0011). CONCLUSION: Having general practice experience prior to medical school was associated with finding general practice appealing, which supports its utility in recruitment. Applicants from more deprived backgrounds were less likely to have had a general practice experience, possibly through lack of accessible opportunities.

Coronavirus Disease 2019 (COVID-19): Potential implications for weak health systems and conflict zones in the Middle East and North Africa region.

This short communication recognizes the underbelly of weak and conflict-prone health systems in the Middle East and North Africa region in the wake of COVID-19 pandemic. The communication highlights how the lack of basic resources, absence of a well-functioning health system and the dearth of well-coordinated communication channels, can bode ill for the successful fight against COVID-19. The article elucidates COVID-19 potential health, social, and economic implications for such countries. The communication cautions that if COVID-19 is left to incubate and makes a home in weak systems, it will have a much better chance of mutating and coming back to infect many people globally. The communication calls on the international institutions in collaboration with developed nations to be prepared to probe up health systems in weak and conflict-prone health systems with much-needed resources in order to nip COVID-19 in the bud.

Infant hydrocephalus in sub-Saharan Africa: Impact of perioperative care in the Zanzibar archipelago. / Hidrocefalia infantil en el África subsahariana: impacto de los cuidados perioperatorios en el archipiélago de Zanzíbar.

INTRODUCTION: Child hydrocephalus in low- and middle-income countries represents one of the most sensitive ethical and health problems facing international health development. The most optimistic estimates indicate that 200,000 newborns annually will develop hydrocephalus or be born with a neural tube defect in East, Central and South Africa (ECSA). It is estimated that less than 10% of these children will be operated by ventriculoperitoneal shunts, and in general in poor quality conditions or with a very high complication rate. OBJECTIVE: To describe the general characteristics, epidemiology and demographic data of childhood hydrocephalus of patients treated at the NED Institute in the Zanzibar archipelago, and assess the clinical details and medium-term results of the impact of the set-up nursing care. MATERIAL AND METHODS: This is a descriptive and analytical observational study of a retrospective nature, in patients diagnosed and treated with childhood hydrocephalus, in the period from September 2016 to September 2018. With the implementation of a series of perioperative nursing protocols in these patients, the results obtained were described and analyzed. RESULTS: A total of 96 patients were treated for childhood hydrocephalus. 51% (n=49) of these patients were male, with a mean age of 9.25 months. All the mothers of the patients were monitored during pregnancy, but only 8% were treated with folic acid during pregnancy. 81% of children were born through vaginal delivery or uncomplicated spontaneous delivery. Regarding the etiology, 27.1% of treated hydrocephalus was associated with an infectious cause and 35.4% with an unknown cause. 67 ventriculoperitoneal shunt surgery and 15 endoscopic ventriculostomies were performed. The complication rate was 23.17%. CONCLUSIONS: The results of this research indicate that childhood hydrocephalus in Zanzibar has etiology, evolution and complications that are similar to or less than those described to date in East Africa. Implementing a series of perioperative protocols and standardized nursing care positively influences the results obtained. Currently, the Mnazi Mmoja Surgical NED Institute is one of the few centers in East Africa with an exhaustive record of healthcare activity and is the first health center that offers further training to nurses.