TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD.

Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss is the de-repression of cryptic exons. Whilst TDP-43 regulated cryptic splicing is increasingly well catalogued, cryptic alternative polyadenylation (APA) events, which define the 3' end of last exons, have been largely overlooked, especially when not associated with novel upstream splice junctions. We developed a novel bioinformatic approach to reliably identify distinct APA event types: alternative last exons (ALE), 3'UTR extensions (3'Ext) and intronic polyadenylation (IPA) events. We identified novel neuronal cryptic APA sites induced by TDP-43 loss of function by systematically applying our pipeline to a compendium of publicly available and in house datasets. We find that TDP-43 binding sites and target motifs are enriched at these cryptic events and that TDP-43 can have both repressive and enhancing action on APA. Importantly, all categories of cryptic APA can also be identified in ALS and FTD post mortem brain regions with TDP-43 proteinopathy underlining their potential disease relevance. RNA-seq and Ribo-seq analyses indicate that distinct cryptic APA categories have different downstream effects on transcript and translation. Intriguingly, cryptic 3'Exts occur in multiple transcription factors, such as ELK1, SIX3, and TLX1, and lead to an increase in wild-type protein levels and function. Finally, we show that an increase in RNA stability leading to a higher cytoplasmic localisation underlies these observations. In summary, we demonstrate that TDP-43 nuclear depletion induces a novel category of cryptic RNA processing events and we expand the palette of TDP-43 loss consequences by showing this can also lead to an increase in normal protein translation.

Distinct patterns of neural response to faces from different races in humans and deep networks.

Social categories such as the race or ethnicity of an individual are typically conveyed by the visual appearance of the face. The aim of this study was to explore how these differences in facial appearance are represented in human and artificial neural networks. First, we compared the similarity of faces from different races using a neural network trained to discriminate identity. We found that the differences between races were most evident in the fully connected layers of the network. Although these layers were also able to predict behavioural judgements of face identity from human participants, performance was biased toward White faces. Next, we measured the neural response in face-selective regions of the human brain to faces from different races in Asian and White participants. We found distinct patterns of response to faces from different races in face-selective regions. We also found that the spatial pattern of response was more consistent across participants for own-race compared to other-race faces. Together, these findings show that faces from different races elicit different patterns of response in human and artificial neural networks. These differences may underlie the ability to make categorical judgements and explain the behavioural advantage for the recognition of own-race faces.

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for continuous extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies, while the containers and reproducible workflows could easily be deployed and extended to evaluate new methods or data sets.

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, and limitations and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation. APAeval is an international community effort, organized by the RNA Society in 2021, to benchmark tools for the identification and quantification of the usage of alternative polyadenylation (APA) sites from short-read, bulk RNA-sequencing (RNA-seq) data. Here, we reviewed 17 tools and benchmarked eight on their ability to perform APA identification and quantification, using a comprehensive set of RNA-seq experiments comprising real, synthetic, and matched 3'-end sequencing data. To support continuous benchmarking, we have incorporated the results into the OpenEBench online platform, which allows for seamless extension of the set of methods, metrics, and challenges. We envisage that our analyses will assist researchers in selecting the appropriate tools for their studies. Furthermore, the containers and reproducible workflows generated in the course of this project can be seamlessly deployed and extended in the future to evaluate new methods or datasets.

Imaging in metastatic breast cancer, CT, PET/CT, MRI, WB-DWI, CCA: review and new perspectives.

BACKGROUND: Breast cancer is the most frequent cancer in women and remains the second leading cause of death in Western countries. It represents a heterogeneous group of diseases with diverse tumoral behaviour, treatment responsiveness and prognosis. While major progress in diagnosis and treatment has resulted in a decline in breast cancer-related mortality, some patients will relapse and prognosis in this cohort of patients remains poor. Treatment is determined according to tumor subtype; primarily hormone receptor status and HER2 expression. Menopausal status and site of disease relapse are also important considerations in treatment protocols. MAIN BODY: Staging and repeated evaluation of patients with metastatic breast cancer are central to the accurate assessment of disease extent at diagnosis and during treatment; guiding ongoing clinical management. Advances have been made in the diagnostic and therapeutic fields, particularly with new targeted therapies. In parallel, oncological imaging has evolved exponentially with the development of functional and anatomical imaging techniques. Consistent, reproducible and validated methods of assessing response to therapy is critical in effectively managing patients with metastatic breast cancer. CONCLUSION: Major progress has been made in oncological imaging over the last few decades. Accurate disease assessment at diagnosis and during treatment is important in the management of metastatic breast cancer. CT (and BS if appropriate) is generally widely available, relatively cheap and sufficient in many cases. However, several additional imaging modalities are emerging and can be used as adjuncts, particularly in pregnancy or other diagnostically challenging cases. Nevertheless, no single imaging technique is without limitation. The authors have evaluated the vast array of imaging techniques - individual, combined parametric and multimodal - that are available or that are emerging in the management of metastatic breast cancer. This includes WB DW-MRI, CCA, novel PET breast cancer-epitope specific radiotracers and radiogenomics.

PARP inhibition utilized in combination therapy with Olaparib-Temozolomide to achieve disease stabilization in a rare case of BRCA1-mutant, metastatic myxopapillary ependymoma.

Myxopapillary ependymoma (MPE) is a primary tumor of the central nervous system (CNS), characteristically an indolent malignancy involving the spinal conus medullaris, Filum terminale or cauda equina. We present a rare case of MPE, recurrent in the pelvic soft tissue with eventual pleural and intra-pulmonary metastasis. Refractory to repeated gross resection, adjuvant radiotherapy, platinum-based chemotherapy and temozolomide exploitation of mutant somatic BRCA1 status with the addition of a poly (ADP-ribose); polymerase inhibitor (PARPi) in a novel combination regimen with olaparib-temozolomide (OT) has achieved stable radiological disease after 10 cycles.

Folic acid fortification of flour to prevent neural tube defects in Europe - A position statement by the European Board and college of obstetrics and gynaecology (EBCOG).

Neural tube defects are disabling birth defects developing during the very early stages of conception. Children born with spina bifida face significant physical, psychological and social consequences. They may have bowel and urinary dysfunction, and no lower limb muscle control, resulting in lifelong wheelchair use. There is robust evidence that periconceptual folic acid supplementation prevents neural tube defects, when compared with no intervention. However, approximately 40% pregnancies in Europe are unplanned, and women may therefore not be taking prophylactic folic acid at the time of conception. There is evidence that low dose folic acid consumption via flour fortification provides further benefits in prevention of neural tube defects.

Degenerative cervical myelopathy education in UK medical schools: a national cross-sectional survey of medical students.

INTRODUCTION: Degenerative cervical myelopathy (DCM) is a common and progressive neurological condition caused by injury of the cervical spinal cord by degenerative spinal pathology. Delayed diagnosis leading to avoidable and irreversible disability is a major current problem limiting patient outcomes. Lack of sufficient representation of DCM in undergraduate and postgraduate medical curricula may contribute to poor recognition of DCM by non-specialist doctors. The objective of this study was to assess the DCM teaching provision in UK medical schools and the DCM knowledge of UK medical students. METHODS: UK medical students completed a web-based survey distributed nationally through university social media pages, university email bulletins and the national student network of Myelopathy.org. The survey comprised a 19-item questionnaire capturing data on student demographics, myelopathy teaching and myelopathy knowledge. Advertisements were repeated monthly over a 12-month recruitment period and participation was incentivised by entry into an Amazon voucher prize draw. Ethical approval for the study was granted by the Psychology Research Ethics Committee, University of Cambridge (PRE.2018.099). RESULTS: A total of 751 medical students from 32 British medical schools completed the survey. Medical students from all year groups participated. Most students (520; 72%) had not received any medical school teaching about DCM. When students had received DCM teaching, the duration of teaching was minimal (75% < 1 h). A total of 350 students (47%) reported conducting private study on DCM. Modal student self-rating of their own knowledge of DCM was 'terrible' (356; 47%). There was no correlation between a student's subjective rating of their knowledge and their answers to objective questions. A total of 723 (96%) of students expressed interest in learning more about DCM, with lectures the preferred format. CONCLUSIONS: DCM appears to be a neglected condition in medical education which has implications for clinical practice. However, student enthusiasm to undertake private study suggests future teaching interventions will be well-received. Future work is necessary to characterise the format of DCM teaching that is most effective and to subsequently measure how educational interventions translate into clinical benefits.

Evidence of impaired macroautophagy in human degenerative cervical myelopathy.

Degenerative cervical myelopathy (DCM) is a common progressive disease of the spinal cord which can cause tetraplegia. Despite its prevalence, few studies have investigated the pathophysiology of DCM. Macroautophagy is a cellular process which degrades intracellular contents and its disruption is thought to contribute to many neurodegenerative diseases. The present study tests the hypothesis that macroautophagy is impaired in DCM. To address this, we utilised a collection of post-mortem cervical spinal cord samples and investigated seven DCM cases and five human controls. Immunohistochemical staining was used to visualise proteins involved in autophagy. This demonstrated significantly reduced numbers of LC3 puncta in cases versus controls (p = 0.0424). Consistent with reduced autophagy, we identified large aggregates of p62 in four of seven cases and no controls. Tau was increased in two of five cases compared to controls. BCL-2 was significantly increased in cases versus controls (p = 0.0133) and may explain this reduction in autophagy. Increased BCL-2 (p = 0.0369) and p62 bodies (p = 0.055) were seen in more severe cases of DCM. This is the first evidence that autophagy is impaired in DCM; the impairment appears greater in more severe cases. Further research is necessary to investigate whether macroautophagy has potential as a therapeutic target in DCM.

Erratum: Generation and analysis of innovative genomically humanized knockin SOD1, TARDBP (TDP-43), and FUS mouse models.

[This corrects the article DOI: 10.1016/j.isci.2021.103463.].

TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A.

Variants of UNC13A, a critical gene for synapse function, increase the risk of amyotrophic lateral sclerosis and frontotemporal dementia1-3, two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-434,5. Here we show that TDP-43 depletion induces robust inclusion of a cryptic exon in UNC13A, resulting in nonsense-mediated decay and loss of UNC13A protein. Two common intronic UNC13A polymorphisms strongly associated with amyotrophic lateral sclerosis and frontotemporal dementia risk overlap with TDP-43 binding sites. These polymorphisms potentiate cryptic exon inclusion, both in cultured cells and in brains and spinal cords from patients with these conditions. Our findings, which demonstrate a genetic link between loss of nuclear TDP-43 function and disease, reveal the mechanism by which UNC13A variants exacerbate the effects of decreased TDP-43 function. They further provide a promising therapeutic target for TDP-43 proteinopathies.

Homelessness during the pandemic: helping the most vulnerable.

Sam Dorney-Smith, Nursing Fellow, Pathway, and Specialist Advisor, Homeless Health Programme, Queen's Nursing Institute, London (samantha.dorney-smith@nhs.net), runner-up in the Nurse of the Year category of the BJN Awards 2021.

Reporting the whole story: Analysis of the 'out-of-scope' questions from the James Lind Alliance Teenage and Young Adult Cancer Priority Setting Partnership Survey.

OBJECTIVE: We conducted a UK-wide survey to identify the top 10 research questions for young people's cancer. We conducted secondary analysis of questions submitted, which were 'out-of-scope' of the original survey aim. We sought to disseminate these questions, to inform practice, policy and the development of potential interventions to support young people with cancer. DESIGN: James Lind Alliance Priority Setting Partnership. PARTICIPANTS: Young people aged 13-24 with a current/previous cancer diagnosis, their families/friends/partners and professionals who work with this population. METHODS: Eight hundred and fifty-five potential research questions were submitted, and 326 were classified as 'out-of-scope'. These questions, along with 49 'free-text' comments, were analysed using thematic analysis. RESULTS: The 375 out-of-scope questions and comments were submitted by: 68 young people, 81 family members/partners/friends and 42 professionals. Ten overarching themes were identified: diagnostic experience; communication; coordination of care; information needs and lack of information; service provision; long-term effects and aftercare support; family support; financial impact; end-of life care; and research methods and current research. CONCLUSIONS: The need to tailor services, information and communication is a striking thread evidenced across the 'out-of-scope' questions. Gaps in information highlight implications for practice in revisiting information needs throughout the cancer trajectory. We must advocate for specialist care for young people and promote the research priorities and these findings to funding bodies, charities, young people and health and social care policymakers, in order to generate an evidence base to inform effective interventions across the cancer trajectory and improve outcomes. PATIENT/PUBLIC CONTRIBUTIONS: Patients and carers were equal stakeholders throughout.

Generation and analysis of innovative genomically humanized knockin SOD1, TARDBP (TDP-43), and FUS mouse models.

Amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) is a fatal neurodegenerative disorder, and continued innovation is needed for improved understanding and for developing therapeutics. We have created next-generation genomically humanized knockin mouse models, by replacing the mouse genomic region of Sod1, Tardbp (TDP-43), and Fus, with their human orthologs, preserving human protein biochemistry and splicing with exons and introns intact. We establish a new standard of large knockin allele quality control, demonstrating the utility of indirect capture for enrichment of a genomic region of interest followed by Oxford Nanopore sequencing. Extensive analysis shows that homozygous humanized animals only express human protein at endogenous levels. Characterization of humanized FUS animals showed that they are phenotypically normal throughout their lifespan. These humanized strains are vital for preclinical assessment of interventions and serve as templates for the addition of coding or non-coding human ALS/FTD mutations to dissect disease pathomechanisms, in a physiological context.

Paternal origins of obesity: Emerging evidence for incorporating epigenetic pathways into the social determinants of health framework.

Over the past 40 years a global discourse on population obesity has emerged, with moral outrage surrounding the rise in childhood obesity during this time. Women are portrayed as predominantly to blame for the intergenerational transmission of obesity, due to gender norms emphasising maternal responsibility during early-life events. Through a structured review of recent studies exploring epigenetic and social mechanisms of obesity risk transmission, we argue that the role of the father in influencing the obesity risk of children during early life is underappreciated. Paternal actions, embedded within a structural network of the social determinants of health, operate both pre-conception to induce epigenetic changes to the spermatozoa and during the gestational period to influence developmental programming. Paternal contributions influenced by social structures including poor diet and stress influence the subsequent metabolic functioning of the child. An examination of epigenetic pathways, operating at the nexus of genomics and human behaviour, sheds new light on shared parental responsibility for the intergenerational origins of obesity. These emergent findings call into question the effectiveness of early-life obesity interventions that focus exclusively on the mother. More broadly, an examination of the epigenetics of obesity reveals a two-way dynamic between social processes and genomic health information. On the one hand, epigenetic pathways could be an explanatory link between the social determinants of health and physiological outcomes such as obesity. Conversely, a critical appraisal of how this emerging epigenetics knowledge is debated and employed can highlight the very processes that reinforce existing gender disparities in the social determinants of health framework. Ultimately this critical appraisal could lead to a reconfiguration of research and health services agendas, towards more equitable responsibilities across genders for preventing obesity.

The Prevalence of Asymptomatic and Symptomatic Spinal Cord Compression on Magnetic Resonance Imaging: A Systematic Review and Meta-analysis.

STUDY DESIGN: Systematic review and meta-analysis. OBJECTIVES: Cervical spinal cord compression (SCC) due to degenerative changes of the spine is a frequent finding on magnetic resonance imaging (MRI). While most people remain asymptomatic, a proportion develop symptoms of degenerative cervical myelopathy (DCM). DCM is an often-progressive neurological disease that can cause quadriplegia. The epidemiology of SCC and DCM is poorly understood. We sought to estimate the prevalence of degenerative cervical SCC and DCM from cross-sectional cohorts undergoing MRI. METHODS: We conducted a systematic review and meta-analysis of MRI reports on human subjects older than 16 years with degenerative SCC. A predetermined search strategy was used to identify relevant literature on MEDLINE. Title and abstract screenings were followed by full text screening. Data was extracted and analyzed by fixed or random-effects models. RESULTS: The present search returned 1506 publications. Following our exclusion criteria, 19 studies were included. Subgroup analysis of 3786 individuals estimated the prevalence of asymptomatic SCC in a healthy population as 24.2% with a significantly higher prevalence of SCC in older populations compared with younger populations and American/European populations compared with Asian populations. Subgroup analysis of 1202 individuals estimated the prevalence of DCM in a healthy population as 2.3%. CONCLUSIONS: We present the first estimates of the prevalence of asymptomatic SCC and DCM. Studies investigating the epidemiology of SCC are heterogeneous in methodology and results. These data indicate the need for more studies into the epidemiology of SCC and DCM performed with consistent methodologies.

An update on the use of immunotherapy in patients with colorectal cancer.

Introduction: Colorectal cancer (CRC) is the third most common malignancy worldwide, with recent trends demonstrating increasing incidence amongst younger patients. Despite multiple treatment options, metastatic disease remains incurable. A new therapeutic strategy to harness the host immune system, specifically with immune checkpoint inhibitors, now has reported results from a number of clinical trials. Areas covered: This review will discuss in detail microsatellite instability (MSI) and other biomarkers for response to immunotherapy, summarize the pivotal clinical trials of immune checkpoint inhibitors in early-stage and metastatic MSI colorectal cancer, explore strategies to induce treatment responses in MSS CRC and highlight the emerging treatments and novel immune-based therapies under investigation. Expert opinion: Immunotherapy is now a standard of care for the proportion of CRC patients with MSI. While overall survival data are still awaited, the promise of profound and durable responses is highly anticipated. The lack of efficacy in MSS CRC is disappointing and strategies to convert these 'cold' tumors are needed. Further elucidation of optimal use of treatment sequences, combinations and novel agents will improve outcomes.

Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF activity is high in human and murine bone marrow pro-B and pre-B cells and decreases at the immature B cell stage. This stage-specific HIF suppression is required for normal B cell development because genetic activation of HIF-1α in murine B cells led to reduced repertoire diversity, decreased BCR editing and developmental arrest of immature B cells, resulting in reduced peripheral B cell numbers. HIF-1α activation lowered surface BCR, CD19 and B cell-activating factor receptor and increased expression of proapoptotic BIM. BIM deletion rescued the developmental block. Administration of a HIF activator in clinical use markedly reduced bone marrow and transitional B cells, which has therapeutic implications. Together, our work demonstrates that dynamic regulation of HIF-1α is essential for normal B cell development.