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A novel ALK transcript expressed in a subset of human cancers, arising from a de novo alternative transcription initiation site within the ALK gene, is described; the ALK transcript encodes three protein isoforms that stimulate tumorigenesis in vivo in mouse models; resultant tumours are sensitive to treatments with ALK inhibitors, indicating a possible therapeutic avenue for patients expressing these isoforms. A novel oncogene activation mechanism Oncogenes are usually activated by genetic abberations. Ping Chi and colleagues have identified a novel isoform of the anaplastic lymphoma kinase (ALK) in a subset of human cancers, arising independently of genomic aberrations at the ALK locus through alternative transcription initiation in ALK intron 19. Tumours driven by the transcript, termed ALK ATI , are sensitive to ALK inhibitors, suggesting ALK inhibitors as possible therapeutics in patients expressing these isoforms. Activation of oncogenes by mechanisms other than genetic aberrations such as mutations, translocations, or amplifications is largely undefined. Here we report a novel isoform of the anaplastic lymphoma kinase (ALK) that is expressed in ∼11% of melanomas and sporadically in other human cancer types, but not in normal tissues. The novel ALK transcript initiates from a de novo alternative transcription initiation (ATI) site in ALK intron 19, and was termed ALK ATI . In ALK ATI -expressing tumours, the ATI site is enriched for H3K4me3 and RNA polymerase II, chromatin marks characteristic of active transcription initiation sites 1 . ALK ATI is expressed from both ALK alleles, and no recurrent genetic aberrations are found at the ALK locus, indicating that the transcriptional activation is independent of genetic aberrations at the ALK locus. The ALK ATI transcript encodes three proteins with molecular weights of 61.1, 60.8 and 58.7 kilodaltons, consisting primarily of the intracellular tyrosine kinase domain. ALK ATI stimulates multiple oncogenic signalling pathways, drives growth-factor-independent cell proliferation in vitro, and promotes tumorigenesis in vivo in mouse models. ALK inhibitors can suppress the kinase activity of ALK ATI , suggesting that patients with ALK ATI -expressing tumours may benefit from ALK inhibitors. Our findings suggest a novel mechanism of oncogene activation in cancer through de novo alternative transcription initiation.

Background Pancreatic ductal adenocarcinoma (PDAC) is characterized by exceedingly high rates of metastatic progression, with the liver representing the most common site of distant spread. Here, we established a platform for multisite immune profiling of human PDAC encompassing the tumor, peripheral circulation, and premetastatic liver, to more comprehensively study how various immune subsets might contribute to patient outcomes. Methods Tumor, liver, and blood samples were obtained from patients undergoing resection for non-metastatic PDAC. Derived immune cells underwent paired single-cell RNA and TCR sequencing. Immune composition, cell-type functional profiles, and T cell clonal expansion patterns were evaluated across tissue sites. Results In total, 106,539 immune cells were sequenced, of which 85,748 met criteria for analysis. We identified 32 cell populations, of which seven demonstrated significant enrichment within a particular tissue, highlighting that this workflow possesses the granularity needed for identifying potential future biomarkers. Functional profiling revealed tissue-specific differences in cell phenotypes. This included terminally differentiated exhausted CD8 T cells within the tumor, highly active Tregs within the premetastatic liver and tumor, and M1 versus M2 polarization of liver and tumor macrophage populations, respectively. Within the tumor, expanded Treg clones were uniquely abundant, and while expanded clones could be tracked to the blood and premetastatic liver, many of these mapped back to known viral antigens. Leveraging previously validated gene sets, we show how these can be applied to predict the tumor reactivity of intratumoral T cells using transcriptional signatures. We demonstrated a high degree of concordance between multiple independent signatures and tracked high-priority TCRs within the blood and liver. Conclusion This study demonstrates the feasibility of a platform, which has already been implemented into ongoing clinical protocols, for immune profiling of human PDAC across the sites most relevant to metastatic progression. Future applications of this work can monitor immune populations throughout metastatic progression to build a temporal database of immune phenotypes and track association with clinical outcomes.

Objective Optical coherence tomography (OCT)‐derived measures of the retina correlate with disability and cortical gray matter atrophy in multiple sclerosis (MS); however, whether such measures predict long‐term disability is unknown. We evaluated whether a single OCT and visual function assessment predict the disability status 10 years later. Methods Between 2006 and 2008, 172 people with MS underwent Stratus time domain‐OCT imaging [160 with measurement of total macular volume (TMV)] and high and low‐contrast letter acuity (LCLA) testing (n = 150; 87%). All participants had Expanded Disability Status Scale (EDSS) assessments at baseline and at 10‐year follow‐up. We applied generalized linear regression models to assess associations between baseline TMV, peripapillary retinal nerve fiber layer (pRNFL) thickness, and LCLA with 10‐year EDSS scores (linear) and with clinically significant EDSS worsening (binary), adjusting for age, sex, optic neuritis history, and baseline disability status. Results In multivariable models, lower baseline TMV was associated with higher 10‐year EDSS scores (mean increase in EDSS of 0.75 per 1 mm3 loss in TMV (mean difference = 0.75; 95% CI: 0.11–1.39; P = 0.02). In analyses using tertiles, individuals in the lowest tertile of baseline TMV had an average 0.86 higher EDSS scores at 10 years (mean difference = 0.86; 95% CI: 0.23–1.48) and had over 3.5‐fold increased odds of clinically significant EDSS worsening relative to those in the highest tertile of baseline TMV (OR: 3.58; 95% CI: 1.30–9.82; Ptrend = 0.008). pRNFL and LCLA predicted the 10‐year EDSS scores only in univariate models. Interpretation Lower baseline TMV measured by OCT significantly predicts higher disability at 10 years, even after accounting for baseline disability status.

BackgroundSurgical axillary staging demonstrating positive nodal disease before neoadjuvant chemotherapy (NAC) necessitates axillary lymph node dissection (ALND) post-NAC. Despite evidence supporting post-NAC surgical staging, we hypothesized that there is persistent use of pre-NAC staging and that it is associated with aggressive clinicopathologic features and a higher rate of subsequent ALND.Patients and MethodsStage I–III breast cancer patients who underwent lymph node staging surgery and received NAC between 2013 and 2017 in the National Cancer Database were included. Sequence of staging surgery and chemotherapy administration was determined. Multivariable regression was used to assess characteristics associated with pre-NAC staging. Rate of ALND was compared between those who had pre- and post-NAC surgical axillary staging.ResultsIn total, 120,538 met inclusion; 68% received NAC first and 32% had pre-NAC staging. Pre-NAC staging surgery was associated with younger age (age < 30 versus 40–49 years, HR 1.1) and decreased with older age (ages 70–79/80+ versus 40–49 years, HR 0.86 and 0.73). Advancing clinical T stage, lobular subtype, higher grade, and HR+/HER2− subtype were also associated with pre-NAC surgical staging. Women who underwent pre-NAC surgical staging were more likely to undergo ALND.ConclusionsOver 30% of women underwent surgical axillary staging prior to NAC, resulting in higher rates of ALND in this cohort. While certain features suggestive of aggressive behavior (grade and T stage) were associated with pre-NAC surgical axillary staging, women with more aggressive tumor subtypes (triple negative/HER2+) were less likely to undergo pre-NAC surgical axillary staging. Pre-NAC surgical axillary staging should be performed only in rare circumstances to avoid unnecessary ALND.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2–host interactions and the progression of Coronavirus disease 2019 (COVID-19). Here, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2 . We uncovered proviral and antiviral factors across highly interconnected host pathways, including clathrin transport, inflammatory signaling, cell-cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high molecular weight glycoproteins, as a prominent viral restriction network that inhibits SARS-CoV-2 infection in vitro and in murine models. These mucins also inhibit infection of diverse respiratory viruses. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and highlights airway mucins as a host defense mechanism. Genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2 identify mucins as key host factors restricting viral infection.

The mechanism of how loss of the tumor suppressor p53 can lead to genomic instability is not fully understood. This study demonstrates that under physiologic low levels of proliferation, homozygous loss of tumor protein 53 ( TP53 ) via genome editing, but not common p53 missense mutations, results in an inability to increase expression of N-Myc down-regulated gene 1 ( NDRG1 ) . In turn, failure to upregulate NDRG1 protein under low proliferative states leads to supernumerary centrosome formation, a known mechanism of aneuploidy. These results provide a mechanistic link between loss of TP53 , proliferation, NDRG1 , and genomic instability and help explain how cells with a low proliferative index and p53 loss can acquire additional genetic alterations that lead to cancer. The tumor protein 53 ( TP53 ) tumor suppressor gene is the most frequently somatically altered gene in human cancers. Here we show expression of N-Myc down-regulated gene 1 ( NDRG1 ) is induced by p53 during physiologic low proliferative states, and mediates centrosome homeostasis, thus maintaining genome stability. When placed in physiologic low-proliferating conditions, human TP53 null cells fail to increase expression of NDRG1 compared with isogenic wild-type controls and TP53 R248W knockin cells. Overexpression and RNA interference studies demonstrate that NDRG1 regulates centrosome number and amplification. Mechanistically, NDRG1 physically associates with γ-tubulin, a key component of the centrosome, with reduced association in p53 null cells. Strikingly, TP53 homozygous loss was mutually exclusive of NDRG1 overexpression in over 96% of human cancers, supporting the broad applicability of these results. Our study elucidates a mechanism of how TP53 loss leads to abnormal centrosome numbers and genomic instability mediated by NDRG1 .

Background: Intraosseous (IO) infusion provides a quick alternative route to vascular circulation through the bone when intravenous access is compromised. Despite its potentially lifesaving benefits, it is often an underutilized procedure in the adult population, partially owing to lack of training that stems from the unavailability of cost-effective, anatomically correct simulators. The aim of this study was to identify and integrate critical improvements to the existing simple and advanced adult proximal tibia IO simulators previously designed at Ontario Tech University. Methods: First, a design thinking (DT) process was conducted with 3 health care professionals to brainstorm a list of improvements. Then, these ideas were moved into a 2-round Delphi methodology with 7 health care professionals to clarify and consolidate potential updates. Finally, this set of short-listed items were discussed with 3 3D-printing designers to determine feasibility of the changes. Results: The DT process generated 6 and 8 ideas for the simple and advanced simulators, respectively. These were carried into the Delphi methodology, through which panellists collectively agreed on 2 upgrades to only the advanced simulator: to offer the ability to laterally expose the tibia and resistance to flow. The 3D-printing designers were able to integrate the features into the design of the advanced simulator. Conclusion: This study provided design details required to develop and manufacture an affordable, customizable, and realistic IO simulator. The revisions are intended to support the development of an effective decentralized simulation-based education model aimed at teaching health care professionals IO skills remotely.

•H3N2 serology titres were highest in those with current season influenza vaccination.•Titres were higher in those with past season vaccination over those with no vaccination recorded.•Influenza vaccination protection was good against influenza requiring emergency care in children.•Vaccine effectiveness in adults was modest. We present England 2021/22 end-of-season adjusted vaccine effectiveness (aVE) against laboratory confirmed influenza related emergency care use in children aged 1–17 and in adults aged 50+, and serological findings in vaccinated vs unvaccinated adults by hemagglutination inhibition assay. Influenza vaccination has been routinely offered to all children aged 2–10 years and adults aged 65 years + in England. In 2021/22, the offer was extended to children to age 15 years, and adults aged 50–64 years. Influenza activity rose during the latter half of the 2021/22 season, while remaining comparatively low due to COVID-19 pandemic control measures. Influenza A(H3N2) strains predominated. A test negative design was used to estimate aVE by vaccine type. Cases and controls were identified within a sentinel laboratory surveillance system. Vaccine histories were obtained from the National Immunisation Management Service (NIMS), an influenza and COVID-19 vaccine registry. These were linked to emergency department presentations (excluding accidents) with respiratory swabbing ≤ 14 days before or ≤ 7 days after presentation. Amongst adults, 423 positive and 32,917 negative samples were eligible for inclusion, and 145 positive and 6,438 negative samples among children. Those admitted to hospital were further identified. In serology against the circulating A(H3N2) A/Bangladesh/4005/2020-like strain, 61 % of current season adult vaccinees had titres ≥ 1:40 compared to 17 % of those unvaccinated in 2020/21 or 2021/22 (p < 0.001). We found good protection from influenza vaccination against influenza requiring emergency care in children (72.7 % [95 % CI 52.7, 84.3 %]) and modest effectiveness in adults (26.1 % [95 % CI 4.5, 42.8 %]). Adult VE was higher for A(H1N1) (81 % [95 % CI 50, 93 %]) than A(H3N2) (33 % [95 % CI 6, 53 %]). Consistent protection was observable across preschool, primary and secondary school aged children. Imperfect test specificity combined with very low prevalence may have biased estimates towards null. With limited influenza circulation, the study could not determine differences by vaccine types.

Intraosseous (IO) access and infusion is a safe and rapid alternative to intravenous access in obtaining vascular access for administering fluids and drugs. Healthcare professionals, such as primary and advanced care paramedics, use IO access and infusion in emergency circumstances where peripheral intravenous routes are inaccessible. IO access skills require hands-on training, which can be done remotely if the participants have access to simulation, instructions, guidance, and feedback. For the purpose of moving the training outside of the simulation laboratories, we have developed (1) an inexpensive and scalable three-dimensional (3D) printed and silicone-based advanced adult proximal tibial IO access and infusion simulator and (2) a unique learning management system (LMS) for remote simulation-based training. The LMS was built using the Django platform and supports experiential learning by providing access to educational and instructional content (including virtual simulation and serious games), allowing peers to communicate among themselves and with subject-matter experts, provide and receive feedback asynchronously, and engage in learning using gamification elements. The aim of this technical report is to describe the process of development and the final product of the LMS as a research and educational tool to scaffold remote learning of emergency IO skills by paramedics-in-training.