A diagnostic challenge of KIT p.V559D and BRAF p.G469A mutations in a paragastric mass.

A patient with gastrointestinal stroma tumor (GIST) and KIT p.V559D and BRAF p.G469A alterations was referred to our institutional molecular tumor board (MTB) to discuss therapeutic implications. The patient had been diagnosed with B-cell chronic lymphocytic leukemia (CLL) years prior to the MTB presentation. GIST had been diagnosed 1 month earlier. After structured clinical annotation of the molecular alterations and interdisciplinary discussion, we considered BRAF/KIT co-mutation unlikely in a treatment-naïve GIST. Discordant variant allele frequencies furthermore suggested a second malignancy. NGS of a CLL sample revealed the identical class 2 BRAF alteration, thus supporting admixture of CLL cells in the paragastric mass, leading to the detection of 2 alterations. Following the MTB recommendation, the patient received imatinib and had a radiographic response. Structured annotation and interdisciplinary discussion in specialized tumor boards facilitate the clinical management of complex molecular findings. Coexisting malignancies and clonal hematopoiesis warrant consideration in case of complex and uncommon molecular findings.

Renal Extramedullary Hematopoiesis in Mast Cell Leukemia with Bone Marrow Fibrosis.

Systemic mastocytosis is defined by the clonal proliferation of abnormal mast cells. The clinical course can range from indolent forms with normal life expectancy to advanced mast cell leukemia with dismal prognosis. An association with other diseases, including myeloproliferative neoplasia, has been described. We present a case of a 75-year patient with a history of cutaneous mastocytosis who was diagnosed with mast cell leukemia more than 9 years ago and did not receive treatment. The patient presented to our clinic with acute kidney failure because of renal extramedullary hematopoiesis. Bone marrow histopathology revealed extensive fibrosis and 50% infiltration by mast cells with a c-KIT D816V mutation. No mutations supporting primary myelofibrosis were identified. Treatment with midostaurin was started, and the patient was discharged after improvement of renal function. Here, we discuss diagnostic challenges between different forms of mast cell leukemia and overlaps with other hematological malignancies.

Leveraging Large Language Models for Decision Support in Personalized Oncology.

Importance: Clinical interpretation of complex biomarkers for precision oncology currently requires manual investigations of previous studies and databases. Conversational large language models (LLMs) might be beneficial as automated tools for assisting clinical decision-making. Objective: To assess performance and define their role using 4 recent LLMs as support tools for precision oncology. Design, Setting, and Participants: This diagnostic study examined 10 fictional cases of patients with advanced cancer with genetic alterations. Each case was submitted to 4 different LLMs (ChatGPT, Galactica, Perplexity, and BioMedLM) and 1 expert physician to identify personalized treatment options in 2023. Treatment options were masked and presented to a molecular tumor board (MTB), whose members rated the likelihood of a treatment option coming from an LLM on a scale from 0 to 10 (0, extremely unlikely; 10, extremely likely) and decided whether the treatment option was clinically useful. Main Outcomes and Measures: Number of treatment options, precision, recall, F1 score of LLMs compared with human experts, recognizability, and usefulness of recommendations. Results: For 10 fictional cancer patients (4 with lung cancer, 6 with other; median [IQR] 3.5 [3.0-4.8] molecular alterations per patient), a median (IQR) number of 4.0 (4.0-4.0) compared with 3.0 (3.0-5.0), 7.5 (4.3-9.8), 11.5 (7.8-13.0), and 13.0 (11.3-21.5) treatment options each was identified by the human expert and 4 LLMs, respectively. When considering the expert as a criterion standard, LLM-proposed treatment options reached F1 scores of 0.04, 0.17, 0.14, and 0.19 across all patients combined. Combining treatment options from different LLMs allowed a precision of 0.29 and a recall of 0.29 for an F1 score of 0.29. LLM-generated treatment options were recognized as AI-generated with a median (IQR) 7.5 (5.3-9.0) points in contrast to 2.0 (1.0-3.0) points for manually annotated cases. A crucial reason for identifying AI-generated treatment options was insufficient accompanying evidence. For each patient, at least 1 LLM generated a treatment option that was considered helpful by MTB members. Two unique useful treatment options (including 1 unique treatment strategy) were identified only by LLM. Conclusions and Relevance: In this diagnostic study, treatment options of LLMs in precision oncology did not reach the quality and credibility of human experts; however, they generated helpful ideas that might have complemented established procedures. Considering technological progress, LLMs could play an increasingly important role in assisting with screening and selecting relevant biomedical literature to support evidence-based, personalized treatment decisions.

Tumour mutational burden and survival with molecularly matched therapy.

BACKGROUND: The impact of tumour mutational burden (TMB) on outcome with molecularly matched therapy is unknown. Higher TMB could predict resistance to molecularly matched therapy through co-occurring driver mutations. METHODS: One hundred and four patients with advanced cancers underwent molecular profiling in the DKTK-MASTER program. Fifty-five patients received systemic therapy excluding immunotherapy. Patients with molecularly matched (n = 35) or non-molecularly informed therapy (n = 20) were analysed for TMB and survival. Results were validated in an independent cohort of patients receiving molecularly matched (n = 68) or non-molecularly informed therapy (n = 40). Co-occurring driver mutations and TMB were analysed in the exploratory cohort and The Cancer Genome Atlas (TCGA) datasets. RESULTS: Patients were stratified by the median TMB of 1.67 mutations per Megabase (mut/Mb) of 35 patients receiving molecularly matched therapy into TMB-high or TMB-low groups. Median overall survival (4 months [95% CI, 3.3-7.6] versus 12.8 months [95% CI, 10-not reached], p < 0.001) and progression-free survival (1.8 months [95% CI, 1.1-3.7] versus 7.9 months [95% CI, 2.8-17.0], p = 0.003) were significantly shorter in the TMB-high group compared to the TMB-low group. In the validation cohort, shorter OS and PFS were identified in the TMB-high group (TMB cut-off of 4 mut/Mb) treated with molecularly matched therapy. No differences were observed in patients receiving non-molecularly informed systemic therapy. A significant correlation between co-occurring driver mutations and TMB (n = 104, r = 0.78 [95% CI, 0.68-0.85], p < 0.001) was found in the exploratory cohort as well as the majority (24/33) of TCGA studies. CONCLUSION: A high TMB was associated with unfavourable outcome in patients receiving molecularly matched therapy, indicating untargeted resistance pathways. Therefore, TMB should be further investigated as a predictive biomarker in precision oncology programs.

Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutated salivary duct carcinoma.

Background and purpose: A subgroup of salivary duct carcinoma (SDC) harbor overexpression of the androgen receptor (AR), and co-occurring mutations in the HRAS- and PIK3CA-genes. The impact of genomic complexity on targeted treatment strategies in advanced cancer is unknown. Materials and methods: We analyzed molecular and clinical data from an institutional molecular tumor board (MTB) to identify AR+, HRAS/PIK3CA co-mutated SDC. Follow-up was performed within the MTB registrational study or retrospective chart review after approval by the local ethics committee. Response was assessed by the investigator. A systematic literature search was performed in MEDLINE to identify additional clinically annotated cases. Results: 4 patients with AR+ HRAS/PIK3CA co-mutated SDC and clinical follow-up data were identified from the MTB. An additional 9 patients with clinical follow-up were identified from the literature. In addition to AR overexpression and HRAS and PIK3CA-alterations, PD-L1 expression and Tumor Mutational Burden > 10 Mutations per Megabase were identified as additional potentially targetable alterations. Among evaluable patients, androgen deprivation therapy (ADT) was initiated in 7 patients (1 Partial Response (PR), 2 Stable Disease (SD), 3 Progressive Disease (PD), 2 not evaluable), tipifarnib was initiated in 6 patients (1 PR, 4 SD, 1 PD). One patient each was treated with immune checkpoint inhibition (Mixed Response) and combination therapies of tipifarnib and ADT (SD) and alpelisib and ADT (PR). Conclusion: Available data further support comprehensive molecular profiling of SDC. Combination therapies, PI3K-inhibitors and immune therapy warrant further investigation, ideally in clinical trials. Future research should consider this rare subgroup of SDC.

Applications of the Microscale Thermophoresis Binding Assay in COVID-19 Research.

As the COVID-19 pandemic progresses, new variants of SARS-CoV-2 continue to emerge. This underscores the need to develop optimized tools to study such variants, along with new coronaviruses that may arise in the future. Such tools will also be instrumental in the development of new antiviral drugs. Here, we introduce microscale thermophoresis (MST) as a reliable and versatile tool for coronavirus research, which we demonstrate through three different applications described in this report: (1) binding of the SARS-CoV-2 spike receptor binding domain (RBD) to peptides as a strategy to prevent virus entry, (2) binding of the RBD to the viral receptor ACE2, and (3) binding of the RBD to ACE2 in complex with the amino acid transporter SLC6A20/SIT1 or its allelic variant rs61731475 (p.Ile529Val). Our results demonstrate that MST is a highly precise approach to studying protein-protein and/or protein-ligand interactions in coronavirus research, making it an ideal tool for studying viral variants and developing antiviral agents. Moreover, as shown in our results, a unique advantage of the MST assay over other available binding assays is the ability to measure interactions with membrane proteins in their near-native plasma membrane environment.

Pathologic Lymph Node Regression After Neoadjuvant Chemotherapy Predicts Recurrence and Survival in Esophageal Adenocarcinoma: A Multicenter Study in the United Kingdom.

PURPOSE: There is limited evidence regarding the prognostic effects of pathologic lymph node (LN) regression after neoadjuvant chemotherapy for esophageal adenocarcinoma, and a definition of LN response is lacking. This study aimed to evaluate how LN regression influences survival after surgery for esophageal adenocarcinoma. METHODS: Multicenter cohort study of patients with esophageal adenocarcinoma treated with neoadjuvant chemotherapy followed by surgical resection at five high-volume centers in the United Kingdom. LNs retrieved at esophagectomy were examined for chemotherapy response and given a LN regression score (LNRS)-LNRS 1, complete response; 2, <10% residual tumor; 3, 10%-50% residual tumor; 4, >50% residual tumor; and 5, no response. Survival analysis was performed using Cox regression adjusting for confounders including primary tumor regression. The discriminatory ability of different LN response classifications to predict survival was evaluated using Akaike information criterion and Harrell C-index. RESULTS: In total, 17,930 LNs from 763 patients were examined. LN response classified as complete LN response (LNRS 1 ≥1 LN, no residual tumor in any LN; n = 62, 8.1%), partial LN response (LNRS 1-3 ≥1 LN, residual tumor ≥1 LN; n = 155, 20.3%), poor/no LN response (LNRS 4-5; n = 303, 39.7%), or LN negative (no tumor/regression; n = 243, 31.8%) demonstrated superior discriminatory ability. Mortality was reduced in patients with complete LN response (hazard ratio [HR], 0.35; 95% CI, 0.22 to 0.56), partial LN response (HR, 0.72; 95% CI, 0.57 to 0.93) or negative LNs (HR, 0.32; 95% CI, 0.25 to 0.42) compared with those with poor/no LN response. Primary tumor regression and LN regression were discordant in 165 patients (21.9%). CONCLUSION: Pathologic LN regression after neoadjuvant chemotherapy was a strong prognostic factor and provides important information beyond pathologic TNM staging and primary tumor regression grading. LN regression should be included as standard in the pathologic reporting of esophagectomy specimens.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.

BACKGROUND: Structured and harmonized implementation of molecular tumor boards (MTB) for the clinical interpretation of molecular data presents a current challenge for precision oncology. Heterogeneity in the interpretation of molecular data was shown for patients even with a limited number of molecular alterations. Integration of high-dimensional molecular data, including RNA- (RNA-Seq) and whole-exome sequencing (WES), is expected to further complicate clinical application. To analyze challenges for MTB harmonization based on complex molecular datasets, we retrospectively compared clinical interpretation of WES and RNA-Seq data by two independent molecular tumor boards. METHODS: High-dimensional molecular cancer profiling including WES and RNA-Seq was performed for patients with advanced solid tumors, no available standard therapy, ECOG performance status of 0-1, and available fresh-frozen tissue within the DKTK-MASTER Program from 2016 to 2018. Identical molecular profiling data of 40 patients were independently discussed by two molecular tumor boards (MTB) after prior annotation by specialized physicians, following independent, but similar workflows. Identified biomarkers and resulting treatment options were compared between the MTBs and patients were followed up clinically. RESULTS: A median of 309 molecular aberrations from WES and RNA-Seq (n = 38) and 82 molecular aberrations from WES only (n = 3) were considered for clinical interpretation for 40 patients (one patient sequenced twice). A median of 3 and 2 targeted treatment options were identified per patient, respectively. Most treatment options were identified for receptor tyrosine kinase, PARP, and mTOR inhibitors, as well as immunotherapy. The mean overlap coefficient between both MTB was 66%. Highest agreement rates were observed with the interpretation of single nucleotide variants, clinical evidence levels 1 and 2, and monotherapy whereas the interpretation of gene expression changes, preclinical evidence levels 3 and 4, and combination therapy yielded lower agreement rates. Patients receiving treatment following concordant MTB recommendations had significantly longer overall survival than patients receiving treatment following discrepant recommendations or physician's choice. CONCLUSIONS: Reproducible clinical interpretation of high-dimensional molecular data is feasible and agreement rates are encouraging, when compared to previous reports. The interpretation of molecular aberrations beyond single nucleotide variants and preclinically validated biomarkers as well as combination therapies were identified as additional difficulties for ongoing harmonization efforts.

Immobilisation of torus fractures of the wrist in children (FORCE): a randomised controlled equivalence trial in the UK.

BACKGROUND: The most common fractures in children are torus (buckle) fractures of the wrist. Controversy exists over treatment, which ranges from splint immobilisation and discharge to cast immobilisation, follow-up, and repeat imaging. This study compared pain and function in affected children offered a soft bandage and immediate discharge with those receiving rigid immobilisation and follow-up as per treating centre protocol. METHODS: In this randomised controlled equivalence trial we included 965 children (aged 4-15 years) with a distal radius torus fracture from 23 hospitals in the UK. Children were randomly allocated in a 1:1 ratio to the offer of bandage group or rigid immobilisation group using bespoke web-based randomisation software. Treating clinicians, participants, and their families could not be masked to treatment allocation. Exclusion criteria included multiple injuries, diagnosis at more than 36 h after injury, and inability to complete follow-up. The primary outcome was pain at 3-days post-randomisation measured using Wong-Baker FACES Pain Rating Scale. We performed a modified intention-to-treat and per protocol analysis. The trial was registered with ISRCTN registry, ISRCTN13955395. FINDINGS: Between Jan 16, 2019, and July 13, 2020, 965 children were randomly allocated to a group, 489 to the offer of a bandage group and 476 to the rigid immobilisation group, 379 (39%) were girls and 586 (61%) were boys. Primary outcome data was collected for 908 (94%) of participants, all of whom were included in the modified intention-to-treat analysis. Pain was equivalent at 3 days with 3·21 points (SD 2·08) in the offer of bandage group versus 3·14 points (2·11) in the rigid immobilisation group. With reference to a prespecified equivalence margin of 1·0, the adjusted difference in the intention-to-treat population was -0·10 (95% CI -0·37 to 0·17) and-0·06 (95% CI -0·34 to 0·21) in the per-protocol population. INTERPRETATION: This trial found equivalence in pain at 3 days in children with a torus fracture of the distal radius assigned to the offer of a bandage group or the rigid immobilisation group, with no between-group differences in pain or function during the 6 weeks of follow-up. FUNDING: UK National Institute for Health and Care Research.

Offer of a bandage versus rigid immobilisation in 4- to 15-year-olds with distal radius torus fractures: the FORCE equivalence RCT.

BACKGROUND: Torus (buckle) fractures of the wrist are the most common fractures in children involving the distal radius and/or ulna. It is unclear if children require rigid immobilisation and follow-up or would recover equally as well by being discharged without any immobilisation or a bandage. Given the large number of these injuries, identifying the optimal treatment strategy could have important effects on the child, the number of days of school absence and NHS costs. OBJECTIVES: To establish whether or not treating children with a distal radius torus fracture with the offer of a soft bandage and immediate discharge (i.e. offer of a bandage) provides the same recovery, in terms of pain, function, complications, acceptability, school absence and resource use, as treatment with rigid immobilisation and follow-up as per usual practice (i.e. rigid immobilisation). DESIGN: A pragmatic, multicentre, randomised controlled equivalence trial. SETTING: Twenty-three UK emergency departments. PARTICIPANTS: A total of 965 children (aged 4-15 years) with a distal radius torus fracture were randomised from January 2019 to July 2020 using a secure, centralised, online-encrypted randomisation service. Exclusion criteria included presentation > 36 hours after injury, multiple injuries and an inability to complete follow-up. INTERVENTIONS: A bandage was offered to 489 participants and applied to 458, and rigid immobilisation was carried out in 476 participants. Participants and clinicians were not blinded to the treatment allocation. MAIN OUTCOME MEASURES: The pain at 3 days post randomisation was measured using the Wong-Baker FACES Pain Rating Scale. Secondary outcomes were the patient-reported outcomes measurement system upper extremity limb score for children, health-related quality of life, complications, school absence, analgesia use and resource use collected up to 6 weeks post randomisation. RESULTS: A total of 94% of participants provided primary outcome data. At 3 days, the primary outcome of pain was equivalent in both groups. With reference to the prespecified equivalence margin of 1.0, the adjusted difference in the intention-to-treat population was -0.10 (95% confidence interval -0.37 to 0.17) and the per-protocol population was -0.06 (95% confidence interval -0.34 to 0.21). There was equivalence of pain in both age subgroups (i.e. 4-7 years and 8-15 years). There was no difference in the rate of complications, with five complications (1.0%) in the offer of a bandage group and three complications (0.6%) in the rigid immobilisation group. There were no differences between treatment groups in functional recovery, quality of life or school absence at any point during the follow-up. Analgesia use was marginally higher at day 1 in the offer of a bandage group than it was in the rigid immobilisation group (83% vs. 78% of participants), but there was no difference at other time points. The offer of a bandage significantly reduced the cost of treatment and had a high probability of cost-effectiveness at a willingness-to-pay threshold of £30,000 per quality-adjusted life-year. LIMITATIONS: Families had a strong pre-existing preference for the rigid immobilisation treatment. Given this, and the inability to blind families to the treatment allocation, observer bias was a concern. However, there was clear evidence of equivalence. CONCLUSIONS: The study findings support the offer of a bandage in children with a distal radius torus fracture. FUTURE WORK: A clinical decision tool to determine which children require radiography is an important next step to prevent overtreatment of minor wrist fractures. There is also a need to rationalise interventions for other common childhood injuries (e.g. 'toddler's fractures' of the tibia). TRIAL REGISTRATION: This trial is registered as ISRCTN13955395 and UKCRN Portfolio 39678. FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 33. See the NIHR Journals Library website for further project information.

BACKGROUND: Torus fractures (also called buckle fractures) of the wrist are the most common type of broken bone in children, affecting 60,000 children in the UK per year. They are the mildest form of broken bone, in which the bone crushes (or buckles). Despite these fractures being so common, there is no 'standard treatment'. The traditional treatment is to use a plaster cast and arrange outpatient follow-up. Recent medical research has suggested that wearing a bandage, or even having no treatment, might result in similar healing. In this study, we looked into whether or not a bandage (which was optional to wear) and no further follow-up resulted in the same recovery as a hard splint and usual follow-up. A total of 965 children aged 4­15 years from 23 emergency departments in the UK took part in the study. Children were evenly divided between the bandage and hard splint groups in a process called randomisation. Prior to the study, families told us that managing pain after injury was the most important issue to them. We asked children and their families to tell us about pain, recovery using the arm, quality of life, complications encountered and school absences. We also looked at the financial costs to families and the NHS. WHAT DID THE TRIAL FIND?: The two treatments resulted in the same outcomes. The majority of those offered a bandage chose to wear it immediately. There was no difference at all in the levels of pain between those treated with a hard splint and usual outpatient follow-up and those offered a bandage and discharge (i.e. no further follow up) from hospital the same day. Similarly, there was no difference in the recovery using the arm, quality of life, complications encountered or school absences. There was a very slight increase in pain killer use in the bandage group at day 1, but not at any other time point. Overall, the cost of the offer of a bandage was slightly lower for families and the NHS. In conclusion, the findings of this study support offering a bandage to be used at the discretion of families to treat children with a torus fracture of the wrist.

Biomarker-driven therapies for metastatic uveal melanoma: A prospective precision oncology feasibility study.

BACKGROUND: Targeted therapies for metastatic uveal melanoma have shown limited benefit in biomarker-unselected populations. The Treat20 Plus study prospectively evaluated the feasibility of a precision oncology strategy in routine clinical practice. PATIENTS AND METHODS: Fresh biopsies were analyzed by high-throughput genomics (whole-genome, whole-exome, and RNA sequencing). A multidisciplinary molecular and immunologic tumor board (MiTB) made individualized treatment recommendations based on identified molecular aberrations, patient situation, drug, and clinical trial availability. Therapy selection was at the discretion of the treating physician. The primary endpoint was the feasibility of the precision oncology clinical program. RESULTS: Molecular analyses were available for 39/45 patients (87%). The MiTB provided treatment recommendations for 40/45 patients (89%), of whom 27/45 (60%) received ≥1 matched therapy. First-line matched therapies included MEK inhibitors (n = 15), MET inhibitors (n = 10), sorafenib (n = 1), and nivolumab (n = 1). The best response to first-line matched therapy was partial response in one patient (nivolumab based on tumor mutational burden), mixed response in two patients, and stable disease in 12 patients for a clinical benefit of 56%. The matched therapy population had a median progression-free survival and overall survival of 3.3 and 13.9 months, respectively. The growth modulation index with matched therapy was >1.33 in 6/17 patients (35%) with prior systemic therapy, suggesting clinical benefit. CONCLUSIONS: A precision oncology approach was feasible for patients with metastatic uveal melanoma, with 60% receiving a therapy matched to identify molecular aberrations. The clinical benefit after checkpoint inhibitors highlights the value of tumor mutational burden testing.

The relationship between environmental context and attentional engagement in podcast listening experiences.

Introduction: Previous research has shown that podcasts are most frequently consumed using mobile listening devices across a wide variety of environmental, situational, and social contexts. To date, no studies have investigated how an individual's environmental context might influence their attentional engagement in podcast listening experiences. Improving understanding of the contexts in which episodes of listening take place, and how they might affect listener engagement, could be highly valuable to researchers and producers working in the fields of object-based and personalized media. Methods: An online questionnaire on listening habits and behaviors was distributed to a sample of 264 podcast listeners. An exploratory factor analysis was run to identify factors of environmental context that influence attentional engagement in podcast listening experiences. Five aspects of podcast listening engagement were also defined and measured across the sample. Results: The exploratory factor analysis revealed five factors of environmental context labeled as: outdoors, indoors & at home, evenings, soundscape & at work, and exercise. The aspects of podcast listening engagement provided a comprehensive quantitative account of contemporary podcast listening experiences. Discussion: The results presented support the hypothesis that elements of a listener's environmental context can influence their attentional engagement in podcast listening experiences. The soundscape & at work factor suggests that some listeners actively choose to consume podcasts to mask disturbing stimuli in their surrounding soundscape. Further analysis suggested that the proposed factors of environmental context were positively correlated with the measured aspects of podcast listening engagement. The results are highly pertinent to the fields of podcast studies, mobile listening experiences, and personalized media, and provide a basis for researchers seeking to explore how other forms of listening context might influence attentional engagement.

Oncogenic KRAS mutations enhance amino acid uptake by colorectal cancer cells via the hippo signaling effector YAP1.

Oncogenic KRAS mutations develop unique metabolic dependencies on nutrients to support tumor metabolism and cell proliferation. In particular, KRAS mutant cancer cells exploit amino acids (AAs) such as glutamine and leucine, to accelerate energy metabolism, redox balance through glutathione synthesis and macromolecule biosynthesis. However, the identities of the amino acid transporters (AATs) that are prominently upregulated in KRAS mutant cancer cells, and the mechanism regulating their expression have not yet been systematically investigated. Here, we report that the majority of the KRAS mutant colorectal cancer (CRC) cells upregulate selected AATs (SLC7A5/LAT1, SLC38A2/SNAT2, and SLC1A5/ASCT2), which correlates with enhanced uptake of AAs such as glutamine and leucine. Consistently, knockdown of oncogenic KRAS downregulated the expression of AATs, thereby decreasing the levels of amino acids taken up by CRC cells. Moreover, overexpression of mutant KRAS upregulated the expression of AATs (SLC7A5/LAT1, SLC38A2/SNAT2, and SLC1A5/ASCT2) in KRAS wild-type CRC cells and mouse embryonic fibroblasts. In addition, we show that the YAP1 (Yes-associated protein 1) transcriptional coactivator accounts for increased expression of AATs and mTOR activation in KRAS mutant CRC cells. Specific knockdown of AATs by shRNAs or pharmacological blockage of AATs effectively inhibited AA uptake, mTOR activation, and cell proliferation. Collectively, we conclude that oncogenic KRAS mutations enhance the expression of AATs via the hippo effector YAP1, leading to mTOR activation and CRC cell proliferation.

Annotation and initial evaluation of a large annotated German oncological corpus.

OBJECTIVE: We present the Berlin-Tübingen-Oncology corpus (BRONCO), a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and speculation. The aim of BRONCO is to foster reproducible and openly available research on Information Extraction from German medical texts. MATERIALS AND METHODS: BRONCO consists of 200 manually deidentified discharge summaries of cancer patients. Annotation followed a structured and quality-controlled process involving 2 groups of medical experts to ensure consistency, comprehensiveness, and high quality of annotations. We present results of several state-of-the-art techniques for different IE tasks as baselines for subsequent research. RESULTS: The annotated corpus consists of 11 434 sentences and 89 942 tokens, annotated with 11 124 annotations for medical entities and 3118 annotations of related attributes. We publish 75% of the corpus as a set of shuffled sentences, and keep 25% as held-out data set for unbiased evaluation of future IE tools. On this held-out dataset, our baselines reach depending on the specific entity types F1-scores of 0.72-0.90 for named entity recognition, 0.10-0.68 for entity normalization, 0.55 for negation detection, and 0.33 for speculation detection. DISCUSSION: Medical corpus annotation is a complex and time-consuming task. This makes sharing of such resources even more important. CONCLUSION: To our knowledge, BRONCO is the first sizable and freely available German medical corpus. Our baseline results show that more research efforts are necessary to lift the quality of information extraction in German medical texts to the level already possible for English.

Metoclopramide treatment blocks CD93-signaling-mediated self-renewal of chronic myeloid leukemia stem cells.

Self-renewal is a key characteristic of leukemia stem cells (LSCs) responsible for the development and maintenance of leukemia. In this study, we identify CD93 as an important regulator of self-renewal and proliferation of murine and human LSCs, but not hematopoietic stem cells (HSCs). The intracellular domain of CD93 promotes gene transcription via the transcriptional regulator SCY1-like pseudokinase 1 independently of ligation of the extracellular domain. In a drug library screen, we identify the anti-emetic agent metoclopramide as an efficient blocker of CD93 signaling. Metoclopramide treatment reduces murine and human LSCs in vitro and prolongs survival of chronic myeloid leukemia (CML) mice through downregulation of pathways related to stemness and proliferation in LSCs. Overall, these results identify CD93 signaling as an LSC-specific regulator of self-renewal and proliferation and a targetable pathway to eliminate LSCs in CML.

Esophageal Columnar Metaplasia in Childhood: A Population-Based Case Series Analysis.

BACKGROUND: Adults with Barrett's esophagus (BE) are often entered into surveillance for esophageal adenocarcinoma (EAC), although cancer risk is relatively low. BE can be detected in children (< 16 years). Little is known about the epidemiology of pediatric BE, and it is unclear what the optimal surveillance regimes are in children. AIM: To evaluate the demographic and clinical characteristics, and future neoplastic progression risk in all pediatric BE patients diagnosed in Northern Ireland between 1993 and 2010. METHODS: Data from the population-based Northern Ireland BE register were matched to the Northern Ireland Cancer Registry for EAC outcomes until end 2013. Age-adjusted incidence of pediatric BE was calculated, and characteristics between pediatric and adult BE patients compared using Chi-square tests. RESULTS: Over 18 years, 42 pediatric BE patients (< 16 years) were identified, equivalent to an age-adjusted incidence of < 2 per 100,000 children. There was a clear age differential, with BE incidence increasing with age within the pediatric population. The majority (85.7%) of patients were male, a significantly higher male/female ratio than adult BE patients (p < 0.001). No pediatric BE patients progressed to high-grade dysplasia (HGD) or EAC, although the eldest patient was aged 34 years by the end of follow-up. CONCLUSIONS: This is the largest series of pediatric BE ever reported. It demonstrates that pediatric BE is rare. The male preponderance of this condition is more apparent in childhood compared with adult cases. No children developed HGD/EAC during follow-up, suggesting that regular surveillance is not required, at least until adulthood.