The genetic basis and cell of origin of mixed phenotype acute leukaemia.

Mixed phenotype acute leukaemia (MPAL) is a high-risk subtype of leukaemia with myeloid and lymphoid features, limited genetic characterization, and a lack of consensus regarding appropriate therapy. Here we show that the two principal subtypes of MPAL, T/myeloid (T/M) and B/myeloid (B/M), are genetically distinct. Rearrangement of ZNF384 is common in B/M MPAL, and biallelic WT1 alterations are common in T/M MPAL, which shares genomic features with early T-cell precursor acute lymphoblastic leukaemia. We show that the intratumoral immunophenotypic heterogeneity characteristic of MPAL is independent of somatic genetic variation, that founding lesions arise in primitive haematopoietic progenitors, and that individual phenotypic subpopulations can reconstitute the immunophenotypic diversity in vivo. These findings indicate that the cell of origin and founding lesions, rather than an accumulation of distinct genomic alterations, prime tumour cells for lineage promiscuity. Moreover, these findings position MPAL in the spectrum of immature leukaemias and provide a genetically informed framework for future clinical trials of potential treatments for MPAL.

CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells.

MOTIVATION: Cell-cell communications regulate internal cellular states, e.g. gene expression and cell functions, and play pivotal roles in normal development and disease states. Furthermore, single-cell RNA sequencing methods have revealed cell-to-cell expression variability of highly variable genes (HVGs), which is also crucial. Nevertheless, the regulation of cell-to-cell expression variability of HVGs via cell-cell communications is still largely unexplored. The recent advent of spatial transcriptome methods has linked gene expression profiles to the spatial context of single cells, which has provided opportunities to reveal those regulations. The existing computational methods extract genes with expression levels influenced by neighboring cell types. However, limitations remain in the quantitativeness and interpretability: they neither focus on HVGs nor consider the effects of multiple neighboring cell types. RESULTS: Here, we propose CCPLS (Cell-Cell communications analysis by Partial Least Square regression modeling), which is a statistical framework for identifying cell-cell communications as the effects of multiple neighboring cell types on cell-to-cell expression variability of HVGs, based on the spatial transcriptome data. For each cell type, CCPLS performs PLS regression modeling and reports coefficients as the quantitative index of the cell-cell communications. Evaluation using simulated data showed our method accurately estimated the effects of multiple neighboring cell types on HVGs. Furthermore, applications to the two real datasets demonstrate that CCPLS can extract biologically interpretable insights from the inferred cell-cell communications. AVAILABILITY AND IMPLEMENTATION: The R package is available at https://github.com/bioinfo-tsukuba/CCPLS. The data are available at https://github.com/bioinfo-tsukuba/CCPLS_paper. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Improvement in Intraoperative Image Quality in Transcranial Magnetic Resonance-Guided Focused Ultrasound Surgery Using Transmitter Gain Adjustment.

INTRODUCTION: Transcranial magnetic resonance-guided focused ultrasound surgery (TcMRgFUS) has the advantage of allowing immediate evaluation of therapeutic effects after each sonication and intraoperative magnetic resonance imaging (MRI) to visualize the lesion. When the image shows that the lesion has missed the planned target and the therapeutic effects are insufficient, the target of the subsequent ablation can be finely adjusted based on the image. The precision of this adjustment is determined by the image quality. However, the current intraoperative image quality with a 3.0T MRI system is insufficient for precisely detecting the lesion. Thus, we developed and validated a method for improving intraoperative image quality. METHODS: Because intraoperative image quality is affected by transmitter gain (TG), we acquired T2-weighted images (T2WIs) with two types of TG: the automatically adjusted TG (auto TG) and the manually adjusted TG (manual TG). To evaluate the character of images with 2 TGs, the actual flip angle (FA), the image uniformity, and the signal-to-noise ratio (SNR) were measured using a phantom. Then, to assess the quality of intraoperative images, T2WIs with both TGs were acquired during TcMRgFUS for 5 patients. The contrast-to-noise ratio (CNR) of the lesion was retrospectively estimated. RESULTS: The images of the phantom with the auto TG showed substantial variations between the preset and actual FAs (p < 0.01), whereas on the images with the manual TG, there were no variations between the two FAs (p > 0.05). The total image uniformity was considerably lower with the manual TG than with the auto TG (p < 0.01), indicating that the image's signal values with the manual TG were more uniform. The manual TG produced significantly higher SNRs than the auto TG (p < 0.01). In the clinical study, the lesions were clearly detected in intraoperative images with the manual TG, but they were difficult to identify in images with the auto TG. The CNR of lesions in images with manual TG was considerably higher than in images with auto TG (p < 0.01). CONCLUSION: Regarding intraoperative T2WIs using a 3.0T MRI system during TcMRgFUS, the manual TG method improved image quality and delineated the ablative lesion more clearly than the current method with auto TG.

Psychological characteristics of Japanese patients and their family members receiving genetic counseling: A single-institute exploratory study.

In Japan, clinical genetic services became available in the 1970s, and genomic medicine, including genetic counseling (GC), developed rapidly. However, research on the outcomes of GC in Japan is limited. Japan has a unique cultural context, and appropriate GC methods have not yet been optimized for this population. The current study aimed to evaluate the psychological status of Japanese patients and their companions undergoing GC and the outcomes of GC. We used the Quality of Care Through the Patients' Eyes-gene cancer (QUOTE-geneCA ), the Genetic Counseling Outcome Scale-24 (GCOS-24), and the State-Trait Anxiety Inventory (STAI) to evaluate patients and their companions' needs and preferences regarding GC, empowerment, and anxiety, respectively. We evaluated stress status during GC by measuring saliva cortisol levels. QUOTE-geneCA results for patients (n = 69) and a group of patients and their companions (n = 96) revealed that participants felt that it was important that skilled medical staff explained medical information and provided advice in an easily understandable manner. Japanese patients and their companions regarded the procedural aspects of counseling as most important and their autonomy in decision-making as less important. GCOS-24 results revealed a significant increase in empowerment scores in 38 patients (by 9.63 points) from pre- to post-GC (p < 0.001; Cohen's d = 0.79). STAI results revealed a significant decrease in state anxiety for patients (6.11 points; p < 0.001; Cohen's d = 0.66). Cortisol levels in patients significantly decreased after GC (p = 0.001). The improvement of empowerment scores from pre- to post-GC among patients and their companions were significantly negatively correlated with pre-GC empowerment scores (p < 0.001), trait anxiety scores (p = 0.001), and the number of people living together (p = 0.011). The change of cortisol levels during GC in patients and their companions was significantly positively correlated with trait anxiety score (p = 0.027). This study suggested that these characteristics of Japanese patients and their companions may predict GC outcomes.

Massively parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity.

As a prototype of genomics-guided precision medicine, individualized thiopurine dosing based on pharmacogenetics is a highly effective way to mitigate hematopoietic toxicity of this class of drugs. Recently, NUDT15 deficiency was identified as a genetic cause of thiopurine toxicity, and NUDT15-informed preemptive dose reduction was quickly adopted in clinical settings. To exhaustively identify pharmacogenetic variants in this gene, we developed massively parallel NUDT15 function assays to determine the variants' effect on protein abundance and thiopurine cytotoxicity. Of the 3,097 possible missense variants, we characterized the abundance of 2,922 variants and found 54 hotspot residues at which variants resulted in complete loss of protein stability. Analyzing 2,935 variants in the thiopurine cytotoxicity-based assay, we identified 17 additional residues where variants altered NUDT15 activity without affecting protein stability. We identified structural elements key to NUDT15 stability and/or catalytical activity with single amino acid resolution. Functional effects for NUDT15 variants accurately predicted toxicity risk alleles in patients treated with thiopurines with far superior sensitivity and specificity compared to bioinformatic prediction algorithms. In conclusion, our massively parallel variant function assays identified 1,152 deleterious NUDT15 variants, providing a comprehensive reference of variant function and vastly improving the ability to implement pharmacogenetics-guided thiopurine treatment individualization.

Development of a Selective Assay of Tyrosine and Its Producing and Metabolizing Enzymes Utilizing Pulse-UV Irradiation-Induced Chemiluminescence.

A new pulse UV irradiation-induced chemiluminescence (CL) determination method was developed for l-tyrosine using the luminol derivative L-012. The proposed method depends on the formation of reactive oxygen species (ROS) upon pulse UV irradiation of l-tyrosine; then, these ROS react with L-012 producing strong CL. The proposed method showed excellent sensitivity and ultraselectivity toward l-tyrosine. The mechanism of the developed CL method was studied using ROS scavengers, HPLC, and mass spectrometry. The method was linear for l-tyrosine in the range of 0.03-50 µM. Minor changes in the l-tyrosine structure, including hydroxylation, dehydroxylation, phosphorylation, or decarboxylation, were found to lead to a strong decrease in CL. Using the excellent selectivity of the proposed method for l-tyrosine, we have developed a CL assay for measuring alkaline phosphatase activity in the range of 0.02-15 U/L with the limit of detection (LOD) of 4 mU/L using the nonchemiluminescent O-phospho-l-tyrosine as a substrate. Furthermore, the CL reaction was applied for tyrosinase activity assay as this enzyme can convert l-tyrosine to the nonchemiluminescent l-dopa. The decrease in CL is correlated with the tyrosinase activity in the range of 0.025-0.75 U/mL with an LOD of 1.5 mU/mL. Moreover, the tyrosinase activity assay was successfully applied for the determination of IC50 of the tyrosinase inhibitors kojic acid and benzoic acid. Therefore, our novel pulse UV irradiation CL method for the determination of l-tyrosine was not only suitable for the determination of this vital amino acid but also extended to the successful determination of its producing and metabolizing enzymes and their inhibitors.

A pilot study of game-based learning programs for childhood cancer survivors.

BACKGROUND: Childhood cancer survivors lacking awareness on their potential risks of late effects often fail to seek adequate follow-up care. Patient education matching their preference is of great importance to improve their adherence to survivorship care. In this study, we developed two age-dependent game-based learning programs, which enable continuous approaches for childhood cancer survivors along their intellectual maturation. Then, we assessed the effectiveness of the programs. METHODS: Childhood cancer survivors over 10 years of age who regularly visited a long-term follow-up clinic were enrolled in this study. They were requested to play either of two different types of game tools, one for school children and another for adolescents and young adults, for one month at home. To evaluate the educational effects of the programs, they were examined for health management awareness, self-esteem, and knowledge on cancer-related late effects before and after the intervention with age-based questionnaires and knowledge tests. RESULTS: Among 83 participants, 49 (59.0%) completed the assessments over the period of 12 months. The health management awareness and knowledge levels increased significantly at 1-month after the intervention as compared to the baseline in both school children and adolescents/young adults (for health management awareness, p = 0.011 in elementary school children; p = 0.007 in junior high school children; p < 0.001 in adolescents/young adults; for knowledge levels, p < 0.001 in school children; p < 0.001 in adolescents/young adults). The effect was maintained for 12 months in school children while it decreased in adolescents and young adults with time. Self-esteem significantly increased at 1-month (p = 0.002 in school children; p = 0.020 in adolescents/young adults) and was maintained for 12 months in both age groups. CONCLUSION: The game-based learning programs enhanced health locus of control and self-esteem in childhood cancer survivors. The game-based learning programs could be applied effectively to survivorship care as a new modality of patient education. TRIAL REGISTRATION: This study was retrospectively registered in UMIN-CTR ( UMIN000043603 ) on March 12, 2021.

Changes of cancer diagnosis disclosure to children in Japan in the last 20 years.

BACKGROUND: The practice of cancer diagnosis disclosure to children has been changed with the times. The regulations of clinical trials in the 2000s might change the practice in Japan. However, the perspective of this topic among children and adults has not been investigated in detail. METHODS: We studied changes in the practice of information sharing with children with cancer at pediatric cancer centers and the perspective of cancer diagnosis disclosure to children among school children, their parents and pediatric oncologists in the last 20 years by comparing the results of questionnaire surveys conducted in 1998, 2008 and 2018. RESULTS: This study revealed that the performing rate has increased with the times, but the institutions actively performing for children aged 7-9 years were 36.4% even in the 2018 survey. More than 70% of children wished diagnosis disclosure if they suffer from cancer in the series of surveys, while the ratio of parents who tell cancer diagnosis to their children hovered at 34.5 to 53.7% (p < 0.001 in all surveys). The ratio of pediatric oncologists having the policy to perform diagnosis disclosure proactively increased from 9.3 to 60.0%, while that of parents having the same policy stayed at 5.3% even in 2018. CONCLUSIONS: The performing rate of information sharing with children with cancer was significantly changed in the last 20 years. The opinion gaps were observed between parents and children and between parents and pediatric oncologists.

Change in children's perception of cancer in the last 10 years in Japan.

BACKGROUND: Social awareness of cancer can be changed with cancer education and proper distribution of cancer information. This study addressed the current situation and historical changes to children's perception of cancer. METHODS: Questionnaire surveys were conducted among healthy school children aged 10-15 years in 2008 and 2018. Knowledge of cancer was surveyed and compared with that of asthma, tuberculosis, and measles. The children were asked about their health information resources. RESULTS: The numbers of participants and collection rates were 438 and 63.9% in 2008, and 320 and 44.7% in 2018. Children's perception of cancer changed significantly in the last decade. The proportion of respondents answering "cancer affects children" changed from 78.3 to 89.5% (P = 0.0001), "cancer is preventable" from 42.0 to 49.7% (P = 0.0425), and "cancer is curable," from 52.4 to 66.0% (P = 0.0003). Significantly more junior high school students answered that cancer is preventable than elementary school children in 2018 (55.9 vs 42.7%, P = 0.0028). The major resources of information on health were television, parents, and books. The proportion of children choosing the Internet significantly increased from 15.3 to 47.8% (P < 0.0001). Significantly more junior high school students selected television and the Internet than elementary school children (94.5 vs 86.9%, P = 0.0202 for television; 57.1 vs 37.9%, P = 0.0007 for the Internet). CONCLUSIONS: The proportion of children correctly perceiving cancer information had increased in the last decade. Junior high school students better understood the information. The Internet is of increasing importance as an information resource for school children.

Peer evaluations of group work in different years of medical school and academic achievement: how are they related?

BACKGROUND: To develop the skills needed in health care teams, training communication and teamwork skills are important in medical education. Small group collaborative learning is one of the methods utilized in such trainings, and peer evaluation is suggested to be useful in reinforcing the effectiveness of group learning activities. In Mie University Faculty of Medicine, group work consisting of book review sessions of liberal arts education in the first grade and problem-based learning (PBL) sessions in preclinical years were conducted using the same peer evaluation system that included three domains: degree of prior learning, contribution to group discussion, and cooperative attitude. This study was conducted to determine the relationships among behaviors during group work and the academic achievement of medical students. METHODS: With the data from a cohort of medical students in three consecutive academic years (n = 340), peer evaluation scores in groupworks of book review sessions, those in PBL sessions and paper test scores of preclinical years were analyzed. The correlations were analyzed with Spearman's correlation coefficient, and the respective scores were compared by using the Wilcoxon signed-ranked test. RESULTS: Significant correlations were observed among the evaluation scores of respective domains in group work and paper test scores. The degree of prior learning had the strongest relationship among the three domains (rs = 0.355, p < 0.001 between book review sessions and PBL; rs = 0.338, p < 0.001 between book review sessions and paper test score; rs = 0.551, p < 0.001 between PBL and paper test score). Peer evaluation scores of respective domains were found to be significantly higher in PBL. CONCLUSION: Medical students maintained their groupwork behaviors to some extent from early school to preclinical years. Those behaviors were positively related to their academic achievement in the later years of the medical education curriculum. Our study highlighted the importance of the early introduction of group work. The results will be useful to motivate medical students to put more effort into group work.