Spatial omics technologies for understanding molecular status associated with cancer progression.

Cancer cells are generally exposed to numerous extrinsic stimulations in the tumor microenvironment. In this environment, cancer cells change their expression profiles to fight against circumstantial stresses, allowing their progression in the challenging tissue space. Technological advancements of spatial omics have had substantial influence on cancer genomics. This technical progress, especially that occurring in the spatial transcriptome, has been drastic and rapid. Here, we describe the latest spatial analytical technologies that have allowed omics feature characterization to retain their spatial and histopathological information in cancer tissues. Several spatial omics platforms have been launched, and the latest platforms finally attained single-cell level or even higher subcellular level resolution. We discuss several key papers elucidating the initial utility of the spatial analysis. In fact, spatial transcriptome analyses reveal comprehensive omics characteristics not only in cancer cells but also their surrounding cells, such as tumor infiltrating immune cells and cancer-associated fibroblasts. We also introduce several spatial omics platforms. We describe our own attempts to investigate molecular events associated with cancer progression. Furthermore, we discuss the next challenges in analyzing the multiomics status of cells, including their morphology and location. These novel technologies, in conjunction with spatial transcriptome analysis and, more importantly, with histopathology, will elucidate even novel key aspects of the intratumor heterogeneity of cancers. Such enhanced knowledge is expected to open a new path for overcoming therapeutic resistance and eventually to precisely stratify patients.

AIE-ESIPT Photoluminescent Probe Based on 3-(3-Hydroxypyridin-2-yl)isoquinolin-4-ol for the Detection of Intracellular Hydrogen Peroxide.

Excited-state intramolecular proton transfer (ESIPT) molecules, which feature large Stokes shifts to avoid self-absorption, play an essential role in photoluminescent bioimaging probes. Herein, we report the development of an ESIPT molecule 3-(3-hydroxypyridin-2-yl)isoquinolin-4-ol (PiQ). PiQ not only undergoes a distinct ESIPT process unlike the symmetrical 2,2'-bipyridyl-3,3'-diol but also exhibits aggregation-induced emission (AIE) characteristics. PiQ self-assembles into aggregates with an average size of 241.0±51.9 nm in aqueous solutions, leading to significantly enhanced photoluminescence. On the basis of the ESIPT and AIE characteristics of PiQ, the latter is functionalized with a hydrogen peroxide-responsive 4-pinacoratoborylbenzyl group (B) and a carboxylesterase-responsive acetyl group (A) to produce a photoluminescent probe B-PiQ-A. The potential of PiQ for applications in bioimaging and chemical sensing is underscored by its efficient detection of both endogenous and exogenous hydrogen peroxide in living cells.

Frequent toothbrushing boosts resilience among children in poverty: results from a population-based longitudinal study.

BACKGROUND: Poverty negatively impacts beneficial aspects of mental development, such as resilience. Toothbrushing, an oral health behavior, has the potential to protect children's resilience through its anti-inflammatory and self-management effects and may be more effective for children, especially children in poverty. This study investigated whether toothbrushing boosts resilience among children, especially children under poverty, and modifies the association between poverty and resilience using a longitudinal population sample of school children. METHODS: Data from the Adachi Child Health Impact of Living Difficulty (A-CHILD Study) were analyzed. A baseline study was conducted in 2015 in which the children were in first grade and followed through fourth grade (N = 3459, response rate: 80%, follow-up rate: 82%). Poverty was assessed by material deprivation (life-related deprivation and child-related deprivation) and annual household income at baseline. Children's toothbrushing frequency was assessed at baseline and classified into less than twice a day or twice or more a day. Children's resilience was assessed at baseline and follow-up using the Children's Resilient Coping Scale (range 0-100). RESULTS: Children who brushed their teeth twice or more a day in first grade had 3.50 points greater resilience scores in fourth grade than those who brushed their teeth less than twice a day in first grade. After adjusting for confounders, including resilience in first grade, among underpoverty children, those who brushed their teeth twice or more a day in first grade had higher resilience scores [2.66 (95% CI = 0.53, 4.79)] than those who brushed their teeth less than twice a day. Among nonpoverished children, toothbrushing frequency in first grade did not significantly correlate with resilience in fourth grade. CONCLUSIONS: The beneficial effect of toothbrushing twice or more a day on resilience was more significant among children in poverty than among those without poverty in elementary school in Japan. Health policy focused on frequent toothbrushing may contribute to boosting resilience among children living in poverty.

A Free Bypass Flap for Chronic Limb-threatening Ischemia.

Background: Recently, significant inframalleolar disease seems to increase in chronic limb-threatening ischemia (CLTI) patients, making identifying sufficient outflow vessels in the foot challenging. In these difficult situations, free tissue transfer is a valuable tool to provide a low-resistance vascular bed to the affected part. However, there remains concern that free tissue transfer may impede adequate perfusion of the higher resistance diseased vascular bed. Methods: To improve perfusion of the affected area directly, the authors have developed a concept of a free bypass flap, adding bypass surgery to free tissue transfer. After anastomosis with the recipient vessels in a conventional manner for free tissue transfer, bypass surgery to the foot is performed by anastomosis of the branch of the flap pedicle with the diseased artery to the foot. A retrospective chart review of nine CLTI patients was performed to analyze the outcomes of free bypass flap transfer between 2018 and 2023. Results: The flap success rate was 100% (n = 9). Postoperative angiography or echo confirmed the patency of all but one bypass vessel (n = 8). There were six fatalities, however, due to causes other than foot lesions, with an average observation period of 16 months. The limb salvage rate was 89% (n = 8). Conclusions: A free bypass flap enhances the overall blood circulation to the foot. Due to its high patency rate of bypass vessels, it is a valuable method for preserving the limbs of highly comorbid patients with CLTI.

Association between Short Stature at Grade 1 and Permanent Teeth Caries at Grade 6 in Elementary School Children in Japan: A Population-Based Cohort Study.

Short stature in children is a marker of low nutritional status and has been suggested to be associated with dental caries. However, longitudinal studies on this topic are scarce. Data from a longitudinal study of elementary school children in Adachi City, Tokyo, Japan, were analyzed. In 2015, caregivers of children at grade 1 answered questionnaires, and information on dental caries and height measured at school health checkups was merged and followed to grade 6 (N = 3576; follow up rate = 83.3%). The association between short stature at grade 1 (-2.01 standard deviation (SD)--3.00 SD, or <-3.00 SD in height-for-age according to the World Health Organization criteria) and the number of decayed, missing, or filled permanent teeth (DMFT) at grade 6 was examined using multivariable Poisson regression with robust standard error. After adjusting for confounders, children with a short stature at grade 1 had a higher DMFT number at grade 6: the mean ratios (95% confidence interval) were 1.17 (0.89-1.54) and 2.18 (1.03-4.64) for children with a height-for-age -2.01 SD--3.00 SD, and those with a height-for-age < -3.00, respectively. Short stature at grade 1 could be a marker of future dental caries in the permanent teeth at grade 6.

Combination of rRT-PCR and Clinical Features to Predict Coronavirus Disease 2019 for Nosocomial Infection Control.

Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), immediately became a pandemic. Therefore, nosocomial infection control is necessary to screen for patients with possible COVID-19. Objective: This study aimed to investigate commonly measured clinical variables to predict COVID-19. Methods: This cross-sectional study enrolled 1087 patients in the isolation ward of a university hospital. Conferences were organized to differentiate COVID-19 from non-COVID-19 cases, and multiple nucleic acid tests were mandatory when COVID-19 could not be excluded. Multivariate logistic regression models were employed to determine the clinical factors associated with COVID-19 at the time of hospitalization. Results: Overall, 352 (32.4%) patients were diagnosed with COVID-19. The majority of the non-COVID-19 cases were predominantly caused by bacterial infections. Multivariate analysis indicated that COVID-19 was significantly associated with age, sex, body mass index, lactate dehydrogenase, C-reactive protein, and malignancy. Conclusion: Some clinical factors are useful to predict patients with COVID-19 among those with symptoms similar to COVID-19. This study suggests that at least two real-time reverse-transcription polymerase chain reactions of SARS-CoV-2 are recommended to exclude COVID-19.

Impact of multiple MEFV variants of unknown significance on the diagnosis and clinical presentation of familial Mediterranean fever.

The detection of variants of unknown significance (VUS) in familial Mediterranean fever (FMF) is common; however, their diagnostic value remains elusive, and the interpretation of multiple VUS remains difficult. Therefore, we examined FMF diagnosis-associated factors 1-year post-genetic testing in patients with only VUS and assessed the impact of multiple VUS on diagnosis and clinical features. A 1-year follow-up was conducted on patients clinically suspected of having FMF without confirmatory diagnosis owing to the presence of only VUS. Clinical features were compared between patients with a single VUS and those with multiple VUS among patients diagnosed with FMF. Among 261 patients followed up, 202 were diagnosed with FMF based on clinical judgment. No specific clinical symptoms or variant patterns at genetic testing were associated with diagnosis at 1 year. Multiple VUS was significantly and independently associated with a lower response to colchicine than single VUS among patients diagnosed with FMF. However, clinical symptoms showed no correlation with the number of VUS. In conclusion, predicting FMF diagnosis 1-year post-genetic testing in patients with only VUS remains challenging. Moreover, the impact of multiple VUS on FMF may be limited owing to the lack of correlation with clinical features, except colchicine response.

CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing.

Familial hypercholesterolemia is an inherited disorder that remains underdiagnosed. Conventional genetic testing methods such as next-generation sequencing (NGS) or target PCR are based on the amplification process. Due to the efficiency limits of polymerase and ligase enzymes, these methods usually target short regions and do not detect large mutations straightforwardly. This study combined the long-read nanopore sequencing and CRISPR-Cas9 system to sequence the target DNA molecules without amplification. We originally designed and optimized the CRISPR-RNA panel to target the low-density lipoprotein receptor gene (LDLR) and proprotein convertase subtilisin/kexin type 9 gene (PCSK9) from human genomic DNA followed by nanopore sequencing. The average coverages for LDLR and PCSK9 were 106× and 420×, versus 1.2× for the background genome. Among them, continuous reads were 52x and 307x, respectively, and spanned the entire length of LDLR and PCSK9. We identified pathogenic mutations in both coding and splicing donor regions in LDLR. We also detected an 11,029 bp large deletion in another case. Furthermore, using continuous long reads generated from the benchmark experiment, we demonstrated how a false-positive 670 bp deletion caused by PCR amplification errors was easily eliminated.

Relationship between nephrotoxicity and area under the concentration-time curve of vancomycin in critically ill patients: a multicenter retrospective study.

We aimed to assess the frequency of acute kidney injury (AKI) in different areas under the concentration-time curve (AUC) values of vancomycin (VAN) using a two-point blood collection method, allowing for accurate AUC assessment in critically ill patients. This multicenter retrospective observational study was conducted in eight hospitals. We retrospectively analyzed the data of patients who had received VAN in an intensive care unit (ICU) between January 2020 and December 2022. The primary outcome was the incidence of AKI. Patients were classified into three groups according to the AUC24-48h at the initial therapeutic drug monitoring (TDM) as follows: <500, 500-600, and ≥600 µg·h/mL. The AUC24-48h values were calculated using the Bayesian estimation software Practical AUC-guided TDM. Among 146 patients [median age (interquartile range), 67 (56-78) years; 39% women], the AUC24-48h <500 µg·h/mL had an AKI rate of 6.5% (7/107), the AUC24-48h 500-600 µg·h/mL had an AKI rate of 28.0% (7/25), and the AUC24-48h ≥600 µg·h/mL had an AKI rate of 42.9% (6/14). In multivariate Cox proportional hazard analysis, the AUC24-48h 500-600 µg·h/mL [hazard ratio 5.4, 95% confidence interval (CI) 1.64-17.63] and the AUC24-48h ≥600 µg·h/mL (hazard ratio 7.0, 95% CI 2.31-21.18) significantly correlated with a higher incidence of AKI compared with the AUC24-48h <500 µg·h/mL. In conclusion, we identified an association between AUC on day 2 and the risk of AKI in ICU patients, suggesting that not only AUCs above 600 µg·h/mL but also those between 500 and 600 µg·h/mL pose a risk for AKI. IMPORTANCE: Vancomycin (VAN) is a glycopeptide antibiotic and one of the most commonly used antibiotics for severe infections caused by methicillin-resistant Staphylococcus aureus. However, higher VAN concentrations have been associated with an increased risk of acute kidney injury (AKI). Herein, we aimed to assess the frequency of AKI in different areas under the concentration-time curve (AUC) values of VAN using a two-point blood collection method, allowing for accurate AUC assessment in critically ill patients. We identified an association between AUC on day 2 and the risk of AKI in intensive care unit patients, suggesting that not only AUCs above 600 µg·h/mL but also those between 500 and 600 µg·h/mL pose a risk for AKI. Therefore, individualized dosing is feasible, with pharmacists being able to optimize VAN doses to attain appropriate targets.

Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis.

BACKGROUND: Cell-cell interaction factors that facilitate the progression of adenoma to sporadic colorectal cancer (CRC) remain unclear, thereby hindering patient survival. METHODS: We performed spatial transcriptomics on five early CRC cases, which included adenoma and carcinoma, and one advanced CRC. To elucidate cell-cell interactions within the tumour microenvironment (TME), we investigated the colocalisation network at single-cell resolution using a deep generative model for colocalisation analysis, combined with a single-cell transcriptome, and assessed the clinical significance in CRC patients. FINDINGS: CRC cells colocalised with regulatory T cells (Tregs) at the adenoma-carcinoma interface. At early-stage carcinogenesis, cell-cell interaction inference between colocalised adenoma and cancer epithelial cells and Tregs based on the spatial distribution of single cells highlighted midkine (MDK) as a prominent signalling molecule sent from tumour epithelial cells to Tregs. Interaction between MDK-high CRC cells and SPP1+ macrophages and stromal cells proved to be the mechanism underlying immunosuppression in the TME. Additionally, we identified syndecan4 (SDC4) as a receptor for MDK associated with Treg colocalisation. Finally, clinical analysis using CRC datasets indicated that increased MDK/SDC4 levels correlated with poor overall survival in CRC patients. INTERPRETATION: MDK is involved in the immune tolerance shown by Tregs to tumour growth. MDK-mediated formation of the TME could be a potential target for early diagnosis and treatment of CRC. FUNDING: Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Science Research; OITA Cancer Research Foundation; AMED under Grant Number; Japan Science and Technology Agency (JST); Takeda Science Foundation; The Princess Takamatsu Cancer Research Fund.

Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma.

The mechanism underlying the development of tumors, particularly at early stages, still remains mostly elusive. Here, we report whole-genome long and short read sequencing analysis of 76 lung cancers, focusing on very early-stage lung adenocarcinomas such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma. The obtained data is further integrated with bulk and spatial transcriptomic data and epigenomic data. These analyses reveal key events in lung carcinogenesis. Minimal somatic mutations in pivotal driver mutations and essential proliferative factors are the only detectable somatic mutations in the very early-stage of AIS. These initial events are followed by copy number changes and global DNA hypomethylation. Particularly, drastic changes are initiated at the later AIS stage, i.e., in Noguchi type B tumors, wherein cancer cells are exposed to the surrounding microenvironment. This study sheds light on the pathogenesis of lung adenocarcinoma from integrated pathological and molecular viewpoints.