Integrative molecular and spatial analysis reveals evolutionary dynamics and tumor-immune interplay of in situ and invasive acral melanoma.

In acral melanoma (AM), progression from in situ (AMis) to invasive AM (iAM) leads to significantly reduced survival. However, evolutionary dynamics during this process remain elusive. Here, we report integrative molecular and spatial characterization of 147 AMs using genomics, bulk and single-cell transcriptomics, and spatial transcriptomics and proteomics. Vertical invasion from AMis to iAM displays an early and monoclonal seeding pattern. The subsequent regional expansion of iAM exhibits two distinct patterns, clonal expansion and subclonal diversification. Notably, molecular subtyping reveals an aggressive iAM subset featured with subclonal diversification, increased epithelial-mesenchymal transition (EMT), and spatial enrichment of APOE+/CD163+ macrophages. In vitro and ex vivo experiments further demonstrate that APOE+CD163+ macrophages promote tumor EMT via IGF1-IGF1R interaction. Adnexal involvement can predict AMis with higher invasive potential whereas APOE and CD163 serve as prognostic biomarkers for iAM. Altogether, our results provide implications for the early detection and treatment of AM.

Pharmacogenomic profiling of intra-tumor heterogeneity using a large organoid biobank of liver cancer.

Inter- and intra-tumor heterogeneity is a major hurdle in primary liver cancer (PLC) precision therapy. Here, we establish a PLC biobank, consisting of 399 tumor organoids derived from 144 patients, which recapitulates histopathology and genomic landscape of parental tumors, and is reliable for drug sensitivity screening, as evidenced by both in vivo models and patient response. Integrative analysis dissects PLC heterogeneity, regarding genomic/transcriptomic characteristics and sensitivity to seven clinically relevant drugs, as well as clinical associations. Pharmacogenomic analysis identifies and validates multi-gene expression signatures predicting drug response for better patient stratification. Furthermore, we reveal c-Jun as a major mediator of lenvatinib resistance through JNK and ß-catenin signaling. A compound (PKUF-01) comprising moieties of lenvatinib and veratramine (c-Jun inhibitor) is synthesized and screened, exhibiting a marked synergistic effect. Together, our study characterizes the landscape of PLC heterogeneity, develops predictive biomarker panels, and identifies a lenvatinib-resistant mechanism for combination therapy.

Correlation between caries activity and salivary microbiota in preschool children.

Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of children. However, the distribution characteristics of oral saliva microbiomes in children with different CA are largely underexplored. The aim of this study was to investigate the microbial community in saliva of preschool children with different CA and caries status, and to analyze the difference of microbial community in saliva of children with different CA and its correlation with ECC. Subjects were divided into 3 groups based on the Cariostat caries activity test: Group H, high CA (n=30); Group M, medium CA (n = 30); Group L, low CA (n=30). Questionnaire survey was used to explore the related influencing factors of CA. According to the caries status (on the basis of decayed mising filled teeth), these subjects were divided into caries-free group (dmft=0, n=19), caries-low group (0 < dmft ≤ 4, n=27) and caries-high group (dmft > 4, n=44). Microbial profiles of oral saliva were analyzed using 16S rRNA gene sequencing. There were significant differences in the microbial structure (P < 0.05). Scardovia and Selenomonas were the biomarkers of both H group and high caries group. The genus Abiotrophia and Lautropia were the biomarkers of both the L group and the low caries group, while the Lactobacillus and Arthrospira spp. were significantly enriched in the M group. The area under the ROC curve of the combined application of dmft score, age, frequency of sugary beverage intake, and the genus Scardovia, Selenomonas, and Campylobacter in screening children with high CA was 0.842. Moreover, function prediction using the MetaCyc database showed that there were significant differences in 11 metabolic pathways of salivary microbiota among different CA groups. Certain bacteria genera in saliva such as Scardovia and Selenomonas may be helpful in screening children with high CA.

Liver tumour immune microenvironment subtypes and neutrophil heterogeneity.

The heterogeneity of the tumour immune microenvironment (TIME), organized by various immune and stromal cells, is a major contributing factor of tumour metastasis, relapse and drug resistance1-3, but how different TIME subtypes are connected to the clinical relevance in liver cancer remains unclear. Here we performed single-cell RNA-sequencing (scRNA-seq) analysis of 189 samples collected from 124 patients and 8 mice with liver cancer. With more than 1 million cells analysed, we stratified patients into five TIME subtypes, including immune activation, immune suppression mediated by myeloid or stromal cells, immune exclusion and immune residence phenotypes. Different TIME subtypes were spatially organized and associated with chemokine networks and genomic features. Notably, tumour-associated neutrophil (TAN) populations enriched in the myeloid-cell-enriched subtype were associated with an unfavourable prognosis. Through in vitro induction of TANs and ex vivo analyses of patient TANs, we showed that CCL4+ TANs can recruit macrophages and that PD-L1+ TANs can suppress T cell cytotoxicity. Furthermore, scRNA-seq analysis of mouse neutrophil subsets revealed that they are largely conserved with those of humans. In vivo neutrophil depletion in mouse models attenuated tumour progression, confirming the pro-tumour phenotypes of TANs. With this detailed cellular heterogeneity landscape of liver cancer, our study illustrates diverse TIME subtypes, highlights immunosuppressive functions of TANs and sheds light on potential immunotherapies targeting TANs.

The roles of inactivated vaccines in older patients with infection of Delta variant in Nanjing, China.

BACKGROUND: The coronavirus disease 2019 (COVID-19) is spreading around the world. The COVID-19 vaccines may improve concerns about the pandemic. However, the roles of inactivated vaccines in older patients (aged ≥60 years) with infection of Delta variant were less studied. METHODS: We classified the older patients with infection of Delta variant into three groups based on the vaccination status: no vaccination (group A, n = 113), one dose of vaccination (group B, n = 46), and two doses of vaccination (group C, n = 22). Two inactivated COVID-19 vaccines (BBIBP-CorV or CoronaVac) were evaluated in this study. The demographic data, laboratory parameters, and clinical severity were recorded. RESULTS: A total of 181 older patients with infection of Delta variant were enrolled. 111 (61.3%) patients had one or more co-morbidities. The days of "turn negative" and hospital stay in Group C were lower than those in the other groups (P < 0.05). The incidences of multiple organ dysfunction syndrome (MODS), septic shock, acute respiratory distress syndrome (ARDS), acute kidney injury, and cardiac injury in Group A were higher than those in the other groups (P < 0.05). The MV-free days and ICU-free days during 28 days in Group A were also lower than those in the other groups (P < 0.05). In patients with co-morbidities, vaccinated cases had lower incidences of MODS (P = 0.015), septic shock (P = 0.015), and ARDS (P = 0.008). CONCLUSIONS: The inactivated COVID-19 vaccines were effective in improving the clinical severity of older patients with infection of Delta variant.

Single-Cell DNA Sequencing Reveals Punctuated and Gradual Clonal Evolution in Hepatocellular Carcinoma.

BACKGROUND & AIMS: Copy number alterations (CNAs), elicited by genome instability, are a major source of intratumor heterogeneity. How CNAs evolve in hepatocellular carcinoma (HCC) remains unknown. METHODS: We performed single-cell DNA sequencing (scDNA-seq) on 1275 cells isolated from 10 patients with HCC, ploidy-resolved scDNA-seq on 356 cells from 1 additional patient, and single-cell RNA sequencing on 27,344 cells from 3 additional patients. Three statistical fitting models were compared to investigate the CNA accumulation pattern. RESULTS: Cells in the tumor were categorized into the following 3 subpopulations: euploid, pseudoeuploid, and aneuploid. Our scDNA-seq analysis revealed that CNA accumulation followed a dual-phase copy number evolution model, that is, a punctuated phase followed by a gradual phase. Patients who exhibited prolonged gradual phase showed higher intratumor heterogeneity and worse disease-free survival. Integrating bulk RNA sequencing of 17 patients with HCC, published datasets of 1196 liver tumors, and immunohistochemical staining of 202 HCC tumors, we found that high expression of CAD, a gene involved in pyrimidine synthesis, was correlated with rapid tumorigenesis and reduced survival. The dual-phase copy number evolution model was validated by our single-cell RNA sequencing data and published scDNA-seq datasets of other cancer types. Furthermore, ploidy-resolved scDNA-seq revealed the common clonal origin of diploid- and polyploid-aneuploid cells, suggesting that polyploid tumor cells were generated by whole genome doubling of diploid tumor cells. CONCLUSIONS: Our work revealed a novel dual-phase copy number evolution model, showed HCC with longer gradual phase was more severe, identified CAD as a promising biomarker for early recurrence of HCC, and supported the diploid origin of polyploid HCC.

IDH Mutation Subgroup Status Associates with Intratumor Heterogeneity and the Tumor Microenvironment in Intrahepatic Cholangiocarcinoma.

Intrahepatic cholangiocarcinoma (ICC) is highly heterogeneous. Here, the authors perform exome sequencing and bulk RNA sequencing on 73 tumor regions from 14 ICC patients to portray the multi-faceted intratumor heterogeneity (ITH) landscape of ICC. The authors show that ITH is highly concordant across genomic, transcriptomic, and immune levels. Comparison of these data to 8 published datasets reveals significantly higher degrees of ITH in ICC than hepatocellular carcinoma. Remarkably, the authors find that high-ITH tumors highly overlap with the IDH (isocitrate dehydrogenase)-mutant subgroup (IDH-SG), comprising of IDH-mutated tumors and IDH-like tumors, that is, those IDH-wildtype tumors that exhibit similar molecular profiles to the IDH-mutated ones. Furthermore, IDH-SG exhibits less T cell infiltration and lower T cell cytotoxicity, indicating a colder tumor microenvironment (TME). The higher ITH and colder TME of IDH-SG are successfully validated by single-cell RNA sequencing on 17 503 cells from 4 patients. Collectively, the study shows that IDH mutant subgroup status, rather than IDH mutation alone, is associated with ITH and the TME of ICC tumors. The results highlight that IDH-like patients may also benefit from IDH targeted therapies and provide important implications for the diagnosis and treatment of ICC.

Health risk assessment and personal exposure to Volatile Organic Compounds (VOCs) in metro carriages - A case study in Shanghai, China.

Air pollution in transportation cabins has recently become a public concern. However, few studies assessed the exposure levels of suspected air pollutants including Volatile Organic Compounds (VOCs). This paper studied the exposure levels of in-carriage VOCs (benzene, toluene, ethylbenzene, xylene, styrene, formaldehyde, acetaldehyde, acetone and acrolein) in Shanghai, China and estimated the health risk in different conditions. The results indicated that VOCs concentrations in metro carriages varied from different train models, due to the difference in carriage size and ventilation system. The concentrations of aromatic VOCs in old metro carriage were 1-2 times higher than the new ones, as better paintings were used in new trains. Poor air circulation and ventilation in the underground track was likely to be the cause of higher VOCs levels (~10%) than the above-ground track. Lower aromatic compounds levels and higher carbonyls levels were observed in metro carriages at suburban areas than those at urban areas, likely due to less aromatic emission sources and more carbonyls emission sources in suburban areas. Acetone and acrolein were found to increase from 7.71 to 26.28µg/m3 with number of commuters increasing from 40 to 200 in the carriages. According to the acceptable level proposed by the World Health Organization (1×10-6-1×10-5), the life carcinogenic risk of commuters by subway (8.5×10-6-4.8×10-5) was little above the acceptable level in Shanghai. Further application of our findings is possible to act as a reference in facilitating regulations for metro systems in other cities around world, so that in-carriage air quality might be improved.

A Class of Multiresponsive Colorimetric and Fluorescent pH Probes via Three Different Reaction Mechanisms of Salen Complexes: A Selective and Accurate pH Measurement.

We report a class of multiresponsive colorimetric and fluorescent pH probes based on three different reaction mechanisms including cation exchange, protonation, and hydrolysis reaction of K(I), Ca(II), Zn(II), Cu(II), Al(III), and Pd(II) Salen complexes. Compared with traditional pure organic pH probes, these complex-based pH probes exhibited a much better selectivity due to the shielding function of the filled-in metal ion in the complex. Their pH sensing performances were affected by the ligand structure and the central metal ion. This work is the first report of "off-on-on'-off" colorimetric and fluorescent pH probes that possess three different reaction mechanisms and should inspire the design of multiple-responsive probes for important analytes in biological systems.

Correction: Fluorescent metal ion chemosensors via cation exchange reactions of complexes, quantum dots, and metal-organic frameworks.

Correction for 'Fluorescent metal ion chemosensors via cation exchange reactions of complexes, quantum dots, and metal-organic frameworks' by Jinghui Cheng, et al., Analyst, 2015, DOI: 10.1039/c5an01398d.

Fluorescent metal ion chemosensors via cation exchange reactions of complexes, quantum dots, and metal-organic frameworks.

Due to their wide range of applications and biological significance, fluorescent sensors have been an active research area in the past few years. In the present review, recent research developments on fluorescent chemosensors that detect metal ions via cation exchange reactions (transmetalation, metal displacement, or metal exchange reactions) of complexes, quantum dots, and metal-organic frameworks are described. These complex-based chemosensors might have a much better selectivity than the corresponding free ligands/receptors because of the shielding function of the filled-in metal ions. Moreover, not only the chemical structure of the ligands/receptors but also the identity of the central metal ions have a tremendous impact on the sensing performances. Therefore, sensing via cation exchange reactions potentially provides a new, simple, and powerful way to design fluorescent chemosensors.

Optical chemosensors based on transmetalation of salen-based Schiff base complexes.

We report our systematic studies of novel, simple, selective, and sensitive optical (both colorimetric and fluorescent) chemosensors for detecting Al(3+) based on transmetalation reactions (metal displacement or exchange reactions) of a series of K(I), Ca(II), Zn(II), Cu(II), and Pt(II) complexes containing different ligands of salen-based Schiff bases. Both the chemical structure of the salen ligand and the identity of the central metal ion have a tremendous impact on the sensing performance, which is mainly determined by the stability constant of the complex. Moreover, the selectivities of the salen-complex-based chemosensors are much better than those of the corresponding free salen ligands because of the shielding function of the filled-in metal ion in the complex. Therefore, the present work potentially provides a new and simple way to design optical probes via complex-based transmetalation reactions.

Therapist Perspectives: Wii Active Videogames Use in Inpatient Settings with People Who Have Had a Brain Injury.

OBJECTIVE: Brain injuries (BIs) are a major public health issue. Clinical experience and literature have identified that it is often challenging to motivate people who have had a BI to engage in repetitive exercises commonly prescribed for rehabilitation. As a result, some therapists include commercial active videogames (AVGs) in their therapy sessions to help make repetitive actions fun and engaging. In this project, we explored how the therapists used commercial AVGs to better understand the major barriers and enablers of use. MATERIALS AND METHODS: We interviewed 17 therapists from two rehabilitation hospitals who work with people who have had a BI. After the interviews were transcribed, we identified salient themes. RESULTS: At the time of the interviews, therapists were using only the Nintendo(®) (Kyoto, Japan) Wii™ console. Common therapeutic goals included balance and weight shifting. Several patient factors, such as cognitive and physical abilities, age, and previous gaming experience, were considered important considerations when deciding to use games. Therapists also indicated many desired changes to games, including better control/interface, better feedback, and the ability to adjust timing, challenge, and stimulation levels. CONCLUSIONS: When considering therapy-centered game design, the needs of both therapists and patients should be considered. There is a necessary balance to consider in game design: They need to (a) be perceived as fun, (b) meet therapy goals, and (c) address therapists' needs (e.g., adjustability to address a range of patient abilities). Additionally, there is a need for a wide variety of available games to address novelty and personal preferences.

Colorimetric and fluorescent pH and Cu2+ probes induced by photoisomerization of a maleonitrile-based Salen ligand.

Both photo-induced cis-trans-isomers of a maleonitrile-based Salen ligand can be used as pH probes covering a broad pH range through three different mechanisms but upon undergoing the formation of a stable complex and Cu(2+)-promoted hydrolysis, respectively, they exhibit totally different responses and mechanisms for sensing Cu(2+).

Near-infrared phosphorescence: materials and applications.

Room-temperature phosphorescent materials that emit light in the visible (red, green, and blue; from 400 to 700 nm) have been a major focus of research and development during the past decades, due to their applications in organic light-emitting diodes (OLEDs), light-emitting electrochemical cells, photovoltaic cells, chemical sensors, and bio-imaging. In recent years, near-infrared (NIR) phosphorescence beyond the visible region (700-2500 nm) has emerged as a new, promising, and challenging research field with potential applications toward NIR OLEDs, telecommunications, night vision-readable displays. Moreover, NIR phosphorescence holds promise for in vivo imaging, because cells and tissues exhibit little absorption and auto-fluorescence in this spectral region. This review describes the overall progress made in the past ten years on NIR phosphorescent transition-metal complexes including Cu(I), Cu(II), Cr(III), Re(I), Re(III), Ru(II), Os(II), Ir(III), Pt(II), Pd(II), Au(I), and Au(III) complexes, with a primary focus on material design complemented with a selection of optical, electronic, sensory, and biologic applications. A critical comparison of various NIR phosphorescent materials reported in the literature and a blueprint for future development in this field are also provided.

Ratiometric optical oxygen sensing: a review in respect of material design.

The quantitative determination of oxygen concentration is essential for a variety of applications ranging from life sciences to environmental sciences. Optical oxygen sensing allows non-invasive measurements with biological objects, parallel monitoring of multiple samples, and imaging. In general, ratiometric optical oxygen sensing is more desirable, due to its advantages of selectivity, insensitivity to ambient or scattered light, and elimination of instrumental fluctuation. Moreover, it can provide the perceived colour change, which would be useful not only for the ratiometric method of detection but also for rapid visual sensing. Mainly focusing on material design for ratiometric measurement, this review describes the overall progress made in the past ten years on ratiometric optical ground-state triplet oxygen sensing and offers a critical comparison of various methods reported in the literature. It also provides a development blueprint for ratiometric optical oxygen sensing.

Synthesis and photophysical properties of water-soluble sulfonato-Salen-type Schiff bases and their applications of fluorescence sensors for Cu2+ in water and living cells.

A series of water-soluble sulfonato-Salen-type ligands derived from different diamines including 1,2-ethylenediamine (Et-1-Et-4), 1,2-cyclohexanediamine (Cy-1 and Cy-2), 1,2-phenylenediamine (Ph-1-Ph-3 and PhMe-1-PhMe-4), and dicyano-1,2-ethenediamine (CN-1) has been designed and prepared. Sulfonate groups of ligands ensure good stability and solubility in water without affecting their excited state properties. These ligands exhibit strong UV/Vis-absorption and blue, green, or orange fluorescence. Time-dependent-density functional theory calculations have been undertaken to reveal the influence of ligand nature, especially sulfonate groups, on the frontier molecular orbitals. Since their fluorescence is selectively quenched by Cu(2+), the sulfonato-Salen-type ligands can be used as highly selective and sensitive turn-off fluorescence sensors for the detection of Cu(2+) in water and fluorescence imaging in living cells.

Tunable fluorescent/phosphorescent platinum(II) porphyrin-fluorene copolymers for ratiometric dual emissive oxygen sensing.

A series of new platinum(II) 5,15-bis(pentafluorophenyl)-10,20-bis(phenyl)porphyrin-9,9-dioctylfluorene copolymers, in which the relative intensities of the blue fluorescence and red phosphorescence can be easily tuned by the initial feed ratio of the two monomers or energy transfer between the fluorescent and phosphorescent units, have been designed and prepared for the application in ratiometric dual emissive oxygen sensing. To the best of our knowledge, this is the first example of a ratiometric oxygen sensor based on dual fluorescent/phosphorescent polymers or copolymers containing transition-metal complexes. It also provides an alternative and easy way to achieve dual emissive oxygen sensing.