A pan-cancer single-cell panorama of human natural killer cells.

Natural killer (NK) cells play indispensable roles in innate immune responses against tumor progression. To depict their phenotypic and functional diversities in the tumor microenvironment, we perform integrative single-cell RNA sequencing analyses on NK cells from 716 patients with cancer, covering 24 cancer types. We observed heterogeneity in NK cell composition in a tumor-type-specific manner. Notably, we have identified a group of tumor-associated NK cells that are enriched in tumors, show impaired anti-tumor functions, and are associated with unfavorable prognosis and resistance to immunotherapy. Specific myeloid cell subpopulations, in particular LAMP3+ dendritic cells, appear to mediate the regulation of NK cell anti-tumor immunity. Our study provides insights into NK-cell-based cancer immunity and highlights potential clinical utilities of NK cell subsets as therapeutic targets.

Gingipains are the important virulence factors of Porphyromonas gingivalis downregulating B10 cells.

Porphyromonas gingivalis is a keystone pathogen in periodontitis. Our previous study indicated that periodontitis induced by P. gingivalis increased the percentage of CD19+ B cells but decreased the ratio of IL-10-producing regulatory B cells (B10) in collagen-induced arthritis (CIA) mice. It is still unclear which virulence factors of P. gingivalis are involved in these processes. Here, we compared the effects of different components of P. gingivalis on the biogenesis of B10 cells and found that the decreased proportion of B10 cells mainly resulted from the undenatured proteins other than the DNA, RNA, or lipopolysaccharides of P. gingivalis. As gingipains are enzymes and virulence factors that play a vital role in the progression in periodontitis through affecting the innate and adaptive immune system, we then compared the influence of the wild-type (WT) strain of P. gingivalis (ATCC 33277) and its isogenic gingipain-null mutant (∆K∆RAB) on the differentiation of splenic B cells into B10 cells. Interestingly, compared to WT strain, ∆K∆RAB treatment increased the frequency of B10 cells as well as the expression of IL-6 in B cells. Furthermore, the acute peritonitis, an ideal model for the quick evaluation of immune effects of agents, induced by ∆K∆RAB, showed the higher IL-6 production and proportion of B10 cells compared with WT. Finally, we performed transcriptomic analysis to better understand the effects and possible mechanisms of gingipains on B cells. Compared with WT, ∆K∆RAB upregulated the PI3K-Akt pathway of B cells, which is important for IL-10 production and B10 cell biogenesis, and more activated Jak-STAT pathway, which is a classical signaling pathway mediated by IL-6. Cumulatively, this study preliminarily revealed that gingipains of P. gingivalis are vital virulence factors downregulating B10 cells and altering immune responses.

Model integrating CT-based radiomics and genomics for survival prediction in esophageal cancer patients receiving definitive chemoradiotherapy.

BACKGROUND: Definitive chemoradiotherapy (dCRT) is a standard treatment option for locally advanced stage inoperable esophageal squamous cell carcinoma (ESCC). Evaluating clinical outcome prior to dCRT remains challenging. This study aimed to investigate the predictive power of computed tomography (CT)-based radiomics combined with genomics for the treatment efficacy of dCRT in ESCC patients. METHODS: This retrospective study included 118 ESCC patients who received dCRT. These patients were randomly divided into training (n = 82) and validation (n = 36) groups. Radiomic features were derived from the region of the primary tumor on CT images. Least absolute shrinkage and selection operator (LASSO) regression was conducted to select optimal radiomic features, and Rad-score was calculated to predict progression-free survival (PFS) in training group. Genomic DNA was extracted from formalin-fixed and paraffin-embedded pre-treatment biopsy tissue. Univariate and multivariate Cox analyses were undertaken to identify predictors of survival for model development. The area under the receiver operating characteristic curve (AUC) and C-index were used to evaluate the predictive performance and discriminatory ability of the prediction models, respectively. RESULTS: The Rad-score was constructed from six radiomic features to predict PFS. Multivariate analysis demonstrated that the Rad-score and homologous recombination repair (HRR) pathway alterations were independent prognostic factors correlating with PFS. The C-index for the integrated model combining radiomics and genomics was better than that of the radiomics or genomics models in the training group (0.616 vs. 0.587 or 0.557) and the validation group (0.649 vs. 0.625 or 0.586). CONCLUSION: The Rad-score and HRR pathway alterations could predict PFS after dCRT for patients with ESCC, with the combined radiomics and genomics model demonstrating the best predictive efficacy.

Comprehensive mapping of alternative polyadenylation site usage and its dynamics at single-cell resolution.

Alternative polyadenylation (APA) plays an important role in posttranscriptional gene regulation such as transcript stability and translation efficiency. However, our knowledge about APA dynamics at the single-cell level is largely unexplored. Here, we developed single-cell polyadenylation sequencing, a strand-specific approach for sequencing the 3' end of transcripts, to investigate the landscape of APA at the single-cell level. By analyzing several cell lines, we found many genes using multiple polyA sites in bulk data are prone to use only one polyA site in each single cell. Interestingly, cell cycle genes were significantly enriched in genes with high variation in polyA site usages. Furthermore, the 414 genes showing a polyA site usage switch after cell synchronization enriched cell cycle genes, while the differentially expressed genes after cell synchronization did not enrich cell cycle genes. We further identified 812 genes showing polyA site usage changes between neighboring cell cycles, which were grouped into six clusters, with cell phase-specific functional categories enriched in each cluster. Deletion of one polyA site in MSL1 and SCCPDH results in slower and faster cell cycle progression, respectively, supporting polyA site usage switch played an important role in cell cycle. These results indicate that APA is an important layer for cell cycle regulation.

Effects of enhanced hygiene measures on severe diarrhea and anastomotic leak after colorectal cancer surgery: the experience of a tertiary referral hospital in China.

Background: The 2019 novel coronavirus (COVID-19) global pandemic has greatly changed the mode of hospital admissions. This study summarized and analyzed the incidence of severe diarrhea and anastomotic leakage during different periods for colorectal cancer surgery. Methods: From January 2017 to September 2020, 2,619 colorectal operations were performed in Peking Union Medical College Hospital. In contrast with previous years, enhanced hand hygiene training, more frequent ventilation of the wards, and separate bed treatments for patients were implemented in 2020. Data on incidence of severe diarrhea and anastomotic leakage were retrieved and collected. Results: The number of cases of severe diarrhea after colorectal surgery was 32 (4.60%), 24 (3.33%), 32 (3.83%), and 11 (2.99%) in 2017, 2018, 2019, and 2020 respectively, while the incidence of anastomotic leakage was 3.30% (23/696), 3.75% (27/720), 2.87% (24/835), and 2.17% (8/368), respectively. There was no significant difference in the incidence of postoperative severe diarrhea or anastomotic leakage across the various years. Conclusions: The number of colorectal surgeries in 2020 was significantly decreased due to the COVID-19 pandemic. Among the different years, no difference was observed regarding the incidence of postoperative flora disorder or anastomosis leakage. Enhanced hygiene measures during the COVID-19 epidemic partially contributed to the decrease of severe diarrhea and anastomotic leakage.

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Integrated decoding hematopoiesis and leukemogenesis using single-cell sequencing and its medical implication.

Single-cell RNA sequencing provides exciting opportunities to unbiasedly study hematopoiesis. However, our understanding of leukemogenesis was limited due to the high individual differences. Integrated analyses of hematopoiesis and leukemogenesis potentially provides new insights. Here we analyzed ~200,000 single-cell transcriptomes of bone marrow mononuclear cells (BMMCs) and its subsets from 23 clinical samples. We constructed a comprehensive cell atlas as hematopoietic reference. We developed counterpart composite index (CCI; available at GitHub: https://github.com/pengfeeei/cci) to search for the healthy counterpart of each leukemia cell subpopulation, by integrating multiple statistics to map leukemia cells onto reference hematopoietic cells. Interestingly, we found leukemia cell subpopulations from each patient had different healthy counterparts. Analysis showed the trajectories of leukemia cell subpopulations were similar to that of their healthy counterparts, indicating that developmental termination of leukemia initiating cells at different phases leads to different leukemia cell subpopulations thus explained the origin of leukemia heterogeneity. CCI further predicts leukemia subtypes, cellular heterogeneity, and cellular stemness of each leukemia patient. Analyses of leukemia patient at diagnosis, refractory, remission and relapse vividly presented dynamics of cell population during leukemia treatment. CCI analyses showed the healthy counterparts of relapsed leukemia cells were closer to the root of hematopoietic tree than that of other leukemia cells, although single-cell transcriptomic genetic variants and haplotype tracing analyses showed the relapsed leukemia cell were derived from an early minor leukemia cell population. In summary, this study developed a unified framework for understanding leukemogenesis with hematopoiesis reference, which provided novel biological and medical implication.

Cross-Tissue Characterization of Heterogeneities of Mesenchymal Stem Cells and Their Differentiation Potentials.

Mesenchymal stem/stromal cells (MSCs) are promising cell sources for regenerative medicine and the treatment of autoimmune disorders. Comparing MSCs from different tissues at the single-cell level is fundamental for optimizing clinical applications. Here we analyzed single-cell RNA-seq data of MSCs from four tissues, namely umbilical cord, bone marrow, synovial tissue, and adipose tissue. We identified three major cell subpopulations, namely osteo-MSCs, chondro-MSCs, and adipo/myo-MSCs, across all MSC samples. MSCs from the umbilical cord exhibited the highest immunosuppression, potentially indicating it is the best immune modulator for autoimmune diseases. MSC subpopulations, with different subtypes and tissue sources, showed pronounced differences in differentiation potentials. After we compared the cell subpopulations and cell status pre-and-post chondrogenesis induction, osteogenesis induction, and adipogenesis induction, respectively, we found MSC subpopulations expanded and differentiated when their subtypes consist with induction directions, while the other subpopulations shrank. We identified the genes and transcription factors underlying each induction at the single-cell level and subpopulation level, providing better targets for improving induction efficiency.

Pretreatment PET/CT imaging of angiogenesis based on 18F-RGD tracer uptake may predict antiangiogenic response.

PURPOSE: To explore the relationship between metabolic uptake of the 18F-ALF-NOTA-PRGD2 (18F-RGD) tracer on positron emission tomography/computerized tomography (PET/CT) and the antiangiogenic effect of apatinib in patients with solid malignancies. MATERIALS AND PATIENTS: Patients with measurable lesions scheduled for second- or third-line single-agent therapy with apatinib were eligible for this prospective clinical trial. All patients underwent 18F-RGD PET/CT examination before the start of treatment. Standardized uptake values (SUVs) of contoured tumor lesions were computed and compared using independent sample t-tests or the Mann-Whitney U test. Receiver-operating characteristic (ROC) curve analysis was used to determine accuracy in predicting response. Survival curves were compared using the Kaplan-Meier method. RESULTS: Of 38 patients who consented to study participation, 25 patients with 42 measurable lesions met the criteria for inclusion in this response assessment analysis. The median follow-up time was 3 months (range, 1-10 months), and the median progression-free survival (PFS) was 3 months (95% confidence interval, 1.04-4.96). The SUVpeak and SUVmean were significantly higher in responding tumors than in non-responding tumors (4.98 ± 2.34 vs 3.59 ± 1.44, p = 0.048; 3.71 ± 1.15 vs 2.95 ± 0.49, P = 0.036). SUVmax did not differ between responding tumors and non-responding tumors (6.58 ± 3.33 vs 4.74 ± 1.83, P = 0.078). An exploratory ROC curve analysis indicated that SUVmean [area under the ROC curve (AUC) = 0.700] was a better parameter than SUVpeak (AUC = 0.689) for predicting response. Using a threshold value of 3.82, high SUVmean at baseline was associated with improved PFS (5.0 vs. 3.4 months, log-rank P = 0.036). CONCLUSION: 18F-RGD uptake on PET/CT imaging pretreatment may predict the response to antiangiogenic therapy, with higher 18F-RGD uptake in tumors predicting a better response to apatinib therapy.

Mastl overexpression is associated with epithelial to mesenchymal transition and predicts a poor clinical outcome in gastric cancer.

Microtubule-associated serine/threonine kinase like (Mastl) is deregulated in a number of types of human malignancy and may be a kinase target for cancer treatment. The aim of the present study was to determine the Mastl expression in gastric cancer and to clarify its clinical and prognostic significance. Immunohistochemistry was performed on a cohort of 126 postoperative gastric cancer samples to detect the expression of Mastl and two epithelial to mesenchymal transition (EMT) markers, epithelial-cadherin and Vimentin. The χ2 test, Kaplan-Meier estimator analysis and Cox's regression model were used to analyze the data. Upregulated Mastl protein expression was observed in the gastric cancer tissues compared with that in the adjacent non-cancerous gastric tissues. Increased Mastl expression was identified in 54/126 (42.9%) gastric cancer samples, and was significantly associated with lymph node metastasis, tumor relapse, EMT status and poor overall survival. Additional analysis demonstrated that the Mastl expression level stratified the patient outcome in stage III, but not stage II tumor subgroups. Cox's regression analysis revealed that increased Mastl expression was an independent prognostic factor for patients with gastric cancer. Mastl expression may be a valuable prognostic marker and a potential target for patients with gastric cancer.

Stereotactic Comparison Study of (18)F-Alfatide and (18)F-FDG PET Imaging in an LLC Tumor-Bearing C57BL/6 Mouse Model.

This study aimed to stereotactically compare the PET imaging performance of (18)F-Alfatide ((18)F-ALF-NOTA-PRGD2, denoted as (18)F-Alfatide) and (18)F-fluorodeoxyglucose (FDG) and immunohistochemistry (IHC) staining in Lewis lung carcinoma (LLC) tumor-bearing C57BL/6 mouse model. (18)F-FDG standard uptake values (SUVs) were higher than (18)F-Alfatide SUVs in tumors, most of the normal tissues and organs except for the bladder. Tumor-to-brain, tumor-to-lung, and tumor-to-heart ratios of (18)F-Alfatide PET were significantly higher than those of (18)F-FDG PET (P < 0.001). The spatial heterogeneity of the tumors was detected, and the tracer accumulation enhanced from the outer layer to the inner layer consistently using the two tracers. The parameters of the tumors were significantly correlated with each other between (18)F-FDG SUV and GLUT-1 (R = 0.895, P < 0.001), (18)F-Alfatide SUV and αvß3 (R = 0.595, P = 0.019), (18)F-FDG SUV and (18)F-Alfatide SUV (R = 0.917, P < 0.001), and GLUT-1 and αvß3 (R = 0.637, P = 0.011). Therefore, (18)F-Alfatide PET may be an effective tracer for tumor detection, spatial heterogeneity imaging and an alternative supplement to (18)F-FDG PET, particularly for patients with enhanced characteristics in the brain, chest tumors or diabetes, meriting further study.

[Expression of osteopontin splice variant and its clinical significance in gastric cancer].

OBJECTIVE: To investigate the expression of osteopontin (OPN) splice variant mRNA, including the three isoforms OPN-A, OPN-B, and OPN-C, to explore its correlation with clinicopathologic features in gastric cancer, and to elucidate their role in tumor invasion and distant metastasis of gastric cancer. METHODS: The expression of OPN-A, OPN-B and OPN-C mRNA were detected by real-time reverse transcriptase-polymerase chain reaction in 66 gastric cancer tissues. The relationship between the expression of OPN-A, OPN-B and OPN-C mRNA and clinicopathologic features of gastric cancer was analyzed. RESULTS: The expression of OPN-C mRNA in the gastric cancer tissue was 3.21-fold higher than that in peritumoral mucosal tissue, showing a significant difference between them (P < 0.001). OPN-C mRNA expression was correlated with the depth of tumor invasion, tumor diameter, lymph node meatastasis, distant meatastasis and had no correlation with differentiation grades. The low expression of OPN-C mRNA was correlated with long survival benefit (P = 0.03). The expression of OPN-A and OPN-B mRNA had no significant relationship with clinicopathologic features of gastric cancer. CONCLUSIONS: One of the isoform of osteopontin (OPN) OPN-C mRNA is overexpressed in gastric cancer. The overexpression of OPN-C mRNA may reflect the progression and is associated with the prognosis of gastric cancer. OPN-C mRNA may have value as a prognostic biomarker in gastric cancer. However, the expression of OPN-A and OPN-B are not correlated with the progression and metastasis of gastric cancer.

Gastric metastasis from small cell lung cancer: a case report.

Small cell lung cancer (SCLC) represents a group of highly malignant tumors that give rise to early and widespread metastases at the time of diagnosis. The preferential metastatic sites are the brain, liver, adrenal glands, bone, and bone marrow. However, metastases of the gastrointestinal system, especially the stomach, are rare; most cases of stomach metastasis are asymptomatic and, as a result, are usually only discovered at autopsy. We report a case of gastric metastasis originating from SCLC. The patient was a 66-year-old man admitted to our hospital due to abdominal pain. He underwent gastroscopy, with the pathological report of the tissue biopsy proving it to be a small cell cancer. Immunohistochemistry was positive for CD56, synaptophysin, and pan-cytokeratin. These results confirmed the diagnosis of gastric metastasis of a neuroendocrine small cell carcinoma from the lung.

Modelling epidermis homoeostasis and psoriasis pathogenesis.

We present a computational model to study the spatio-temporal dynamics of epidermis homoeostasis under normal and pathological conditions. The model consists of a population kinetics model of the central transition pathway of keratinocyte proliferation, differentiation and loss and an agent-based model that propagates cell movements and generates the stratified epidermis. The model recapitulates observed homoeostatic cell density distribution, the epidermal turnover time and the multilayered tissue structure. We extend the model to study the onset, recurrence and phototherapy-induced remission of psoriasis. The model considers psoriasis as a parallel homoeostasis of normal and psoriatic keratinocytes originated from a shared stem cell (SC) niche environment and predicts two homoeostatic modes of psoriasis: a disease mode and a quiescent mode. Interconversion between the two modes can be controlled by interactions between psoriatic SCs and the immune system and by normal and psoriatic SCs competing for growth niches. The prediction of a quiescent state potentially explains the efficacy of multi-episode UVB irradiation therapy and recurrence of psoriasis plaques, which can further guide designs of therapeutics that specifically target the immune system and/or the keratinocytes.

[Expression of osteopontin mRNA and its clinical significance in gastric cancer].

OBJECTIVE: To investigate the expression of osteopontin mRNA and its correlation with clinicopathologic features of gastric cancer and elucidate its role in tumor invasion and distant metastasis. METHODS: The expression of OPN mRNA was detected by semi-quantitive RT-PCR. The relationship between the relative content of OPN mRNA and clinicopathologic features of gastric cancer was analyzed. RESULTS: In 66 cancer tissue samples, a 330 bp band was detected in 50 cases, the positive rate of OPN mRNA expression was 75.8% (50/66). The expression in all 20 cases of normal gastric mucosa was negative. The expression was associated with the depth of tumor invasion, diameter, lymph node metastasis and but had no correlation with differentiation grades. The 66 patients were followed up for 10 approximately 27 months (mean 16 months). The OPN mRNA expression positive group (50 cases) had recurrence in 15 patients and the negative group (16 cases) had only 1 case with recurrence (P = 0.05); 10 patients died in OPN mRNA expression positive group but no patient died in OPN staining negative group (P = 0.05). CONCLUSION: OPN mRNA is over-expressed in gastric cancer. It reflects the progression of disease and association with poor prognosis of gastric cancer. OPN may play an important role in the process of distant metastasis in gastric cancer.