Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer.

Gastric cancer (GC) is the third leading cause of cancer deaths and the fourth most prevalent malignancy worldwide. The high incidence and mortality rates of gastric cancer result from multiple factors such as ineffective screening, diagnosis, and limited treatment options. In our study, we sought to systematically identify predictive molecular networks and key regulators to elucidate complex interacting signaling pathways in GC. We performed an integrative network analysis of the transcriptomic data in The Cancer Genome Atlas (TCGA) gastric cancer cohort and then comprehensively characterized the predictive subnetworks and key regulators by the matched genetic and epigenetic data. We identified 221 gene subnetworks (modules) in GC. The most prognostic subnetworks captured multiple aspects of the tumor microenvironment in GC involving interactions among stromal, epithelial and immune cells. We revealed the genetic and epigenetic underpinnings of those subnetworks and their key transcriptional regulators. We computationally predicted and experimentally validated specific mechanisms of anticancer effects of GKN2 in gastric cancer proliferation and invasion in vitro. The network models and the key regulators of the tumor microenvironment in GC identified here pave a way for developing novel therapeutic strategies for GC.

GDP-D-mannose pyrophosphorylase from Pogonatherum paniceum enhances salinity and drought tolerance of transgenic tobacco.

Pogonatherum paniceum is a highly drought- and salt-tolerant plant species that is typically used for ecological restoration and the conservation of soil and water in many countries. Understanding the molecular mechanisms underlying plant abiotic stress responses, especially to salinity and drought stresses, in species such as P. paniceum could be important to broader crop improvement efforts. GDP-D-mannose pyrophosphorylase (GMPase) is the limiting enzyme in the synthesis of L-ascorbic acid (AsA), which plays a crucial role in the detoxification of reactive oxygen species (ROS). We have cloned and characterized the cDNA of the PpGMP gene of P. paniceum encoding a GMPase. The full-length cDNA sequence contains 1411 nucleotides encoding a putative protein with 361 amino acid residues and an approximate molecular mass of 39.68 kDa. The GMPase transcript was up-regulated in P. paniceum plants subjected to salinity and drought stress, respectively. Transgenic tobacco expressing PpGMPase exhibited enhanced salinity and drought resistance, a higher seed germination rate, better growth performance, a higher AsA content, a more stable redox state, higher superoxide dismutase (SOD) activity, and lower levels of malonaldehyde (MDA) and H2O2 under drought and salinity stress. Taken together, expression of PpGMPase in tobacco conferred salinity and drought stress tolerance by increasing the content of AsA, thereby enhancing ROS-detoxifying functions. Thus, PpGMP is a potential candidate gene for crop improvement.

The Dose/Fractionation Debate in Limited-Stage Small Cell Lung Cancer.

To explore the most suitable dosage regimen for limited-stage small cell lung cancer (LS-SCLC) and provide references for clinical selection, strict inclusion criteria were applied, and studies were screened from Pubmed, Embase, and Web of Science. Subsequently, data on two-year overall survival rates and dosage regimens were collected, and scatter plots were constructed to provide a comprehensive perspective. The survival benefits of various dosage regimens were evaluated, and a linear quadratic equation was utilized to fit the relationship between the biologically effective dose (BED10) and the two-year overall survival rate. Among the five randomized controlled trials, the two-year overall survival rate of ConvTRT regimens with BED10 > 60 Gy (rough value) was only at or below the median of all ConvTRT regimens or all included study regimens, indicating that increasing the number and total dose of ConvTRT does not necessarily lead to better prognosis. In the exploration of HypoTRT regimens, there was a linear positive correlation between BED10 and the two-year overall survival rate (p < 0.0001), while the exploration of HyperTRT regimens was relatively limited, with the majority focused on the 45 Gy/30 F regimen. However, the current 45 Gy/30 F regimen is not sufficient to control LS-SCLC, resulting in a high local recurrence rate. High-dose ConvTRT regimens have long treatment durations and may induce tumor regrowth which may cause reduced efficacy. Under reasonable toxicity reactions, HyperTRT or HypoTRT with higher radiotherapy doses is recommended for treating LS-SCLC.

Shared-Specific Feature Learning With Bottleneck Fusion Transformer for Multi-Modal Whole Slide Image Analysis.

The fusion of multi-modal medical data is essential to assist medical experts to make treatment decisions for precision medicine. For example, combining the whole slide histopathological images (WSIs) and tabular clinical data can more accurately predict the lymph node metastasis (LNM) of papillary thyroid carcinoma before surgery to avoid unnecessary lymph node resection. However, the huge-sized WSI provides much more high-dimensional information than low-dimensional tabular clinical data, making the information alignment challenging in the multi-modal WSI analysis tasks. This paper presents a novel transformer-guided multi-modal multi-instance learning framework to predict lymph node metastasis from both WSIs and tabular clinical data. We first propose an effective multi-instance grouping scheme, named siamese attention-based feature grouping (SAG), to group high-dimensional WSIs into representative low-dimensional feature embeddings for fusion. We then design a novel bottleneck shared-specific feature transfer module (BSFT) to explore the shared and specific features between different modalities, where a few learnable bottleneck tokens are utilized for knowledge transfer between modalities. Moreover, a modal adaptation and orthogonal projection scheme were incorporated to further encourage BSFT to learn shared and specific features from multi-modal data. Finally, the shared and specific features are dynamically aggregated via an attention mechanism for slide-level prediction. Experimental results on our collected lymph node metastasis dataset demonstrate the efficiency of our proposed components and our framework achieves the best performance with AUC (area under the curve) of 97.34%, outperforming the state-of-the-art methods by over 1.27%.

Risk factors of local control in adrenal metastases treated by stereotactic body radiation therapy - a systematic review and meta-analysis.

Purpose: This study is aimed to explore risk factors affect the therapy outcomes of adrenal metastases (AM) for stereotactic body radiation therapy (SBRT) and guide clinical dose selection. Methods and materials: PubMed, Embase and Web of Science were searched in September 22, 2022 in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PRISMA). Subgroup analysis and meta-regression were used to search for sources of heterogeneity and identify risky outcomes factors. Publication bias test and sensitivity analysis were also conducted. Results: Thirty-three studies with full text from 2009 to 2022 about AM with SBRT on 1483 patients were included. Pooled 1- and 2-year local control (LC) and overall survival(OS) were 81.7% (95% confidence interval [CI], 75.6%-86.5%), 62.8% (95% CI, 53.8%-71.8%), 67.4% (95%CI, 61.8%-73.1%) and 46.5% (95%CI, 40.4%-52.6%), respectively. Biological effective dose (BED, α/ß=10Gy) and dose per fraction affected 1-year LC (Qm=23.89, 15.10; P<0.0001, 0.0001). In the range of 60-80Gy (BED10), the group of dose per fraction ≥ 9Gy achieved the excellent 1-year LC (< 9Gy: ≥ 9Gy =78%, 91%; χ2 = 10.16, P = 0.001). Tracking technology significantly affected 1- and 2-year OS (Qm = 5.73, 8.75; P = 0.017, 0.003) and high tracking adoption group showed excellent 1- and 2- year OS (78.7% [95%CI, 68.6%- 88.9%]; and 62.9% [95%CI, 53.1%-72.7%]). Conclusion: Increasing the dose per fraction appropriately may help control locally AM lesious. Tracking technology might contribute to improve survival of advanced patients with AM. But these results need prospective studies to verify them.

Lymph Node Metastasis Prediction From Whole Slide Images With Transformer-Guided Multiinstance Learning and Knowledge Transfer.

The gold standard for diagnosing lymph node metastasis of papillary thyroid carcinoma is to analyze the whole slide histopathological images (WSIs). Due to the large size of WSIs, recent computer-aided diagnosis approaches adopt the multi-instance learning (MIL) strategy and the key part is how to effectively aggregate the information of different instances (patches). In this paper, a novel transformer-guided framework is proposed to predict lymph node metastasis from WSIs, where we incorporate the transformer mechanism to improve the accuracy from three different aspects. First, we propose an effective transformer-based module for discriminative patch feature extraction, including a lightweight feature extractor with a pruned transformer (Tiny-ViT) and a clustering-based instance selection scheme. Next, we propose a new Transformer-MIL module to capture the relationship of different discriminative patches with sparse distribution on WSIs and better nonlinearly aggregate patch-level features into the slide-level prediction. Considering that the slide-level annotation is relatively limited to training a robust Transformer-MIL, we utilize the pathological relationship between the primary tumor and its lymph node metastasis and develop an effective attention-based mutual knowledge distillation (AMKD) paradigm. Experimental results on our collected WSI dataset demonstrate the efficiency of the proposed Transformer-MIL and attention-based knowledge distillation. Our method outperforms the state-of-the-art methods by over 2.72% in AUC (area under the curve).

Modulating the electrocatalytic activity of mononuclear nickel complexes toward water oxidation by tertiary amine group.

Water oxidation is the bottleneck of water splitting, which is a promising strategy for hydrogen production. Therefore, it is significant to develop efficient water oxidation catalysts. Herein, electrochemical water oxidation catalyzed by three nickel complexes, namely [Ni(bptn)(H2O)](ClO4)2 (1), [Ni(mbptn)(CH3CN)](ClO4)2 (2), and [Ni(tmbptn)(H2O)](ClO4)2 (3) (bptn = 1,9-bis(2-pyridyl)-2,5,8-triazanonane, mbptn = 5-methyl-1,9-bis(2-pyridyl)-2,5,8-triazanonane, and tmbptn = 1,9-bis(2-pyridyl)-2,5,8-triazanonane), is studied under near-neutral condition (pH 9.0). Meanwhile, the homogeneous catalytic behaviors of the three mononuclear nickel complexes were investigated and confirmed by scanning electron microscopy, energy dispersive spectrometry, X-ray photoelectron spectroscopy and electrochemical method. Complex 1 stabilized by a pentadentate ligand with three N-H fragments homogeneously catalyzes water oxidation to oxygen with the lowest onset overpotential. Complex 2 stabilized by a similar ligand with two N-H groups and one N-CH3 group exhibits relatively higher onset overpotential but higher catalytic current and turnover frequency. However, complex 3 with three N-CH3 coordination environment shows the highest onset overpotential and the highest catalytic current at higher potential. Comparison of catalytic behaviors and ligand structure of the three complexes reveals that the methyl group on the polypyridine amine ligand affects the water oxidation activity of the complexes obviously. The electronic effect of N-CH3 coordination environment leads to higher redox potential of the metal center and potential demand for water oxidation, while it leads to higher reaction activity of high-valent intermediates, which account for higher catalytic current and efficiency of water oxidation. This work reveals that electrocatalytic water oxidation performance of nickel complexes can be finely modulated by constructing suitable N-CH3 coordination.

Role of postoperative radiotherapy in dermatofibrosarcoma protuberans: a propensity score-matched analysis.

OBJECTIVE: This study aimed to evaluate the role of postoperative radiotherapy (RT) in dermatofibrosarcoma protuberans (DFSP) and identify the prognostic factors influencing the disease-free survival (DFS). METHODS: A total of 184 patients with DFSP were analyzed from 2000 to 2016. The regression model was used to examine the prognostic factors for DFS. Baseline covariates were balanced using a propensity score model. The role of RT was assessed by comparing the DFS of the surgery + RT group with that of the surgery group. RESULTS: The median follow-up was 58 months (range, 6-203 months). The 5-year DFS rate was 89.8%. The univariate analysis showed that age ≥ 50 years, presence of fibrosarcoma, margins < 2 cm, and tumor size ≥5 cm were associated with worse DFS (P = 0.002, P <  0.001, P = 0.030, and P = 0.032, respectively). The multivariate Cox regression model revealed that age, margin width, lesion number, and histological subtype independently affected DFS. The Ki-67 expression was related to age and histological subtype. Patients with Ki-67 ≥ 17% showed a worse DFS than those with Ki-67 < 17% (35.8% vs 87.8%, P = 0.002). In the matched cohort, DFS was significantly higher in the S + RT group than in the S group (5-year DFS, 88.1% vs 56.2%, P = 0.044). CONCLUSIONS: Age, margin width, lesion number, and histological subtype were independent risk factors for DFS in patients with DFSP. The high expression of Ki-67 could predict a poor prognosis. Postoperative RT could improve DFS for patients with DFSP.

Decreased expression of the NKG2D ligand ULBP4 may be an indicator of poor prognosis in patients with nasopharyngeal carcinoma.

U16-binding protein 4 (ULBP4), a human ligand for natural killer group 2, member D (NKG2D) receptor on NK cells and subsets of T cells, is thought to activate anticancer immune responses. However, the expression pattern and prognostic effect of ULBP4 in nasopharyngeal carcinoma (NPC) has not been investigated. We first compared ULBP4 expression between archival 15 NPC tissues and 8 normal nasopharynx (NP) tissues using qPCR. Then ULBP4 expression among 111 NPC specimens was validated on immunohistochemical examination. In addition, the association of ULBP4 expression with clinical characteristics and survival outcomes was analyzed. Furthermore, the impact of ULBP4 expression in NPC cells on the cytotoxic activity of NK cells was investigated. Both mRNA and protein ULBP4 expressions of NPC tissues were significantly lower than those in normal NP tissues. However, no association of ULBP4 expression with clinical characteristics was observed. Patients with NPC having decreased expression of UBLP4 had significantly poorer overall survival (OS), progression-free survival (PFS), and distant metastasis-free survival (DMFS) than those with preserved levels of ULBP4. On multivariate analyses, low expression of ULBP4 was of borderline significance for OS, PFS, and DMFS (P = 0.060, 0.053, and 0.076, respectively). Further, LDH analysis demonstrated that the cytotoxic activitity of NK cells against C666-1 or 5-8F NPC cells with lenti-ULBP4 was considerably increased as compared to those with lenti-vector at various E/T ratios. Hence, restoration of ULBP4 expression may be a novel therapeutic strategy for treatment of NPC. However, further study is required to confirm these findings.

The elevated preoperative fasting blood glucose predicts a poor prognosis in patients with esophageal squamous cell carcinoma: The Fujian prospective investigation of cancer (FIESTA) study.

Diabetes as a latent risk factor for cancer has been extensively investigated, while its postoperative prognosis for esophageal cancer is rarely reported. We therefore sought to assess whether the elevated fasting blood glucose before surgery was associated with poor survival in esophageal cancer patients by eliciting a subset of data from the ongoing Fujian prospective investigation of cancer (FIESTA) study. Over 15-year follow-up, 2535 patients receiving three-field lymphadenectomy were assessable. Only patients with esophageal squamous cell carcinoma (ESCC) (n=2396) were analyzed due to the lower prevalence of the other histological types. In ESCC patients, the follow-up duration ranged from 0.5 to 180 months (median 38.2 months). The median survival time (MST) was remarkably shorter in males than in females (80.7 vs. 180+ months, Log-rank test: P<0.001). In males, the survival was worse in patients with diabetes than those without (MST: 27.9 vs. 111.1 months, Log-rank test: P<0.001). In females, the survivor was improved in patients with diabetes (MST: 71.5 months), but was still worse than patients without diabetes (MST: 180+ months, Log-rank test: P<0.001). The overall multivariate hazard ratio for per unit increment in fasting blood glucose was 1.11 (95% confidence interval or CI: 1.09-1.14, P<0.001) and 1.08 (95% CI: 1.03-1.13, P=0.002) in males and females, respectively. Further survival tree analysis consolidated the discrimination ability of fasting blood glucose for the survival of ESCC patients. Taken together, our findings convincingly demonstrated that the elevated preoperative fasting blood glucose can predict poor survival of ESCC patients, especially in males.