Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity toward advanced stages.

Lung adenocarcinoma is a type of cancer that exhibits a wide range of clinical radiological manifestations, from ground-glass opacity (GGO) to pure solid nodules, which vary greatly in terms of their biological characteristics. Our current understanding of this heterogeneity is limited. To address this gap, we analyze 58 lung adenocarcinoma patients via machine learning, single-cell RNA sequencing (scRNA-seq), and whole-exome sequencing, and we identify six lung multicellular ecotypes (LMEs) correlating with distinct radiological patterns and cancer cell states. Notably, GGO-associated neoantigens in early-stage cancers are recognized by CD8+ T cells, indicating an immune-active environment, while solid nodules feature an immune-suppressive LME with exhausted CD8+ T cells, driven by specific stromal cells such as CTHCR1+ fibroblasts. This study also highlights EGFR(L858R) neoantigens in GGO samples, suggesting potential CD8+ T cell activation. Our findings offer valuable insights into lung adenocarcinoma heterogeneity, suggesting avenues for targeted therapies in early-stage disease.

Identification and validation of DHCR7 as a diagnostic biomarker involved in the proliferation and mitochondrial function of breast cancer.

BACKGROUND: Energy metabolism has a complex intersection with pathogenesis and development of breast cancer (BC). This allows for the possibility of identifying energy-metabolism-related genes (EMRGs) as novel prognostic biomarkers for BC. 7-dehydrocholesterol reductase (DHCR7) is a key enzyme of cholesterol biosynthesis involved in many cancers, and in this paper, we investigate the effects of DHCR7 on the proliferation and mitochondrial function of BC. METHODS: EMRGs were identified from the Gene Expression Omnibus (GEO) and MSigDB databases using bioinformatics methods. Key EMRGs of BC were then identified and validated by functional enrichment analysis, interaction analysis, weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) regression, Cox analysis, and immune infiltration. Western blot, qRT-PCR, immunohistochemistry (IHC), MTT assay, colony formation assay and flow cytometry assay were then used to analyze DHCR7 expression and its biological effects on BC cells. RESULTS: We identified 31 EMRGs in BC. These 31 EMRGs and related transcription factors (TFs), miRNAs, and drugs were enriched in glycerophospholipid metabolism, glycoprotein metabolic process, breast cancer, and cell cycle. Crucially, DHCR7 was a key EMRG in BC identified and validated by WGCNA, LASSO regression and receiver operating characteristic (ROC) curve analysis. High DHCR7 expression was significantly associated with tumor immune infiltration level, pathological M, and poor prognosis in BC. In addition, DHCR7 knockdown inhibited cell proliferation, induced apoptosis and affected mitochondrial function in BC cells. CONCLUSIONS: DHCR7 was found to be a key EMRG up-regulated in BC cells. This study is the first to our knowledge to report that DHCR7 acts as an oncogene in BC, which might become a novel therapeutic target for BC patients.

Genome-wide association study reveals the genes associated with the leaf inclusion contents in Chinese medical tree Eucommia ulmoides.

Eucommia ulmoides is an economic tree that can biosynthesize secondary metabolites with pharmacological functions. Genetic basis of biosynthesis of these compounds is almost unknown. Therefore, genomic-wide association study was performed to exploit the genetic loci maybe involved in biosynthetic pathways of 5 leaf inclusions (aucubin, chlorogenic acid, gutta-percha, polyphenols, total flavonoids). It was shown that contents of the 5 leaf metabolites have a wide variation following normal distribution. A total of 2 013 102 single nucleotide polymorphism (SNP) markers were identified in a population containing 62 individual clones. Through genome-wide association study analysis, many SNP loci were identified perhaps associated with phenotypes of the leaf inclusions. Higher transcriptional levels of the candidate genes denoted by significant SNPs in leaves suggested they may be involved in biosynthesis of the leaf inclusions. These genetic loci provide with invaluable information for further studies on the gene functions in biosynthesis of the leaf inclusions and selective breeding of the plus trees.

Nei Endonuclease VIII-Like1 (NEIL1) Inhibits Apoptosis of Human Colorectal Cancer Cells.

The study is aimed at investigating the role of Nei endonuclease VIII-like1 (NEIL1) in the pathogenesis of colorectal cancer (CRC). The human CRC (HCT116 and SW480) cells were subjected to the siRNA silencing and recombinant plasmid overexpression of NEIL1. Transfection of siNEIL1 significantly inhibited the cell growth. It also increased the Bax expression levels, while it decreased the Bcl-2 expression levels in human CRC cells, leading the Bax/Bcl-2 balance toward apoptosis. Moreover, the apoptosis was promoted through the caspase-9 signaling pathway. One the other hand, high expression of NEIL1 promoted the cell viability and reduced the apoptosis, inducing the balance of Bax/Bcl-2 in the human colon cancer cells to be antiapoptotic. In addition, the caspase-9 signaling pathway inhibited apoptosis, contrary to the results obtained by downregulating NEIL1 expression. Furthermore, NEIL1 was negatively regulated by miR-7-5p, indicating that miR-7-5p inhibited the NEIL1 expression after transcription. Overexpression of miR-7-5p reversed the effects of NEIL1 on these CRC cells. In conclusion, NEIL1 promotes the proliferation of CRC cells, which is regulated negatively by miR-7-5p. These findings suggest that NEIL1 is a potential therapeutic target for CRC.

A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression.

Single-molecule real-time (SMRT) sequencing can be used to identify a wide variety of chemical modifications of the genome, such as methylation. Here, we applied this approach to identify N6-methyl-adenine (m6A) and N4-methyl-cytosine (m4C) modification in the genome of Bacillus pumilus BA06. A typical methylation recognition motif of the type I restriction-modification system (R-M), 5'-TCm6AN8TTGG-3'/3'-AGTN8m6AACC-5', was identified. We confirmed that this motif was a new type I methylation site using REBASE analysis and that it was recognized by a type I R-M system, Bpu6ORFCP, according to methylation sensitivity assays in vivo and vitro. Furthermore, we found that deletion of the R-M system Bpu6ORFCP induced transcriptional changes in many genes and led to increased gene expression in pathways related to ABC transporters, sulfur metabolism, ribosomes, cysteine and methionine metabolism and starch and sucrose metabolism, suggesting that the R-M system in B. pumilus BA06 has other significant biological functions beyond protecting the B. pumilus BA06 genome from foreign DNA.

Evaluation of the diagnostic value of circulating tumor cells with CytoSorter® CTC capture system in patients with breast cancer.

PURPOSE: In this study, we aimed to investigate the viability of utilizing CytoSorter® system to detect circulating tumor cells (CTCs) and to evaluate the diagnostic value of CTCs in breast cancer (BC). METHODS: A total of 366 females patients suspected of having BC and 30 healthy female volunteers were enrolled in this study. CTCs were enriched by CytoSorter® , a microfluidic-based CTCs capturing platform. CTC detection was performed before operation or biopsy. Based on the biopsy results, patients were divided into two groups, namely patients with BC and patients with benign breast diseases (BBD). Patients with BBD and healthy volunteers were serving as controls. The correlation between CTC enumeration and patients' clinicopathological characteristics was evaluated. The receiver operating characteristic (ROC) curve was plotted to assess the diagnostic potency of CytoSorter® system in BC. RESULTS: Based on the biopsy results, 130 BC patients at different cancer stages and 236 patients with BBD were enrolled in the study. Seven subjects were dropped out from the study. CTCs were detected in 109 of 128 BC patients, in one of 29 healthy volunteers, and in 37 of 232 patients with BBD. Maximum CTC counts detected in BC patients, healthy volunteers, and patients with BBD were 8, 1, and 4, respectively. Statistical analysis showed CTCs could be used to distinguish BC patients from healthy volunteers and patients with BBD (P < .0001). Circulating tumor cells were statistically associated with patients' cancer stage (P = .0126), tumor size (tumor node metastasis [TNM] T stage, P = .0253), cancer type (invasive vs noninvasive, P = .0141), and lymph node metastasis (P = .0436). More CTCs were found in patients at advanced cancer stage or TNM T stage and in patients with invasive tumor or lymph node metastasis. Furthermore, CTC detection rates in BC patients at Tis and T1-4 stages were 50%, 81.67%, 91.07%, 100%, and 100%, respectively. When the CTC cut-off value was set to 2, the ROC curve gave an area under the curve (AUC) of 0.86 with a specificity and sensitivity of 95.4% and 76.56%, respectively. Taken together, CTCs could be used as a diagnostic aid in assistance of cancer screening and staging. CONCLUSION: Circulating tumor cells were successfully isolated in BC patients using CytoSorter® system. CTCs can be used to differentiate BC patients from the patients with BBD or healthy volunteers, and as a diagnostic aid for early cancer diagnosis and cancer staging.

Hepatocellular carcinoma with en bloc diaphragmatic resection: A single-center experience over 14 years.

BACKGROUND: Diaphragmatic resection is not common in patients undergoing hepatectomy for hepatocellular carcinoma (HCC). This study aims to evaluate retrospectively the clinical characteristics and surgical results of HCC patients undergoing hepatectomy plus diaphragmatic resection. METHODS: Between January 2000 and December 2013, 52 HCC patients underwent curative resections combined with diaphragmatic resection, with 11 patients had pathological diaphragmatic invasion (DI), 41 patients had diaphragmatic fibrous adhesion (DFA). The clinicopathological features and results were compared between the two groups. RESULTS: 86.5% of the patients had HBV infection. Diameter of tumors was 8.6 ±â€¯3.4 cm, and 34.6% had multiple tumors. In addition, 28.8% had microvascular invasion, 3.8% had macrovascular invasion, but none of the patients had lymph node metastasis or distant metastasis. Moreover, 21.2% had tumor rupture before surgical resection. The DI group exhibited similar clinicopathological features with the DFA group. There were no treatment-related deaths, and major complication was postoperative pleural effusion (46.2%). Other clinical pulmonary issues, such as pneumothorax (5.8%) and pneumonia (3.8%), were also detected. OS at 1, 3 and 5 years was 82.0%, 41.2% and 35.7%, respectively. There was no significant difference in OS and DFS between the DI and DFA groups (P = 0.499 and P = 0.956, respectively). CONCLUSIONS: En bloc resection of diaphragm was associated with acceptable morbidity and mortality, and there was no difference in OS and DFS between HCC patients with DI or DFA. Therefore, it would be advisable to perform en bloc diaphragmatic resection when HCC patients present with gross diaphragmatic involvement.

Hepatocellular Carcinoma in Children and Adolescents: Clinical Characteristics and Treatment.

BACKGROUND: Hepatocellular carcinoma (HCC) occurs rarely in children and adolescents (C&A), and its clinical characteristics, prognostic factors, and treatment were rarely explored. METHODS: This retrospective study focused on 65 HCC patients aged ≤20 years from August 1994 to August 2012. Cox regression models and Kaplan-Meier curves were used to investigate prognostic factors and compare overall survival (OS), respectively. RESULTS: We found 61.5% of patients to have multiple tumors, 30.8% to have portal vein tumor thrombus, and 16.9% to have distant metastasis. Diameter of tumors was 10.2 ± 4.1 cm. OS at 5 years was 15.8%. Multivariate analyses showed initial treatment (P < 0.001) to be a predictor for OS. For moderate-stage HCC, the median OS of patients who underwent resection was longer than that of patients who underwent transarterial chemoembolization (TACE) or supportive treatment (ST) (P < 0.001). For advanced-stage HCC, the median OS of patients who underwent TACE was longer than that of patients who underwent ST (P = 0.045). CONCLUSIONS: HCC in C&A tends to be more advanced than that in adults, and resection remains the mainstay of treatment for those patients. Moreover, compared with ST, TACE may benefit C&A with moderate- and advanced-stage HCC, which needs further study.

Elevated neutrophil-to-lymphocyte ratio is an independent poor prognostic factor in patients with intrahepatic cholangiocarcinoma.

We investigated whether elevated neutrophil-to-lymphocyte ratio ( NLR ) was associated with poor anti-tumor immunity and prognosis in patients with intrahepatic cholangiocarcinoma ( ICC ). Clinicopathologic data of 102 patients with ICC who underwent hepatectomy was retrospectively analyzed. The Kaplan-Meier method and Cox regression model were used to analyze the survival and prognosis. The percentage of overall lymphocytes , T cells and CD8+ T cells in the high NLR group was lower than that in the low NLR group. The percentage of PD-1+CD4+ and PD-1+CD8+ T cells was higher and the percentage of IFN-γ+CD4+ and IFN-γ+CD8+ T cells was lower in the high NLR group than that in the low NLR group ( p = 0.045, p = 0.008; p = 0.012, p = 0.006 ). Density of tumor-infiltrating CD3+ T cells in the high NLR group was lower than that in the low NLR group ( p < 0.001 ). Elevated NLR was an independent predictor for poor overall survival ( OS; p = 0.035 ) and recurrence-free survival ( RFS; p = 0.008 ). These results indicate that elevated NLR is associated with poor anti-tumor immunity and could be a poor biomarker for prognosis in patients with ICC.

Transforming growth factor-ß1-induced epithelial-mesenchymal transition generates ALDH-positive cells with stem cell properties in cholangiocarcinoma.

Epithelial-mesenchymal transition (EMT) is a major factor that facilitates the invasiveness and metastasis of cancer. Recent studies have demonstrated that EMT plays a key role in generating cancer stem cells (CSCs). This study aimed to investigate the effect of EMT on CSCs that were identified as positive for aldehyde dehydrogenase (ALDH) in cholangiocarcinoma (CCA). We demonstrated that transforming growth factor-ß1 (TGF-ß1)-induced EMT in the human cholangiocarcinoma (CCA) cell line, TFK-1, resulted in the acquisition of mesenchymal traits, as well as the expression of ALDH, which was accompanied by decreased sensitivity to the chemotherapeutic agent, 5-fluorouracil. ALDH-positive cells isolated from TFK-1 cells had higher proliferation potential in vitro and tumourigenic ability in vivo. They also expressed mesenchymal markers. Moreover, the expression levels of TGF-ß1 and ALDH1 were correlated with poor prognosis in patients. We conclude that ALDH acts as a marker for CSCs in CCA, and TGF-ß1-induced EMT is involved in the generation of CSCs. These findings offer a new tool for the study of CCA stem cells and illustrate a direct link between EMT and the gain of stem-cell properties.

Identification of weak transitions using moving-window two-dimensional correlation analysis: treatment with scaling techniques.

In the present study, the theory of the data treatment with scaling techniques for moving-window two-dimensional (scaling-MW2D) correlation analysis was first proposed. This new analytical method of spectroscopy can significantly enhance the resolving capacity of the moving-window two-dimensional (MW2D) correlation infrared spectroscopy in the direction of the perturbation variable. So, it strengthened the ability of MW2D to highlight the weak transitions. The in situ infrared spectra of four common polymers, including polyamide 66 (PA66), polystyrene-block-polybutadiene-block-polystyrene block copolymer (SBS), isotactic polypropylene (iPP), and polyoxymethylene (POM), were employed to illustrate the advantages of scaling-MW2D. In the applications of the present study, the conventional autocorrelation MW2D can only distinguish the melting point of PA66, the maximum crystallization temperature of POM, and the primary oxidation of SBS. However, the autocorrelation scaling-MW2D not only can more easily determine the above transitions, but also can identify PA66 brill transition, the dissociation of adsorbed water in PA66, POM secondary crystallization, the glass transition of hard blocks in SBS, and the generation of the aldehyde and hydroxyl groups during SBS oxidation. Our further study found that the selection of the scaling factor α was very important. The golden point α = 0.618 was the best value, and satisfactory application results can be achieved. The slice scaling-MW2D was also investigated. The scaling-MW2D method of spectroscopy can be used elsewhere. The application of this analytical method should not be limited to the infrared spectra, and it also should not be limited to transitions in polymers. This method can be easily extended and applied to other materials and spectra.

Efficient, stable, small, and water-soluble doped ZnSe nanocrystal emitters as non-cadmium biomedical labels.

Mn2+-doped ZnSe quantum dots (Mn:ZnSe d-dots) with a tunable photoluminescence (PL) peak position were made to be water soluble by coating them with a monolayer of mercaptopropionic acid, a very short hydrophilic thiol. If the dopant centers were located close to the surface, thiol-coating partially quenched the PL. With about 2-3 monolayers of pure ZnSe on the surface, the PL of d-dots was actually enhanced upon thiol coating. When the doping centers were placed reasonably inside a d-dot, with about four monolayers of pure ZnSe between the doping centers and the surface ligands, the thiol ligands did not quench the PL of the d-dots, even though they did completely quench the PL of intrinsic ZnSe quantum dots. The overall size of such d-dots/ligand complex is only about 7-8 nm, implying an excellent permeability in biological issues. These d-dots were found to be exceptionally stable against continuous UV radiation in air for at least 25 days. They were also stable in boiling water with air bubbling under room light for hours. Recognition of a biotin pattern by d-dots conjugated with avidine was carried to illustrate the suitability of these efficient (about 40% PL quantum yield), stable, small, and water-soluble d-dots as biomedical labeling reagents.