Combining bulk and scRNA-seq to explore the molecular mechanisms governing the distinct efferocytosis activities of a macrophage subpopulation in PDAC.

Pancreatic ductal adenocarcinoma (PDAC), a very aggressive tumour, is currently the third leading cause of cancer-related deaths. Unfortunately, many patients face the issue of inoperability at the diagnostic phase leading to a quite dismal prognosis. The onset of metastatic processes has a crucial role in the elevated mortality rates linked to PDAC. Individuals with metastatic advances receive only palliative therapy and have a grim prognosis. It is essential to carefully analyse the intricacies of the metastatic process to enhance the prognosis for individuals with PDAC. Malignancy development is greatly impacted by the process of macrophage efferocytosis. Our current knowledge about the complete range of macrophage efferocytosis activities in PDAC and their intricate interactions with tumour cells is still restricted. This work aims to resolve communication gaps and pinpoint the essential transcription factor that is vital in the immunological response of macrophage populations. We analysed eight PDAC tissue samples sourced from the gene expression omnibus. We utilized several software packages such as Seurat, DoubletFinder, Harmony, Pi, GSVA, CellChat and Monocle from R software together with pySCENIC from Python, to analyse the single-cell RNA sequencing (scRNA-seq) data collected from the PDAC samples. This study involved the analysis of a comprehensive sample of 22,124 cells, which were classified into distinct cell types. These cell types encompassed endothelial and epithelial cells, PDAC cells, as well as various immune cells, including CD4+ T cells, CD8+ T cells, NK cells, B cells, plasma cells, mast cells, monocytes, DC cells and different subtypes of macrophages, namely C0 macrophage TGM2+, C1 macrophage PFN1+, C2 macrophage GAS6+ and C3 macrophage APOC3+. The differentiation between tumour cells and epithelial cells was achieved by the implementation of CopyKat analysis, resulting in the detection and categorization of 1941 PDAC cells. The amplification/deletion patterns observed in PDAC cells on many chromosomes differ significantly from those observed in epithelial cells. The study of Pseudotime Trajectories demonstrated that the C0 macrophage subtype expressing TGM2+ had the lowest level of differentiation. Additionally, the examination of gene set scores related to efferocytosis suggested that this subtype displayed higher activity during the efferocytosis process compared to other subtypes. The most active transcription factors for each macrophage subtype were identified as BACH1, NFE2, TEAD4 and ARID3A. In conclusion, the examination of human PDAC tissue samples using immunofluorescence analysis demonstrated the co-localization of CD68 and CD11b within regions exhibiting the presence of keratin (KRT) and alpha-smooth muscle actin (α-SMA). This observation implies a spatial association between macrophages, fibroblasts, and epithelial cells. There is variation in the expression of efferocytosis-associated genes between C0 macrophage TGM2+ and other macrophage cell types. This observation implies that the diversity of macrophage cells might potentially influence the metastatic advancement of PDAC. Moreover, the central transcription factor of different macrophage subtypes offers a promising opportunity for targeted immunotherapy in the treatment of PDAC.

SIVA-1 enhances acquired chemotherapeutic drug resistance of gastric cancer in vivo by regulating the ARF/MDM2/p53 pathway.

SIVA-1 has been shown to affect apoptotic processes in various different cell lines, and SIVA-1 significantly contributes to the decreased responsiveness of cancer cells to some chemotherapy agents. However, whether SIVA-1 has potential application in gastric cancer remains unknown. Therefore, the objective of this investigation was to clarify the distinct function of SIVA-1 in chemotherapeutic drug resistance within a living murine model with gastric malignancy, and initially elucidate the underlying mechanisms. In an established multidrug-resistant gastric cancer xenograft mouse model, lentivirus, named Lv-SIVA-1, was injected into xenograft tumors, and increased the mRNA and protein expression of endogenous SIVA-1 in tumors. Immunohistochemical assays of xenograft tumor showed that SIVA-1 was significantly upregulated, and the protein expression levels of SIVA-1 were highly increased, as detected by Western blotting. In addition, we detected the role of SIVA-1 in cell proliferation and cell apoptosis in gastric cancer cells by TUNEL and found that SIVA-1 decreased tumor cell apoptosis and promoted tumor growth in vivo. Using a TMT assay between tumor tissues of experimental and control groups, differentially expressed proteins were examined and three potential biomarkers of multidrug resistance (ARF, MDM2, and p53) were screened. We further investigated the molecular mechanism by which SIVA-1 played an efficient role against chemotherapies and found that overexpressed SIVA-1 leads to increased ARF and MDM2 expression and suppressed expression of p53 in tumor tissue. In conclusion, SIVA-1 plays a significant role in the multidrug resistance of gastric tumors. In addition, overexpressed SIVA-1 positively regulates cell proliferation, adjusts cycle progression, and reduces the response to drug treatment for gastric cancer in an ARF/MDM2/p53-dependent manner. This novel research provides a basis for chemical management of gastric cancer through regulation of SIVA-1 expression.

Epidemiological and survival outcomes of neuroendocrine carcinoma of the breast: a SEER data analysis.

Background: Neuroendocrine carcinoma of the breast (NECB) is a rare subtype of breast cancer, comprising only 0.1% to 5% of all breast cancer cases. Despite its rarity, it is important to gain a better understanding of the epidemiological, clinical, and prognostic features of NECB. The purpose of the study was to obtain population-based evaluations of the epidemiological and survival outcomes of NECB. Methods: The data of patients with neuroendocrine carcinoma diagnosed and enrolled between 2000 and 2017 were obtained from the Surveillance, Epidemiology, and End Results (SEER) database. Descriptive statistical analyses were used to assess the distribution and tumor-related characteristics of these patients. Kaplan-Meier curves and univariate and multivariate Cox proportional risk models were used to analyze variables that might be associated with prognosis. Results: This study included 7,856 patients with neuroendocrine carcinoma. The median age of the patients was 64 years, and most of them were female, White, and diagnosed at ≥60 years old. The most common pathological type was neoplasm. Survival analysis indicated that there were significant differences in age, marital status, registration location, American Joint Committee on Cancer (AJCC) stage, breast subtype, surgery of primary tumor, and no cancer cause surgery patients with NECB. The results also indicated that treatment with surgery, including surgery of primary tumor, surgery combined with radiation, and no cancer cause surgery, were all effective in improving the prognosis compared with not providing surgical treatment. Conclusions: In conclusion, NECB is a very rare lesion for which age, marital status, registration location, and surgery, AJCC stage, breast subtype were found to be independent prognostic factors.

The identification, adaptive evolutionary analyses and mRNA expression levels of homeobox (hox) genes in the Chinese mitten crab Eriocheir sinensis.

BACKGROUND: Arthropods are the largest group in the animal kingdom and are morphologically characterized by heterorhythmic segments. Brachyuran decapod crustaceans undergo brachyurization metamorphosis in the early developmental process, characterized by a reduced abdomen that is folded beneath the cephalothorax and inserted between the pereiopods or in a special cavity. As the main cause of major alterations in the evolution of animal body plans, Hox genes encode transcription factors and are involved in bilaterian anterior-posterior axis patterning. RESULTS: We found eight Hox genes (labial, proboscipedia, Deformed, zerknüllt, Sex combs reduced, Antennapedia, Ultrabithorax, fushi tarazu, abdominal-A and Abdominal-B) in Eriocheir sinensis. The phylogenetic topology of 13 arthropod Hox genes was closely related to traditional taxonomic groupings. Genome collinearity analysis was performed using genomic data and chromosomal location data of E. sinensis and Portunus trituratus. We found that their chromosomes were highly collinear, and there was a corresponding collinear relationship between the three Hox genes (lab, ftz and Abd-B). The mRNA expression levels of Scr and Antp fluctuated significantly in different developmental stages of E. sinensis, especially in the brachyurization stages. Evolutionary analysis indicated the presence of positively selected sites in Ubx. CONCLUSIONS: In this study, we used genome-wide analysis to identify and analyze all members of the Hox genes in E. sinensis. Our data will contribute to a better understanding of Hox genes in E. sinensis and provide useful molecular evolutionary information for further investigation on their roles in the brachyurization of crabs.

Expression analysis of alpha keratins and corneous beta-protein genes during embryonic development of Gekko japonicus.

Epidermal appendages of birds and reptiles, including claws, feathers, scales, and setae, are primarily composed of alpha keratins (KRTs) and corneous beta-proteins (CBPs). A comprehensive and systematic knowledge of KRTs and CBPs in Schlegel's Japanese gecko (Gekko japonicus) is still lacking. In this study, 22 candidate Gecko japonicus keratin (GjKRT) family genes (12 type I genes, 10 type II genes) were identified in the G. japonicus genome. The majority of GjKRT genes across various subgroups had undergone a prolonged and highly conservative evolutionary process. Through a combination of morphological observation, RNA-seq analysis, and qRT-PCR assay, it was possible to discern the dynamic alterations in the expression of GjKRTs and Gecko japonicus corneous beta-proteins genes (GjCBPs). These findings strongly indicate that GjKRTs gradually accumulate to constitute an α-layer, which is subsequently succeeded by the formation of the corneous beta layer containing GjCBPs at late stages (40-42) of embryonic development. The epidermal appendages in G. japonicus may result from the joint accumulation of KRTs and CBPs, with stages 40-42 being critical for their development. These findings provide novel insights into KRTs and CBPs of G. japonicus and offer a foundation for investigating the functions of GjKRT and GjCBP gene families. Furthermore, this knowledge contributes to unraveling the molecular mechanisms underlying the formation of epidermal appendages in G. japonicus.

Comparing the diagnostic efficacy of [18F]FDG PET/CT and [18F]FDG PET/MRI for detecting bone metastases in breast cancer: a meta-analysis.

BACKGROUND: This meta-analysis aimed to evaluate the comparative diagnostic efficacy of [18F]FDG PET/CT and [18F] FDG PET/MRI in detecting bone metastases in breast cancer patients. METHODS: An extensive search was conducted in the PubMed, Embase, Web of Science, and Cochrane Library databases to identify available publications up to February 2023. Studies were included if they evaluated the diagnostic efficacy of [18F]FDG PET/CT and [18F]FDG PET/MRI in patients with breast cancer bone metastases. Sensitivity and specificity were assessed using the DerSimonian and Laird method, followed by transformation via the Freeman-Tukey double inverse sine transformation. RESULTS: 16 articles (including 4 head-to-head comparison articles) involving 1,261 patients were included in the meta-analysis. The overall sensitivity of [18F]FDG PET/CT in patient-based analysis, lesion-based analysis, and head-to-head comparison were 0.73, 0.89, and 0.87, respectively, while the overall sensitivity of [18F]FDG PET/MRI were 0.99, 0.99, and 0.99. The results indicated that [18F]FDG PET/MRI appears to a higher sensitivity in comparison to [18F]FDG PET/CT(all P < 0.05). In contrast, the overall specificity of [18F]FDG PET/CT in patient-based analysis, lesion-based analysis, and head-to-head comparison were 1.00, 0.99, and 1.00, respectively, while the overall specificity of [18F]FDG PET/MRI were 1.00, 0.99, and 0.98. These results suggested that [18F]FDG PET/CT has a similar level of specificity compared to [18F]FDG PET/MRI. CONCLUSIONS: Our meta-analysis indicates that [18F]FDG PET/MRI demonstrates superior sensitivity and similar specificity to [18F]FDG PET/CT in detecting bone metastases in breast cancer patients. Further prospective research is required to confirm these findings and assess the clinical application of these techniques.

Epidemiology and nomogram for predicting the cancer-specific survival of ovarian granulosa cell tumor: A seer database study.

OBJECTIVE: ovarian granulosa cell tumor (OGCT) is a kind of infrequent ovarian malignant tumor with limited epidemiological data available. we established a predictive nomograph to verify the clinical prognosis. METHODS: 1005 diagnosed with ovarian granulosa cell tumor (OGCT) were extracted from Surveillance, Epidemiology, and End Results (SEER) public database from 2000-2018. Kaplan-Meier analysis was applied to distinguish risk factors, univariate and multivariate Cox analyses were used to determine the independent prognostic factors for cancer-specific survival (CSS) of OGCT patients. The obtained prognostic variables were combined to construct a nomogram model for predicting CSS in OGCT patients. RESULTS: Model performance was detected and evaluated with ROC curves and calibration plots. Data collected from 1005 patients were divided into two groups: training cohort(n=703,70%) and validation cohort(n=302,30%). The multivariate Cox model identified five covariates including age, marital status, AJCC stages, surgery and chemotherapy as independent interfering factors of CSS. The nomogram has shown a promising and excellent accuracy in evaluating 3 -, 5 -, 8-year CSS in OGCT patients. In terms of the CSS of the training cohort, the AUC values of the 3 -, 5 -, 8-year ROC curves were 0.819,0.8,0.819, while in terms of the CSS of the validation cohort, the AUC values of the validation cohort were 0.822,0.84,0.823, respectively. All the calibration curves showed pleasant consistency between predicted and actual survival rates. The nomogram model established in the study can improve the veracity of prognosis prediction, thereby improving the accuracy of individualized survival risk assessment, and providing targeted and constructive recommendations for specific treatment options. CONCLUSION: Age, advanced clinical stage, widower and without surgery therapy are independent risk factors for poor prognosis and the nomogram we constructed can help clinicians efficiently recognize high-risk OGCT patients to guide targeted therapies and improve their outcomes.

Phylogenetic Analysis and Genetic Structure of Schlegel's Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences.

Gekko japonicus, i.e., Schlegel's Japanese Gecko, is an important species which is widely distributed in East Asia. However, the information about population genetics of this species from China remains unclear. To address this issue, we used sequences from a fragment of the mitochondrial protein-coding gene cytochrome c oxidase I to estimate genetic diversity, genetic structure, and historical demography of G. japonicus populations from China. Phylogenetic analysis indicated that G. japonicus had a close relationship with Gekko wenxianensis. A total of 14 haplotypes were obtained, of which haplotype 1 was the most common and widely distributed. The genetic diversity of G. japonicus was comparatively low across different geographic populations. The populations of G. japonicus were divided into four groups which exhibited low levels of genetic differentiation, and expressed an unclear pattern of population structuring. In addition, potential population expansion of G. japonicus has occurred as well. Overall, these results demonstrate that the populations of G. japonicus reveal low genetic diversity in China, which is attributed to the founder and bottleneck events among populations. Our results will provide meaningful information on the population genetics of G. japonicus and will provide some insights into the study of origin of populations.

Significance of Oncotype DX 21-Gene Test and Expression of Long Non-Coding RNA MALAT1 in Early and Estrogen Receptor-Positive Breast Cancer Patients.

OBJECTIVE: To investigate the association between the recurrence score (RS) obtained by Oncotype DX 21-gene test and long non-coding RNA (lncRNA) MALAT1 expression in early and estrogen receptor-positive (ER+) breast cancer. MATERIALS AND METHODS: The Oncotype DX 21-gene test and MALAT1 expression detection were performed in tumor samples from 76 ER+ and early breast cancer patients with the Surplex liquid chip. The RS value was calculated based on the expression of total 21 genes. The level of MALAT1 was measured in both tumor tissue and para-tumor tissue, and relatively quantified with an internal control gene. Mann-Whitney U-test or Kruskal-Wallis test were used to analyze the association between MALAT1 level and different clinical pathological characteristics, including age, tumor stage, disease grade, lymph node status, Ki-67 expression, and progesterone receptor (PR) status. The association between the RS and different characteristics was analyzed by Wilcoxon rank-sum test. Correlation between two parameters was analyzed by Spearman's rank correlation analysis. RESULTS: The expression of MALAT1 was more abundant in tumor tissue (2.992 ± 2.256) than that in adjacent normal tissue (1.641±1.438, Z=-2.594, p=0.009), and it was not correlated with any clinical pathological characteristics. According to the old criteria for RS stratification, 52.7% of patients were in low risk (RS<18), 36.8% of patients were in medium risk (18≤RS≤30), and 10.5% of patients were in high risk (RS>30). While under the new criteria, 18.4% were in low risk group (RS<11), 63.2% were in a medium risk group (11≤RS≤26), and 18.4% were in a high risk group (RS>26). The Oncotype DX 21-gene results only correlated with Ki-67 expression under both new and old criteria, and it was not related with other cancer characteristics. The expression of lncRNA MALAT1 was significantly correlated with the Oncotype DX 21-gene results under the old criteria. CONCLUSION: MALAT1 is a novel breast cancer biomarker independent of tumor stage, disease grade and lymph node status. MALAT1 level is associated with the Oncotype DX 21-gene RS value. Therefore, combination of MALAT1 and the Oncotype DX 21-gene test may be used to predict prognosis in ER+ and early stage breast cancer.

ALOX12 inhibition sensitizes breast cancer to chemotherapy via AMPK activation and inhibition of lipid synthesis.

Arachidonate lipoxygenase12 (Alox12) and its metabolites 12S-hydroxyeicosatetraenoic acid (12S-HETE) have been implicated in influencing tumor transformation and progression. In this study, we have systematically evaluated the expression, function and the downstream effectors of Alox12 in breast cancer using loss- and gain-of-function approaches. We demonstrated that both mRNA and protein levels of Alox12 were significantly increased in multiple breast cancer cell lines compared to normal breast cells. The upregulation of Alox12 expression was also observed in breast cancer tissues and their matched normal breast tissues obtained from patients. Functionally, we demonstrated that Alox12 overexpression was sufficient to stimulate growth in normal breast cells but not breast cancer cells. This also protects breast cancer cell from chemotherapy-induced growth arrest and apoptosis. In contrast, Alox12 depletion inhibited breast cancer growth and survival, and significantly enhanced the chemotherapeutic agents' efficacy. Mechanism studies showed that Alox12 depletion activated AMP-activated protein kinase (AMPK), leading to the inhibition of acetyl-CoA carboxylase1 (ACC1) enzyme activity and lipid synthesis. The recuse of the effects of Alox12 depletion using Alox12 metabolites 12S-HETE further confirmed that AMPK and its subsequent inhibition of ACC1 activity and lipid synthesis were the downstream signaling of Alox12 inhibition. Our findings highlighted the important role of Alox12 in breast cancer, particularly in response to chemotherapy. Our work also demonstrate that inhibiting Alox12 is a possible alternative therapeutic strategy to overcome chemoresistance in breast cancer.

Diagnostic Value of Contrast-Enhanced Spectral Mammography for Screening Breast Cancer: Systematic Review and Meta-analysis.

BACKGROUND: Contrast-enhanced spectral mammography (CESM) is a new image examination technology that has developed over the past few years. As CESM technology keeps improving, a current meta-analysis review is needed to systematically evaluate the potential diagnostic value of CESM. METHODS: A total of 18 studies were included in the review. Sensitivity, specificity, and other important parameters of CESM accuracy for breast cancer diagnosis were pooled and analyzed using random-effects models. Summary receiver operating characteristic curves were calculated for overall accuracy estimation. RESULTS: The summary estimates for CESM in the diagnosis of breast cancer were as follows: the pooled sensitivity and specificity were 0.89 (95% confidence interval [CI], 0.88-0.91) and 0.84 (95% CI, 0.82-0.85), respectively. Positive likelihood ratio was 3.73 (95% CI, 2.68-5.20), negative likelihood ratio was 0.10 (95% CI, 0.06-0.15), and diagnostic odds ratio was 71.36 (95% CI, 36.28-140.39). The area under the curve was 0.96 (standard error = 0.011). CONCLUSION: CESM has a high diagnostic accuracy for evaluating breast cancer and can be considered as a useful test for initial assessment of breast lesions.