Non-cancerous Tissues Research Articles

Genetic overlap between breast cancer and sarcopenia: exploring the prognostic implications of SLC38A1 gene expression

BackgroundSarcopenia, an age-related syndrome characterized by a decline in muscle mass, not only affects patients’ quality of life but may also increase the risk of breast cancer recurrence and reduce survival rates. Therefore, investigating the genetic mechanisms shared between breast cancer and sarcopenia is significant for the prevention, diagnosis, and treatment of breast cancer.MethodsThis study downloaded gene expression datasets and clinical data related to breast cancer and skeletal muscle aging from the GEO database. Data preprocessing, integration, differential gene identification, functional enrichment analysis, and construction of protein-protein interaction networks were performed using R language. Subsequently, COX proportional hazards model analysis and survival analysis were conducted, and survival curves and nomograms were generated. The expression levels of genes in tissues were detected using qRT-PCR, and the Radiant DICOM viewer software was used to delineate the pectoralis major muscle area in CT images.ResultsWe identified 152 differentially expressed genes (P < .05) and 226 sarcopenia-related genes (r > .4) associated with skeletal muscle aging. The TCGA-BRCA dataset revealed 106 genes associated with breast cancer (P < .05, logFC = 1). Functional enrichment analysis indicated significant enrichment in cell proliferation and growth pathways. The PPI network identified critical molecules involved in muscle aging and tumor progression. After dimensionality reduction, a strong correlation was observed between the expression of the muscle aging-related gene set and the prognosis of breast cancer patients (P < .01). The expression of SLC38A1 identified through multivariate COX analysis was significantly associated with poor prognosis in breast cancer patients (P = .03). Incorporating SLC38A1 expression, the prognostic model precisely forecasted breast cancer survival (P < .01). External validation confirmed the higher expression of the SLC38A1 gene in breast cancer tissues compared to adjacent non-cancerous tissues (P < .01). The SLC38A1 index, calculated in combination with the patient’s age and BMI, can optimize the prognostic prediction model, providing a powerful tool for personalized treatment of breast cancer.ConclusionHigh SLC38A1 gene expression was significantly associated with poor prognosis in breast cancer patients. The combination of SLC38A1 expression and the pectoralis major muscle area provided an optimized prognostic prediction model, offering a potential tool for personalized breast cancer treatment.

NMR-based metabolomics combined with metabolic pathway analysis reveals metabolic heterogeneity of colorectal cancer tissue at different anatomical locations and stages.

Colorectal cancer (CRC) still remains the leading cause of cancer death worldwide. This study aimed to profile the metabolic differences of colorectal cancer tissues (CCT) at different stages and sites, as compared with their distant noncancerous tissues (DNT), to investigate the temporal and spatial heterogeneities of metabolic characterization. Our NMR-based metabolomics fingerprinting revealed that many of the metabolite levels were significantly altered in CCT compared to DNT and esophageal cancer tissues, indicating deregulations of glucose metabolism, one-carbon metabolism, glutamine metabolism, amino acid metabolism, fatty acid metabolism, TCA cycle, choline metabolism, and so forth. A total of five biomarker metabolites, including glucose, glutamate, alanine, valine and histidine, were identified to distinguish between early and advanced stages of CCT. Metabolites that distinguish the different anatomical sites of CCT include glucose, glycerol, glutamine, inositol, succinate, and citrate. Those significant metabolic differences in CRC tissues at different pathological stages and sites suggested temporal and spatial heterogeneities of metabolic characterization in CCT, providing a metabolic foundation for further study on biofluid metabolism in CRC early detection.

CircRNA_036186 mediates HNSCC progression by regulating 14-3-3ζ.

Head and neck squamous cell carcinoma (HNSCC) is a prevalent and lethal malignancy, accounting for 95% of head and neck cancers. Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activating protein ZETA (14-3-3ζ) is central to various signalling pathways and is pivotal in tumour progression. Cancerous and corresponding non-cancerous tissue samples were collected from five patients diagnosed with HNSCC. circRNA and mRNA expression profiles were analyzed using high-throughput sequencing techniques. Potential circRNA-microRNA (miRNA)-mRNA interactions were predicted using bioinformatics tools. The study found that CircRNA_036186 regulates the expression of 14-3-3ζ in HNSCC through miR-193b-5p. These findings suggest that CircRNA_036186 has the potential to be a biomarker and therapeutic target for HNSCC and provide some theoretical basis for further research on the role of circRNA in HNSCC.

ADAM17 promotes colorectal cancer migration and invasion by regulating the TGF-β/Smad signaling pathway

ObjectiveInvestigate ADAM17 expression in colorectal cancer (CRC) at molecular and cellular levels and its potential mechanism in promoting tumorigenesis by regulating CRC cell migration and invasion. Materials and methodsThe study measured ADAM17 mRNA and protein levels in colorectal cancer cells and tissues using qPCR and immunohistochemical staining, and assessed the cells' proliferation, migration, and invasion abilities. ResultsADAM17 expression was significantly higher in CRC tissues than in non-cancerous tissues and was linked to metastasis and poor prognosis in CRC patients. Silencing ADAM17 reduced cell migration and invasion. Mechanistically, knocking down ADAM17 decreased the expression of TGF-β/Smad pathway-related proteins, which inhibited proteins associated with migration and invasion, thus impairing these cellular processes. ConclusionADAM17 likely promotes the migration and invasion of CRC cells by regulating the TGF-β/Smad signaling pathway. This study aids in understanding the molecular mechanisms of CRC metastasis and development, and supports the development of new therapeutic targets.

GCNT3 promotes the proliferation, apoptosis, invasion, and migration of breast cancer through the PI3K/AKT pathway.

Breast cancer (BRCA) constitutes one of the principal causes of death among women. The objective of this study was to explore the impact of glucose-aminotransferase 3 (GCNT3) on the growth, invasion, and metastasis of BRCA cells. Additionally, the aim of this research was to clarify the underlying molecular mechanisms through which GCNT3 influences the development and progression of BRCA and to ascertain the potential of GCNT3 as a novel BRCA biomarker. Analysis involved data sourced from the The Cancer Genome Atlas database (TCGA). Expression levels of GCNT3 were measured using Western blot analysis and immunohistochemistry (IHC). Additionally, cell functionality tests were performed posttransfection with GCNT3-specific interference plasmids to assess the influence of GCNT3 in BRCA by using EdU assay, transwell assay, and flow cytometric assay, as well as PI3K/AKT signaling pathway. GCNT3 levels were notably elevated in BRCA tissues compared to adjacent noncancerous tissues. Reducing GCNT3 expression significantly diminished the proliferation, invasion, and migration capabilities of BRCA cells (P<0.05) and concurrently increased apoptosis (P<0.05). The data also indicated that GCNT3 may be involved in activating the PI3K/AKT signaling pathway. Elevated GCNT3 expression in BRCA tissues suggests the potential of GCNT3 to be a biomarker for predicting BRCA prognosis. The regulation of p-PI3K and p-AKT levels by GCNT3 appears to considerably inhibit BRCA cell development and progression.

Overexpression of proteasome 26S subunit non-ATPase 6 protein and its clinicopathological significance in intrahepatic cholangiocarcinoma

BACKGROUND Currently, intrahepatic cholangiocarcinoma (ICC) poses a continuing, significant health challenge, but the relationship has yet to be established between ICC and the proteasome 26S subunit non-ATPase 6 (PSMD6). AIM To investigate the protein expression and clinicopathological significance of PSMD6 in ICC. METHODS The potential impact of the PSMD6 gene on the growth of ICC cell lines was analyzed using clustered regularly interspaced short palindromic repeat knockout screening technology. Forty-two paired specimens of ICC and adjacent non-cancerous tissues were collected. PSMD6 protein expression was determined by immunohistochemistry. Receiver operating characteristic curve analysis was performed to validate PSMD6 expression level, and its association with ICC patients’ various clinicopathological characteristics was investigated. RESULTS The PSMD6 gene was found to be essential for the growth of ICC cell lines. PSMD6 protein was significantly overexpressed in ICC tissues (P &lt; 0.001), but showed no significant association with patient age, gender, pathological grade, or tumor-node-metastasis stage (P &gt; 0.05). CONCLUSION PSMD6 can promote the growth of ICC cells, thus playing a pro-oncogenic role.

NALCN Promoter Methylation as a Biomarker for Metastatic Risk in a Cohort of Non-Small Cell Lung Cancer Patients

Liquid biopsy enables real-time monitoring of tumor development and response to therapy through the analysis of CTCs and ctDNA. NALCN is a sodium leak channel that is frequently involved in tumor evolution and immunity and acts as a tumor suppressor. Deletion of NALCN has been shown to increase cancer metastasis and the number of CTCs in peripheral blood. In this study, we investigated for the first time NALCN promoter methylation in (a) Aza-treated cell lines (A549, TE671, BT20, and MDA-MB-468), (b) paired NSCLC tissues (n = 22), and (c) plasma cell-free DNA (ctDNA) from patients with NSCLC (early stage n = 39, metastatic n = 39) and DNA from 10 healthy donors (HD) using a newly developed highly specific and sensitive real-time MSP method. Treatment with 5′-aza-dC induced the expression of NALCN only in the A549 cell line, suggesting that DNA methylation regulates its expression in certain cancers. The mRNA expression levels of NALCN were quantified in non-small cell lung cancer (NSCLC) and adjacent non-cancerous tissues, and it was found to be underexpressed in 54.5% of tumor tissues, with significantly higher expression in recurrence-free patients (p = 0.009) than in patients who relapsed. The NALCN methylation level was not statisticallysignificantlycorrelated with the corresponding expression (p = 0.439), while Kaplan–Meier analysis showed an association between NALCN promoter hypermethylation and worse disease-free intervals (DFIs) (p = 0.017). Evaluation of NALCN methylation in ctDNA revealed that it was detected in 5.1% of early and 10.2% of advanced cases. Our results strongly suggest that epigenetic inactivation of NALCN may be a predictor of metastasis in NSCLC. Our results should be validated in further studies based on a larger patient cohort to further investigate whether DNA methylation of the NALCN promoter could serve as a potential prognostic DNA methylation biomarker and predictor of metastasis in NSCLC.

MiR-200 family as new potential prognostic factor of overall survival of patients with WHO G2 and WHO G3 brain gliomas

Gliomas are the predominant cause of cancer-related deaths among the young population. Even after incorporation of IDH1/2 mutations and 1p19q codeletion there are doubts regarding adjuvant treatment in WHO G2/G3 gliomas. miRNA molecules control about 30% of all genes, also many oncogenes, tumor suppressor genes and genes responsible for the response to ionizing radiation and systemic treatment. Patients with brain gliomas exhibit miRNA disorders. We aimed to evaluate the expression of miR-200 family members in relation to selected clinico-pathological factors and their prognostic value. We enrolled 53 patients diagnosed with WHO G2/G3 brain gliomas treated between 2012–2016. RT-qPCR based expression of miR-200 family was assessed in tumor and surrounding non-cancerous tissue. An analysis of selected clinico-pathological features was carried out. A logistic regression model was prepared for the miRNA signature. The predictive potential of the signature was assessed using the ROC curve. A stepwise backward regression model was used to select variables with a significant predictive potential related to OS. It was shown that miR-200a-3p, miR-200a-5p, miR-200c-5p, miR-141-3p and miR-429 can be independent predictors of survival. Better 2- and 5-year OS was associated with higher expression of miR-200a-3p, miR141-3p and lower expression of miR-200a-5p, miR-200c-5p, miR-429. The strongest predictors of survival were miR-200a-5p, miR-200b-3p, miR-200c-5p, miR-141-3p, miR-429, tumor volume and CTV. Members of the miR-200 family exhibit prognostic value for 2- and 5-year OS. Presented predictive models of survival may be clinically useful for treatment optimization.

High expression of BBOX1 in paracancerous tissue is associated with poor prognosis in hepatocellular carcinoma patients

The molecular profile of paracancerous tissue has been reported to be prognostic for recurrence in patients with different cancers. This study investigated the clinical significance of the protein expression of gamma-butyrobetaine hydroxylase 1 (BBOX1) in tumor and paracancerous tissues of hepatocellular carcinoma (HCC) patients. This study assessed the role of BBOX1 mRNA in tumor and paracancerous tissues in HCC via bioinformatics analysis. The protein levels of BBOX1 in paired tumor and paracancerous tissues from 83 HCC patients were determined by immunohistochemistry. The associations among BBOX1 protein levels, clinicopathological characteristics and the survival probability of HCC patients were also analyzed. The results revealed that BBOX1 mRNA expression was significantly lower in HCC tissues than in noncancerous tissues. HCC patients with low BBOX1 mRNA expression had a significantly poorer overall survival than those with high BBOX1 expression did. Immunohistochemical analysis of BBOX1 protein expression further confirmed that its levels were markedly lower in HCC tissues than in paracancerous tissues. High BBOX1 expression in paracancerous tissues correlated with poor overall survival and disease-free survival in HCC patients. These findings suggest that the paracancerous BBOX1 expression might be a credible indicator for overall survival or disease-free survival in HCC patients.

Abstract A030: Polycomb repressive complex 2 (PRC2) mediates the epigenetic regulation of cancer-associated fibroblasts in esophageal cancer

Abstract Cancer-associated fibroblasts (CAFs) are a heterogenous cell population that can promote esophageal cancer progression through multiple molecular mechanisms including increased cancer cell proliferation and migration, immunosuppression, and therapeutic resistance. Despite the divergence of CAFs from normal fibroblasts with regards to phenotype and functions, CAFs rarely exhibit widespread genetic alterations. Instead, it is proposed that CAFs are regulated at the epigenetic level. Our objective is to delineate this epigenetic regulation of CAFs in esophageal cancer. Ultimately, we aim to identify the epigenetic regulatory complexes that mediate CAF heterogeneity and pro-tumorigenic functions. To this end, we completed RNA-seq and ATAC-seq on fibroblasts isolated from esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAC) and non-cancerous esophageal tissue. Enrichment analysis identified the polycomb repressive complex 2 (PRC2) as a potential regulator of ESCC and EAC CAFs. PRC2 catalyzes the methylation (mono-, di- or tri-) of lysine 27 on histone 3 (H3K27me1/2/3) resulting in transcriptional repression. Inhibition of two key proteins of PRC2 (EZH2 and SUZ12) through either pharmacological or genetic modulation, altered expression of multiple CAF phenotype related proteins and inhibited CAF functions including CAF proliferation. Ongoing studies, using co-cultures of fibroblasts and tumor cells, seek to identify if inhibition of PRC2 can prevent the initial transition of normal esophageal fibroblasts into CAFs. Importantly, we are conducting in vivo studies to determine if selective PRC2 inhibition in CAFs can inhibit esophageal tumor progression with specific focus on primary tumor growth and metastatic spread. In summary, initial studies have identify that PRC2 complex mediates CAF phenotype and functions, and we aim to establish the larger impact of these CAF specific effects on esophageal cancer. Citation Format: Karen J. Dunbar, Raul Navaridas Fernandez de Bobadil, Katherine M. Cunningham, Emily Esquea, Gizem Efe, Anil K. Rustgi. Polycomb repressive complex 2 (PRC2) mediates the epigenetic regulation of cancer-associated fibroblasts in esophageal cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A030.

Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures.

High-plex proteomic technologies have made substantial contributions to mechanism studies and biomarker discovery in complex diseases, particularly cancer. Despite technological advancements, inherent limitations in individual proteomic approaches persist, impeding the achievement of comprehensive quantitative insights into the proteome. In this study, we employed two widely used proteomic technologies, mass spectrometry (MS) and reverse phase protein array (RPPA) to analyze identical samples, aiming to systematically assess the outcomes and performance of the different technologies. Additionally, we sought to establish an integrated workflow by combining these two proteomic approaches to augment the coverage of protein targets for discovery purposes. We used 14 fresh frozen tissue samples from triple-negative breast cancer (TNBC: seven tumors versus seven adjacent non-cancerous tissues) and cell line samples to evaluate both technologies and implement this dual-proteomic strategy. Using a single-step protein denaturation and extraction protocol, protein samples were subjected to reverse-phase liquid chromatography (LC) followed by electrospray ionization (ESI)-mediated MS/MS for proteomic profiling. Concurrently, identical sample aliquots were analyzed by RPPA for profiling of over 300 proteins and phosphoproteins that are in key signaling pathways or druggable targets in cancer. Both proteomic methods demonstrated the expected ability to differentiate samples by groups, revealing distinct proteomic patterns under various experimental conditions, albeit with minimal overlap in identified targets. Mechanism-based analysis uncovered divergent biological processes identified with the two proteomic technologies, capitalizing on their complementary exploratory potential.

Proteomic profiling of oral squamous cell carcinoma tissues reveals altered immune-related proteins: implications for personalized therapy

ABSTRACT Objectives Oral squamous cell carcinoma poses a substantial global health challenge marked by rising mortality rate. Recently, immunotherapy has shown promising results in cancer management by enhancing immune response. Thus, identifying additional immune-related markers is critical for advancing immunotherapy treatments. Methods Data-independent acquisition (DIA) mass spectrometry approach was used to explore differentially expressed immune-related proteins in oral cancer tissues compared to adjacent non-cancerous tissues. Functional significance was identified through Gene Ontology, pathway, and network analysis. Gene expression of identified proteins was validated using transcriptomic data. Results DIA analysis identified 29,459 precursors corresponding to 3429 proteins. Among these, 1060 proteins were differentially expressed, with 166 being immune-related. Differentially regulated proteins were involved in innate immune response, mitochondrial ATP synthesis, and neutrophil degranulation. Pathway analysis of immune-related proteins showed perturbation in anti-tumor immunity-related pathways such as interferon signaling, TCR signaling, PD-1 signaling, and antigen processing and presentation. Significance of these pathways was further reinforced by the strong interactions identified in the protein–protein interaction network analysis. Additionally, gene expression analysis showed similar mRNA expression patterns for key proteins involved in altered pathways, including ISG15, IFIT1/3, HLA-A/C and OAS2/3. Conclusions Further validation of these proteins could establish them as potential targets for personalized therapy.

Abstract A016: Early pancreatic cancer detection using extracellular vesicle DNA methylation signatures in blood

Abstract In 2020, there were 495,773 new cases and 466,003 deaths for pancreatic cancer worldwide. Furthermore, pancreatic cancer is emerging to be the leading cause of cancer related deaths in the U.S. by the year 2030, surpassing lung and colon cancer. The majority of pancreatic cancer patients (∼80%) are diagnosed at the most advanced (metastatic) stage, for which the 5-year survival is 3%. Dramatically, studies show that if it can be detected at an early stage when surgical removal is feasible, the 5-year survival rate significantly increased to 37%. This data highlights the crucial importance of early detection for pancreatic cancer treatment with curative intent. Unfortunately, currently there are no reliable techniques for routine screening to identify pancreatic cancer at early stages. In this Abstract, we developed and validated the performance of those DNA methylation markers to detect pancreatic cancer in a cohort of pancreatic cancer patients. Firstly, we collected a large amount of genome-wide methylation microarray data (targeting over 450,000 methylation sites) of tissue samples from several publicly available databases, including samples of solid pancreatic tumors (n = 384), noncancerous pancreatic tissues (n = 126) and healthy whole blood (n = 453). The raw microarray data were preprocessed using a pipeline implemented in R, which removes inaccurate measurements and corrects for bias caused by technical issues. A two-stage feature selection procedure was designed and implemented in Python, which makes use of various filters and a multivariate embedded method, support vector machine recursive feature elimination (SVM-RFE). The features were evaluated using two metrics, classification performance and stability, based on a tradeoff of which we selected a set of differentially methylated loci for discriminating the samples. The set of prospective markers includes 129 hypermethylated and 142 hypomethylated tumor-specific loci, 8 hypermethylated and 8 hypomethylated pancreatic tissue specific loci. To validate the performance of those pancreatic cancer-specific methylation markers, as a feasibility study, we isolated extracellular vesicles from cancer cells and plasma of cancer patients using lipid nanoprobe (LNP). Extracellular vesicles (EVs) are lipid-bilayer-enclosed vesicles of sub- micrometer size that are secreted by virtually all cell types. In a pilot study encompassing 11 pancreatic cancer patients (Stage I-IV) and age-matched 10 healthy donors (HD), we employed quantitative methylation-specific polymerase chain reaction assays (qMSP) to examine the promoter methylation status of the genes within plasma EV DNA. The receiver operating characteristic (ROC) curves were employed to assess the performance of a combined promoter methylation signature in EV DNA for the detection of pancreatic cancer. Our findings indicate that the promoter methylation of genes can be specific to pancreatic cancer, suggesting the efficient packaging of methylation information from genomic DNA into EVs. Citation Format: Hongzhang He, Siyang Zheng. Early pancreatic cancer detection using extracellular vesicle DNA methylation signatures in blood [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A016.

STEM-13. NUCLEAR LOCALIZATION OF ALPHA-1-ANTICHYMOTRYPSIN INCREASES IN GLIOBLASTOMA FOLLOWING STANDARD OF CARE TREATMENT

Abstract Glioblastoma (GBM) is the most common malignant primary brain tumor in adults with a median survival of 8-14 months and 5-year survival rate of 6.9%. Its aggressive nature arises mostly from molecular heterogeneity and resistance to standard of care (SOC), including radiation and temozolomide (TMZ). Recurrence is nearly inevitable, driven by highly invasive brain tumor initiating cells (BTICs). Our previous studies revealed that exposing BTICs to cerebrospinal fluid (CSF) from GBM patients increases cell migration and proliferation compared to non-cancer CSF. Transcriptomic analysis identified the upregulation of the SERPINA3 gene, which encodes alpha-1-antichymotrypsin (ACT). Silencing of SERPINA3 reduces BTIC migration and proliferation and abolishes the promigratory response to GBM-derived CSF, highlighting SERPINA3 as a potential therapeutic target. ACT has been reported to bind to DNA, although the implications of this interaction are unknown. We have previously observed higher levels of intranuclear ACT in human GBM compared to non-cancer brain tissues. We hypothesize that the nuclear localization of SERPINA3 in GBM contributes to increased malignancy, opening the possibility of therapeutically targeting its intranuclear transport. Here, we determined the intracellular localization of ACT in BTICs and GBM and compared it to non-cancer tissues. Additionally, we evaluated whether SOC affected intranuclear localization of ACT. Patient-derived BTICs were treated with TMZ, radiation, and a combination of both, to assess changes in ACT expression via Western Blot, PCR, and ICC. A decrease in cell confluency was correlated with a significant decrease (p&amp;lt;0.05) in SERPINA3 mRNA and overall protein expression when BTICs were treated with TMZ alone or in combination. Interestingly, confocal microscopy revealed a significant increase (p&amp;lt;0.05) in its nuclear localization, particularly with TMZ treatment, indicating a change in its intracellular distribution. Overall, nuclear translocation of SERPINA3 increases in response to SOC with potential implications as a treatment resistance mechanism.

Xenotropic and polytropic retrovirus receptor 1 (XPR1) promotes progression of papillary thyroid carcinoma via the BRAF-ERK1/2-P53 signaling pathway.

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Xenotropic and polytropic retrovirus receptor 1 (XPR1), identified as a cellular receptor, plays roles in many pathophysiological processes. However, the underlying function and molecular mechanisms of XPR1 in PTC remain unclear. Therefore, this study aimed to elucidate the role of XPR1 in the process of PTC and the potential mechanisms. RNA-sequencing was performed for gene differential expression analysis in PTC patients' tissues. Immunohistochemical assay, real-time PCR, and western blotting assay were used to determine the expression of XPR1, BRAF, and P53 in PTC tissues. The function of XPR1 on the progression of PTC was explored using in vitro and in vivo experiments. The molecular mechanism of XPR1 was investigated using gene silencing, ELISA, immunofluorescence, western blotting, and real-time PCR assays. We found that XPR1 was markedly upregulated in PTC tissues compared to adjacent noncancerous tissues, suggesting that high expression of XPR1 could be correlated with poor patient disease-free survival in PTC. In addition, the expression of BRAF and P53 in PTC tissues was substantially higher than in adjacent noncancerous tissues. Silencing of XPR1 reduced the proliferation, migration, and invasion capacities of TPC-1 cells in vitro and effectively inhibited the tumorigenecity of PTC in vivo. More importantly, silencing of XPR1 in TPC-1 cells significantly decreased the expression of XPR1, BRAF, and P53 both in vitro and in vivo. Interestingly, we demonstrated that XPR1 may positively activate the BRAF-ERK-P53 signaling pathway, further promoting PTC progression. The findings reveal a crucial role of XPR1 in PTC progression and prognosis via the BRAF-ERK1/2-P53 signaling pathway, providing potential therapeutic targets for treating PTC.

ScRNA-Seq Analysis Revealed CAFs Regulating HCC Cells via PTN Signaling.

Cancer-associated fibroblasts (CAFs) play a pivotal role in shaping the microenvironment of hepatocellular carcinoma (HCC). However, the mechanisms through which CAFs influence the progression of HCC remain incompletely understood. Single-cell RNA sequencing datasets (GSE158723 and GSE112271) were retrieved from the Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) and analyzed using R software. Our analysis suggested that CAFs may promote liver cancer cell development, possibly through the interaction of pleiotrophin (PTN) and syndecan-2 (SDC2). Clinical samples from HCC patients were collected and processed into frozen sections and single-cell suspensions for Masson staining, immunofluorescence staining, and flow cytometry. Additionally, Huh7 liver cancer cells and LO2 normal liver cells were cultured and subjected to immunofluorescence assays using cell slides. The proportion of CAFs in cancerous tissues was higher than in adjacent non-cancerous tissues, and pleiotrophin (PTN) expression was elevated in cancer tissues compared to adjacent tissues. These findings aligned with the results of the single-cell RNA sequencing (scRNA-seq) analysis. Furthermore, SDC2 expression was significantly upregulated in Huh7 liver cancer cells compared to LO2 normal liver cells. This study suggests that CAFs may contribute to HCC progression via the PTN/SDC2 signaling pathway. Our findings provide deeper insights into the interactions between CAFs and HCC cells within the tumor microenvironment (TME).

Challenges and prospects of cell-free DNA in precision oncology

Cell-free DNA (cfDNA), predominantly derived from apoptotic or necrotic cells, is emerging as a potential biomarker due to non-invasiveness and cost-effectiveness1. Additionally, another type of cfDNA such as cell-free mitochondrial DNA (cf-mtDNA) that is released from cells under stress or damage condition, may play a key role in the immune system. Thus, the presence of cfDNA in the circulation of cancer patients with differential observations between the cancer and the healthy individuals may be used to improve diagnosis by liquid biopsies2. In the past decades, liquid biopsy has been significantly advanced, particularly in detecting cfDNA, which has opened a new research era in cancer diagnostics worldwide. However, there is a big hindrance in integrating cfDNA analysis with clinical diagnosis, For example, a high rate of false positives is caused by insensitive assays, which may be improved by refining the processing of sequencing data. That is due to the technical differences of feature analysis (e.g., fragmentomics and methylation patterns) and their heterogeneity limited the application of cfDNA in the clinics3–5. Currently, there are many efforts on the way to solve the problems. Especially, the top priority is to enhance assay sensitivity and specificity and to adapt analytical techniques in oncology.Nowadays, liquid biopsy technology based on circulating free DNA (cfDNA) brings new hope for future clinical applications such as minimally invasive early screening for tumors, with the key to effectiveness lying in the integration of next-generation sequencing (NGS) with advanced separation technologies. A comparison between the RNA expression datasets and the cfDNA fragment frequencies has revealed distinct genomic characteristics between cancer patients and healthy individuals. Research has found that there are specific fragmentation patterns of cfDNA in the promoter regions of some highly expressed genes6,7. Notably, cfSort is the first supervised tissue deconvolution approach powered by deep learning, leveraging a high-resolution methylation atlas from 521 non-cancer tissue samples across 29 major human tissue types. This model accurately identifies the origin of cfDNA, demonstrating the clinical value of sequencing data in disease diagnosis and treatment monitoring8. In this perspective, we outline the current trend of cfDNA research and highlight its potential limitations in oncology (Fig. 1). It provides valuable insights for cancer diagnosis and management which may help pave the way for the future adoption of cfDNA in oncology.

B7-H3 is widely expressed in soft tissue sarcomas

PurposeTargeted therapy development in soft tissue sarcoma (STS) has been burdened by the heterogeneity of this group of rare tumors. B7 homolog 3 protein (B7-H3) is a molecule in the same family as programmed death-ligand 1 (PD-L1). It has limited expression in noncancerous tissues and is overexpressed in many cancers, making it an attractive target for cancer therapy, and clinical trials targeting B7-H3 are actively underway. While available data demonstrate high expression levels of B7-H3 in individual sarcoma subtypes, its expression patterns across STS subtypes are not well described. The purpose of this study was to characterize the expression patterns of B7-H3 in STS.Patients and methodsThis retrospective analysis evaluated STS tumor specimens from patients with a variety of different subtypes. Specimens were evaluated by immunohistochemistry (IHC) for expression and staining pattern of B7-H3 both in tumors and in associated vasculature.ResultsSpecimens from 153 sarcoma patients included 15 different STS subtypes. B7-H3 was broadly expressed in 97% of samples (95% CI 0.93–0.99) and 69.2% demonstrated high levels of B7-H3 expression (95% CI 0.61–0.76). No significant association between B7-H3 positivity or expression level and prior treatment(s), tumor size, tumor grade, or patient age. B7-H3 positivity in vessels was found in 94.7% (145/153) of samples. In tumors that had been previously assessed for PD-L1 and PD-1, there was no correlation between B7-H3 positivity or expression and the positivity or expression level of PD-L1 or PD-1.ConclusionThese data show high levels of B7-H3 positivity across soft tissue sarcoma subtypes, suggesting its feasibility as a therapeutic target for future sarcoma treatments. Future clinical trials are needed to evaluate whether targeting B7-H3 can provide clinical benefit to help patients with sarcoma.

Radioresistance and brain metastases: a review of the literature and applied perspective.

Intracranial metastatic disease is a serious complication of cancer, treated through surgery, radiation, and targeted therapies. The central role of radiation therapy makes understanding the radioresistance of metastases a priori a key interest for prognostication and therapeutic development. Although historically defined clinic-radiographically according to tumour response, developments in new techniques for delivering radiation treatment and understanding of radioprotective mechanisms led to a need to revisit the definition of radioresistance in the modern era. Factors influencing radioresistance include tumour-related factors (hypoxia, cancer stem cells, tumour kinetics, tumour microenvironment, metabolic alterations, tumour heterogeneity DNA damage repair, non-coding RNA, exosomes, methylomes, and autophagy), host-related factors (volume effect & dose-limiting non-cancerous tissue, pathophysiology, and exosomes), technical factors, and probabilistic factors (cell cycle and random gravity of DNA damage). Influences on radioresistance are introduced and discussed in the context of brain metastases.

Contributions of Tissue Inhibitor of Metalloproteinase-1 Genotypes to the Risk of Metastasis in Gastric Cancer.

In gastric cancer (GCa) tissues, the mRNA and protein levels of tissue inhibitor of metalloproteinase-1 (TIMP-1) are significantly elevated compared to adjacent non-cancerous tissues. Moreover, the abnormal up-regulation of TIMP-1 has been associated with a poor prognosis. However, the role of TIMP-1 genotypes in susceptibility to GCa has seldom been investigated. This study aimed to evaluate the influence of TIMP-1 genotypes on GCa susceptibility and their potential interactions with clinico-pathological factors, including age, sex, body mass index, smoking, alcohol consumption, Helicobacter pylori (H. pylori) infection, and metastasis status. TIMP-1 rs4898, rs6609533, and rs2070584 genotypes were analyzed in 161 patients with GCa and 483 non-cancer control subjects from a Taiwanese population using PCR-RFLP methodology and direct sequencing. The genotypic (p for trend=0.1987) and allelic (p=0.0733) frequencies of TIMP-1 rs4898 did not differ significantly between GCa cases and controls. Under the dominant model, combined CT+CC genotypes were not associated with GCa risk [odds ratio (OR)=0.74, 95% confidence interval (95%CI)=0.51-1.07, p=0.1272]. Similarly, no significant association was found for TIMP-1 rs6609533 or rs2070584 polymorphisms. Importantly, patients with GCa carrying the TIMP-1 rs4898 TT genotype exhibited a significantly enhanced risk of GCa when they had smoking (p=0.0140) and alcohol drinking habits (p=0.0011). Furthermore, the CC genotype of TIMP-1 rs4898 was linked to a lower risk of distant metastasis. The TIMP-1 rs4898 CC genotype may serve as a prognostic biomarker and could inform lifestyle modifications aimed at GCa prevention. Validation of TIMP-1 genotypic profile in diverse populations is warranted.