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Chen F, Yang J, Fang M, Wu Y, Su D, Sheng Y. Necroptosis-related lncRNA to establish novel prognostic signature and predict the immunotherapy response in breast cancer. J Clin Lab Anal 2022; 36:e24302. [PMID: 35229919 PMCID: PMC8993638 DOI: 10.1002/jcla.24302] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Necroptosis is a type of programmed cell death, and recent researches have showed that lncRNAs could regulate the process of necroptosis in multiple cancers. We tried to screen necroptosis‐related lncRNAs and investigate the immune landscape in breast cancer (BC). Methods The samples of breast normal and cancer tissue were acquired from TCGA and GTEx databases. A risk prognostic model was constructed based on the identified necroptosis‐related lncRNAs by Cox regression and least absolute shrinkage and selection operator (LASSO) method. Moreover, the forecast performance of this model was verified and accredited by synthetic approach. Subsequently, an accurate nomogram was constructed to predict the prognosis of BC patients. The biological differences were investigated through GO, GSEA, and immune analysis. The immunotherapy response was estimated through tumor mutation burden (TMB) and tumor immune dysfunction and exclusion (TIDE) score. Results A total of 251 necroptosis‐related lncRNAs were identified by differential coexpression analysis, and SH3BP5‐AS1, AC012073.1, AC120114.1, LINC00377, AL133467.1, AC036108.3, and AC020663.2 were involved in the risk model, which had an excellent concordance with the prediction. The pathway analyses showed that immune‐related pathways were relevant to the necroptosis‐related lncRNAs risk model. And the risk score was significantly correlated with immune cell infiltration, as well as the ESTIMATE score. Most notably, the patients of higher risk score were characterized with increased TMB and decreased TIDE score, indicating that these patients showed better immune checkpoint blockade response. Conclusion These findings were conducive to understand the function of necroptosis‐related lncRNAs in BC and provide a potential promising therapeutic strategy for BC.
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Jin M, Zhang Z, Li Y, Teng D, Shi X, Ba J, Chen B, Du J, He L, Lai X, Teng X, Li Y, Chi H, Liao E, Liu C, Liu L, Qin G, Qin Y, Quan H, Shi B, Sun H, Tang X, Tong N, Wang G, Zhang JA, Wang Y, Xue Y, Yan L, Yang J, Yang L, Yao Y, Ye Z, Zhang Q, Zhang L, Zhu J, Zhu M, Ning G, Mu Y, Zhao J, Teng W, Shan Z. U-Shaped Associations Between Urinary Iodine Concentration and the Prevalence of Metabolic Disorders: A Cross-Sectional Study. Thyroid 2020; 30:1053-1065. [PMID: 32188373 DOI: 10.1089/thy.2019.0516] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background: Iodine is important in both thyroid function and human metabolism. Studies have explored the effect of iodine on metabolic disorders through thyroid function. This study aimed to investigate the relationship between iodine status and metabolic disorders, such as metabolic syndrome (MetS), hypertension, impaired glucose metabolism, central obesity, and dyslipidemia. Methods: A total of 51,795 subjects aged ≥18 years from the TIDE (Thyroid Disorders, Iodine Status and Diabetes, a national epidemiological cross-sectional study) program were included. The prevalence of metabolic disorders and its related diseases was calculated based on the level of urinary iodine concentrations (UICs) using the chi-square method. To further explore whether the prevalence was associated with UIC, quadratic and UIC-stratified logistic regression models were used. Results: The prevalence of metabolic disorders as a function of UIC was found to be U-shaped with a lower prevalence of 76.0% at an UIC of 300-499 μg/L. Participants with an UIC of 300-499 μg/L showed an association with metabolic disorders (odds ratio [OR] = 0.857, 95% confidence interval [CI 0.796-0.922]) and hypertension (OR = 0.873 [CI 0.814-0.936]). An UIC of 300-799 μg/L was found to be associated with the occurrence of MetS and impaired glucose tolerance. An UIC of 500-799 μg/L was associated with the occurrence of prediabetes (OR = 0.883 [CI 0.797-0.978]). An UIC of ≥300 μg/L was associated with the occurrence of hypertriglyceridemia, hypercholesterolemia, and high levels of low-density lipoprotein cholesterol. Furthermore, an UIC of <100 μg/L showed an association with hypertension (OR = 1.097 [CI 1.035-1.162]) and hypercholesterolemia (OR = 1.178 [CI 1.117-1.242]). Conclusions: The association between UICs in adults and metabolic disorders and its related diseases is U-shaped. The association between UIC and metabolic disorders disappears in cases of iodine deficiency (<100 μg/L) or excess (≥500 μg/L).
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Zhang F, Li Y, Yu X, Wang X, Lin Z, Song B, Tian L, Feng C, Shan Z, Teng W. The Relationship and Gender Disparity Between Thyroid Nodules and Metabolic Syndrome Components Based on a Recent Nationwide Cross-Sectional Study and Meta-Analysis. Front Endocrinol (Lausanne) 2021; 12:736972. [PMID: 34621243 PMCID: PMC8490942 DOI: 10.3389/fendo.2021.736972] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/30/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MetS) has a potential connection with thyroid disease, but its relationship with thyroid nodules (TNs) is still controversial. This study aims to clarify the relationship between MetS and TNs, and this relationship in the subgroup of gender. METHODS The recent nationwide cross-sectional study called Thyroid Disorders, Iodine Status, and Diabetes Epidemiological survey provided the newest data on the relationship between MetS and TNs from China and included 56,729 subjects. We also researched related literature in PubMed, EMBASE, Cochrane Library, and MEDLINE until Oct 30, 2020, in order to perform a meta-analysis. The relevant articles were examined, and the eligible studies were included to assess the association between MetS and TNs. RESULTS The meta-analysis included 15 studies (involving 468,845 subjects). Of these, 14 studies were from the databases, and one study was this cross-sectional data. The meta-analysis showed that TNs were associated with a higher prevalence of MetS (OR=1.87, 95% CI: 1.44-2.45) and the components of MetS, including central obesity (OR=1.41, 95% CI: 1.15-1.72), hypertriglyceridemia (OR=1.13, 95% CI: 1.10-1.15), low high-density lipoprotein cholesterolemia (OR=1.11, 95% CI: 1.02-1.20), abnormal blood pressure (OR=1.68, 95% CI: 1.62-1.75), and hyperglycemia (OR=1.59, 95% CI: 1.46-1.74). Central obesity displayed gender differences, being a risk factor in males (OR=1.38, 95% CI: 1.02-1.86) but not in females (OR=1.47, 95% CI: 0.97-2.23). CONCLUSION TNs were indeed associated with a higher prevalence of MetS. In addition, its component diseases, such as central obesity, hypertriglyceridemia, abnormal blood pressure, and hyperglycemia, were also associated with TNs. Females with MetS or its components had a higher risk of suffering from TNs than males.
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Etard C, Joshi S, Stegmaier J, Mikut R, Strähle U. Tracking of Indels by DEcomposition is a Simple and Effective Method to Assess Efficiency of Guide RNAs in Zebrafish. Zebrafish 2017; 14:586-588. [PMID: 28767326 DOI: 10.1089/zeb.2017.1454] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A bottleneck in CRISPR/Cas9 genome editing is variable efficiencies of in silico-designed gRNAs. We evaluated the sensitivity of the TIDE method (Tracking of Indels by DEcomposition) introduced by Brinkman et al. in 2014 for assessing the cutting efficiencies of gRNAs in zebrafish. We show that this simple method, which involves bulk polymerase chain reaction amplification and Sanger sequencing, is highly effective in tracking well-performing gRNAs in pools of genomic DNA derived from injected embryos. The method is equally effective for tracing INDELs in heterozygotes.
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Pallocca M, Angeli D, Palombo F, Sperati F, Milella M, Goeman F, De Nicola F, Fanciulli M, Nisticò P, Quintarelli C, Ciliberto G. Combinations of immuno-checkpoint inhibitors predictive biomarkers only marginally improve their individual accuracy. J Transl Med 2019; 17:131. [PMID: 31014354 PMCID: PMC6480695 DOI: 10.1186/s12967-019-1865-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/28/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND There are no accepted universal biomarkers capable to accurately predict response to immuno-checkpoint inhibitors (ICI). Although recent literature has been flooded with studies on ICI predictive biomarkers, available data show that currently approved companion diagnostics either leave out many possible responders, as in the case of PD-L1 testing for first-line metastatic lung cancer, or apply to a small subset of patients, such as the recently approved treatment for microsatellite instability-high or mismatch repair deficiency tumors. In this study, we conducted a survey of the available data on ICI trials with matched genomic or transcriptomic datasets in order to cross-validate the proposed biomarkers, to assess whether their prediction power was confirmed and, mainly, to investigate if their combination was able to generate a better predictive tool. METHODS We extracted clinical information and sequencing data details from publicly available datasets, along with a list of possible biomarkers obtained from the recent literature. After an operation of data harmonization, we validated the performance of all the biomarkers taken individually. Furthermore, we tested two strategies to combine the best performing biomarkers in order to improve their predictive value. RESULTS When considered individually, some of the biomarkers, such as the ImmunoPhenoScore, and the IFN-γ signature, did not confirm their originally proposed predictive power. The best absolute scoring biomarkers are TIDE, one of the ICB resistance signatures and CTLA4 with a mean AUC > 0.66. Among the combinations tested, generalized linear models showed the best performance with an AUC of 0.78. CONCLUSIONS We confirmed that the available biomarkers, taken individually, fail to provide a satisfactory predictive value. Unfortunately, also combination of some of them only provides marginal improvements. Hence, in order to generate a more robust way to predict ICI efficacy it is necessary to analyze and combine additional biomarkers and interrogate a wider set of clinical data.
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Liu Z, He J, Han J, Yang J, Liao W, Chen N. m6A Regulators Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization In Nasopharyngeal Carcinoma. Front Immunol 2022; 12:762243. [PMID: 35069534 PMCID: PMC8776994 DOI: 10.3389/fimmu.2021.762243] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 12/03/2021] [Indexed: 02/05/2023] Open
Abstract
Background The role of RNA N6-methyladenosine (m6A) modification in tumor progression and metastasis has been demonstrated. Nonetheless, potential biological function of m6A modification patterns in nasopharyngeal carcinoma (NPC) remains unknown. Methods The m6A modification patterns were comprehensively evaluated based on 26 m6A regulators in NPC, and m6A subtype and also m6A score were identified and systematically correlated with representative tumor characteristics. Results Two distinct m6A subtypes were determined and were highly consistent with immune activated and immune suppressed phenotypes, respectively. More representative m6A scores of individual tumors could predict tumor microenvironment (TME) infiltration, mRNA based stemness index (mRNAsi), EBV gene expression, genetic variation, and prognosis of NPC patients. Low m6A score, characterized by activation of immunity and suppression of mRNAsi and EBV gene, indicated an activated TME phenotype and better PFS and also lower risk of recurrence and metastasis. High m6A score, characterized by activation of Wnt and NF-κB signaling pathway and lack of effective immune infiltration, indicated an immune suppressed TME phenotype and poorer survival. Low m6A score was also correlated with increased tumor mutation burden (TMB) and better response to immunotherapy, and vice versa. A significant therapeutic advantage in patients with low m6A score was confirmed with an anti-PDL1 immunotherapy cohort. Conclusions m6A patterns played an important role in the diversity and complexity of TME. m6A score could be used to evaluate the m6A pattern of individual tumor to enhance our understanding of TME infiltration and guide more effective immunotherapy strategies.
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Zhang F, Teng D, Tong N, Wang G, Li Y, Yu X, Shan Z, Teng W. Gender-Specific Associations Between Metabolic Disorders and Thyroid Nodules: A Cross-Sectional Population-Based Study from China. Thyroid 2022; 32:571-580. [PMID: 35317620 DOI: 10.1089/thy.2021.0686] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background: Metabolic disorders (MDs) and the metabolic syndrome (MetS) may be associated with thyroid diseases. The aim of this study was to investigate the relationship between MDs and various types of thyroid nodules (TNs), according to gender. Methods: We analyzed cross-sectional data from the Thyroid Disorders, Iodine Status, and Diabetes Epidemiological (TIDE) survey in China. A total of 56,729 subjects ≥18 years of age were included. Thyroid gland morphology was assessed by thyroid standardized ultrasonography. A multivariate logistic regression model was used to explore the odds ratio (OR) and confidence intervals [CIs] for any associations between MDs and TNs. Subgroup analyses were conducted according to gender and TN type (solitary, S-TN; multiple, M-TNs). Results: The prevalence of TNs was increased in several MDs, and was higher in women than men regardless of whether they suffered from MDs (22.0%, CI [21.6-22.5%] vs. 15.7%, CI [15.3-16.7%], p < 0.001). TNs were associated with the presence of MDs (OR = 1.189, CI [1.107-1.278], p < 0.001), hypercholesterolemia (OR = 1.235, CI [1.177-1.296], p < 0.001), high low-density lipoprotein cholesterol (LDL-C; OR = 1.249, CI [1.186-1.316], p < 0.001), and hyperuricemia (OR = 1.206, CI [1.126-1.293], p < 0.001). MDs and MetS were, respectively, significantly associated with TNs, S-TNs, and M-TNs in men, while MDs were significantly associated with the three TN profiles in women. With respect to dyslipidemia, hypercholesterolemia and high LDL-C had the strongest association with TNs, whereas hypertriglyceridemia had no effect. Conclusions: TNs (especially M-TNs) may be associated with MDs and their various components, and there appear to be some gender-specific associations.
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Huang X, Liu Y, Qian C, Shen Q, Wu M, Zhu B, Feng Y. CHSY3 promotes proliferation and migration in gastric cancer and is associated with immune infiltration. J Transl Med 2023; 21:474. [PMID: 37461041 PMCID: PMC10351153 DOI: 10.1186/s12967-023-04333-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/09/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The glycosyltransferase CHSY3 is a CHSY family member, yet its importance in the context of gastric cancer development remains incompletely understood. The present study was thus developed to explore the mechanistic importance of CHSY3 as a regulator of gastric cancer. METHODS Expression of CHSY3 was verified by TCGA, GEO and HPA databases. Kaplan-Meier curve, ROC, univariate cox, multivariate cox, and nomogram models were used to verify the prognostic impact and predictive value of CHSY3. KEGG and GO methods were used to identify signaling pathways associated with CHSY3. TIDE and IPS scores were used to assess the immunotherapeutic value of CHSY3. WGCNA, Cytoscape constructs PPI networks and random forest models to identify key Hub genes. Finally, qRT-PCR and immunohistochemical staining were performed to verify CHSY3 expression in clinical specimens. The ability of CHSY3 to regulate tumor was further assessed by CCK-8 assay and cloning assay, EDU assay, migration assay, invasion assay, and xenograft tumor model analysis. RESULTS The expression of CHSY3 was discovered to be abnormally upregulated in GC tissues through TCGA, GEO, and HPA databases, and the expression of CHSY3 was associated with poor prognosis in GC patients. Correlation analysis and Cox regression analysis revealed higher CHSY3 expression in higher T staging, an independent prognostic factor for GC. Moreover, elevated expression of CHSY3 was found to reduce the benefit of immunotherapy as assessed by the TIDE score and IPS score. Then, utilizing WGCNA, the PPI network constructed by Cytoscape, and random forest model, the Hub genes of COL5A2, POSTN, COL1A1, and FN1 associated with immunity were screened. Finally, the expression of CHSY3 in GC tissues was verified by qRT-PCR and immunohistochemical staining. Moreover, the expression of CHSY3 was further demonstrated by in vivo and in vitro experiments to promote the proliferation, migration, and invasive ability of GC. CONCLUSIONS The results of this study suggest that CHSY3 is an important regulator of gastric cancer progression, highlighting its promise as a therapeutic target for gastric cancer.
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Jacobsen T, Liao C, Beisel CL. The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs. FEMS Microbiol Lett 2020; 366:5475644. [PMID: 31004485 DOI: 10.1093/femsle/fnz085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/19/2019] [Indexed: 12/19/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) nuclease Acidaminococcus sp. Cas12a (AsCas12a, also known as AsCpf1) has become a popular alternative to Cas9 for genome editing and other applications. AsCas12a has been associated with a TTTV protospacer-adjacent motif (PAM) as part of target recognition. Using a cell-free transcription-translation (TXTL)-based PAM screen, we discovered that AsCas12a can also recognize GTTV and, to a lesser degree, GCTV motifs. Validation experiments involving DNA cleavage in TXTL, plasmid clearance in Escherichia coli, and indel formation in mammalian cells showed that AsCas12a was able to recognize these motifs, with the GTTV motif resulting in higher cleavage efficiency compared to the GCTV motif. We also observed that the -5 position influenced the activity of DNA cleavage in TXTL and in E. coli, with a C at this position resulting in the lowest activity. Together, these results show that wild-type AsCas12a can recognize non-canonical GTTV and GCTV motifs and exemplify why the range of PAMs recognized by Cas nucleases are poorly captured with a consensus sequence.
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Research Support, U.S. Gov't, Non-P.H.S. |
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Abstract
The targeted nuclease revolution (ZFN, TALEN, and CRISPR/Cas9) has led to a myriad of reports describing genotyping methodologies for genome edited founders (F0-crispants) and their offspring (F1). As such, choosing a specific genotyping methodology for your Xenopus CRISPR/Cas9 experiments can be challenging. In this chapter we will discuss, with emphasis on Xenopus tropicalis (X. tropicalis), different methods for assessing genome editing efficiencies within F0 CRISPR/Cas9 founders and for identification of their hetero-, compound hetero-, and homozygous mutant F1 offspring. For F0 crispants, we will provide the protocols and the respective (dis)advantages of genotyping with heteroduplex mobility assay (HMA), subclone Sanger sequencing, and sequence trace decomposition. Furthermore, we provide a previously unpublished pipe-line for rapid genotyping of F1 offspring-high resolution melting analysis (HRMA) and sequence trace decomposition-procured from breeding with F0 crispants. As such, we report here the current state-of-the-art cost- and time-effective approaches to perform genotyping of CRISPR/Cas9 experiments for the Xenopus tropicalis researcher.
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Wang Q, Zhang X, Du K, Wu X, Zhou Y, Chen D, Zeng L. Machine learning identifies characteristics molecules of cancer associated fibroblasts significantly correlated with the prognosis, immunotherapy response and immune microenvironment in lung adenocarcinoma. Front Oncol 2022; 12:1059253. [PMID: 36439484 PMCID: PMC9682016 DOI: 10.3389/fonc.2022.1059253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/24/2022] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a highly lethal disease with a dramatic pro-fibrocytic response. Cancer-associated fibroblasts (CAFs) have been reported to play a key role in lung adenocarcinoma. METHODS Marker genes of CAFs were obtained from the Cell Marker website. Single sample gene set enrichment analysis (ssGSEA) was used for CAFs quantification. R and GraphPad Prism software were utilized for all analysis. Quantitative real-time PCR (qRT-PCR) was utilized to detect the RNA level of specific molecules. RESULTS Based on the ssGSEA algorithm and obtained CAFs markers, the LUAD patients with low- and high-CAFs infiltration were successfully identified, which had different response patterns to immunotherapy. Through the machine learning algorithm - LASSO logistic regression, we identified 44 characteristic molecules of CAFs. Furthermore, a prognosis signature consisting of seven characteristic genes was established, which showed great prognosis prediction ability. Additionally, we found that patients in the low-risk group might have better outcomes when receiving immunotherapy of PD-1, but not CTLA4. Also, the biological enrichment analysis revealed that immune response-related pathways were significantly associated with CAFs infiltration. Meanwhile, we investigated the underlying biological and microenvironment difference in patients with high- and low-risk groups. Finally, we identified that AMPD1 might be a novel target for LUAD immunotherapy. Patients with a high level of AMPD1 were correlated with worse responses to immunotherapy. Moreover, immunohistochemistry showed that the protein level of AMPD1 was higher in lung cancer. Results of qRT-PCR demonstrated that AMPD1 was upregulated in A549 cells compared with BEAS-2B. Meanwhile, we found that the knockdown of AMPD4 can significantly reduce the expression of CTLA4 and PDCD1, but not CD274 and PDCD1LG2. CONCLUSION We comprehensively explored the role of CAFs and its characteristics molecules in LUAD immunotherapy and developed an effective signature to indicate patients prognosis and immunotherapy response. Moreover, AMPD1 was identified as a novel target for lung cancer immunotherapy.
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Song B, Lu C, Teng D, Shan Z, Teng W. Association between different metabolic phenotypes of obesity and thyroid disorders among Chinese adults: a nationwide cross-sectional study. Front Endocrinol (Lausanne) 2023; 14:1158013. [PMID: 37152970 PMCID: PMC10162017 DOI: 10.3389/fendo.2023.1158013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Background Increased body mass index (BMI) and metabolic abnormalities both have potential associations with thyroid disease. The aim of this study was to investigate the correlation between different metabolic phenotypes of obesity and thyroid disorders using nationwide data from China. Methods Data were collected from a cross-sectional survey called the Thyroid Disorders, Iodine Status, and Diabetes Epidemiological Survey conducted between 2015 and 2017 in China. A total of 69007 subjects aged 18 years or older were defined and divided into six groups on the basis of BMI and metabolic health status: metabolically healthy normal weight (MHNW), metabolically unhealthy normal weight (MUNW), metabolically healthy overweight (MHOW), metabolically unhealthy overweight (MUOW), metabolically healthy obesity (MHO), and metabolically unhealthy obesity (MUO). We estimated the odds ratios (ORs) and confidence intervals [CIs] for different thyroid disorders according to metabolic phenotypes using multivariate logistic regression models. Results In our study, we found that the prevalence of subclinical hypothyroidism was almost as high in the MUNW group as in the MUO group, the prevalence of overt hyperthyroidism was highest in the MUNW group and Graves' disease was highest in the MHO group. Our results also suggested that the prevalence of goiter and thyroid nodules increased with increased BMI values and that the MUO group had the highest incidence. Multivariate logistic regression analysis indicated that subjects with unhealthy metabolic phenotypes (MUNW, MUOW, and MUO) all had an increased risk of subclinical hypothyroidism, regardless of their BMI. MUNW subjects had an approximately 1.6-fold higher risk of overt hyperthyroidism and a 1.8-fold higher risk of Graves' disease than their metabolically healthy counterparts (MHNW). The present study also demonstrated that the MUO group had the highest risk of goiter and thyroid nodules among the metabolic phenotypes of obesity. Conclusion Based on our study, we found that metabolic abnormalities and obesity play different roles in various thyroid diseases. Metabolically unhealthy individuals, both with and without obesity, have a higher risk of thyroid disorders than metabolically healthy individuals without obesity.
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Yu W, Liu F, Lei Q, Wu P, Yang L, Zhang Y. Identification of Key Pathways and Genes Related to Immunotherapy Resistance of LUAD Based on WGCNA Analysis. Front Oncol 2022; 11:814014. [PMID: 35071018 PMCID: PMC8770266 DOI: 10.3389/fonc.2021.814014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 01/15/2023] Open
Abstract
Immunotherapy resistance is a major barrier in the application of immune checkpoint inhibitors (ICI) in lung adenocarcinoma (LUAD) patients. Although recent studies have found several mechanisms and potential genes responsible for immunotherapy resistance, ways to solve this problem are still lacking. Tumor immune dysfunction and exclusion (TIDE) algorithm is a newly developed method to calculate potential regulators and indicators of ICI resistance. In this article, we combined TIDE and weighted gene co-expression network analysis (WGCNA) to screen potential modules and hub genes that are highly associated with immunotherapy resistance using the Cancer Genome Atlas (TCGA) dataset of LUAD patients. We identified 45 gene co-expression modules, and the pink module was most correlated with TIDE score and other immunosuppressive features. After considering the potential factors in immunotherapy resistance, we found that the pink module was also highly related to cancer stemness. Further analysis showed enriched immunosuppressive cells in the extracellular matrix (ECM), immunotherapy resistance indicators, and common cancer-related signaling pathways in the pink module. Seven hub genes in the pink module were shown to be significantly upregulated in tumor tissues compared with normal lung tissue, and were related to poor survival of LUAD patients. Among them, THY1 was the gene most associated with TIDE score, a gene highly related to suppressive immune states, and was shown to be strongly expressed in late-stage patients. Immunohistochemistry (IHC) results demonstrated that THY1 level was higher in the progressive disease (PD) group of LUAD patients receiving a PD-1 monoclonal antibody (mAb) and positively correlated with SOX9. Collectively, we identified that THY1 could be a critical biomarker in predicting ICI efficiency and a potential target for avoiding tumor immunotherapy resistance.
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Zhang R, Wang H, Xiao J, Lu J, Li M, Zhou Y, Sun H, Liu L, Huang T, Zhao Q. CAV1 Impacts the Tumor Immune Microenvironment and Has Potential Value of Predicting Response to Immunotherapy in Esophageal Cancer. DNA Cell Biol 2023; 42:27-42. [PMID: 36638349 DOI: 10.1089/dna.2022.0025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Caveolin-1 (CAV1) is one of the members of the caveolae, and the role of CAV1 in esophageal cancer (ESCA) is not completely clear. In this study, we found that expression of CAV1 was downregulated in ESCA in The Cancer Genome Atlas and the Genotype-Tissue Expression (GTEx) database and we also use immunohistochemistry of tissue microarray for verification. Then, we used bioinformatics methods to investigate the prognostic value of CAV1, influence on immune cell infiltration in tumor microenvironment (TME) and responding to immunotherapy in ESCA. Our result indicated that CAV1 designs an inflamed TME in ESCA based on the evidence that CAV1 positively correlated with immunomodulators, immune score, stomal score, cancer immunity cycles, tumor-infiltrating immune cells, T cell inflamed score, and immune checkpoints. Immunophenoscore, Tumor Immune Dysfunction and Exclusion algorithms, and the mutation analysis show that the downregulated CAV1 expression indicated higher tumor mutation burden and higher rate of response to immune checkpoint inhibitors (ICIs) in the low-expression group. In a word, our study demonstrated the impact of CAV1 to the TME in ESCA and it may be a new target for ESCA immunotherapy. In addition, the expression of CAV1 can predict the clinical response to ICIs, which may provide clinical treatment guidance.
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Lomov NA, Viushkov VS, Petrenko AP, Syrkina MS, Rubtsov MA. [Methods of Evaluating the Efficiency of CRISPR/Cas Genome Editing]. Mol Biol (Mosk) 2019; 53:982-997. [PMID: 31876277 DOI: 10.1134/s0026898419060119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/04/2019] [Indexed: 11/23/2022]
Abstract
The CRISPR/Cas system is currently widely used for genome editing. The procedure of genome editing includes two necessary steps: (i) searching for the most effective guide RNA, and (ii) analyzing clones for presence of the desired mutation. This review presents the methods used to assess the efficiency of the CRISPR/Cas system and to confirm mutation in the target locus and discusses their advantages and disadvantages. It aims to provide information that could help researchers to choose a technique most appropriate for their specific tasks and available resources.
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Kang H, Zhu X, Cui Y, Xiong Z, Zong W, Bao Y, Jia P. A Comprehensive Benchmark of Transcriptomic Biomarkers for Immune Checkpoint Blockades. Cancers (Basel) 2023; 15:4094. [PMID: 37627121 PMCID: PMC10452274 DOI: 10.3390/cancers15164094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Immune checkpoint blockades (ICBs) have revolutionized cancer therapy by inducing durable clinical responses, but only a small percentage of patients can benefit from ICB treatments. Many studies have established various biomarkers to predict ICB responses. However, different biomarkers were found with diverse performances in practice, and a timely and unbiased assessment has yet to be conducted due to the complexity of ICB-related studies and trials. In this study, we manually curated 29 published datasets with matched transcriptome and clinical data from more than 1400 patients, and uniformly preprocessed these datasets for further analyses. In addition, we collected 39 sets of transcriptomic biomarkers, and based on the nature of the corresponding computational methods, we categorized them into the gene-set-like group (with the self-contained design and the competitive design, respectively) and the deconvolution-like group. Next, we investigated the correlations and patterns of these biomarkers and utilized a standardized workflow to systematically evaluate their performance in predicting ICB responses and survival statuses across different datasets, cancer types, antibodies, biopsy times, and combinatory treatments. In our benchmark, most biomarkers showed poor performance in terms of stability and robustness across different datasets. Two scores (TIDE and CYT) had a competitive performance for ICB response prediction, and two others (PASS-ON and EIGS_ssGSEA) showed the best association with clinical outcome. Finally, we developed ICB-Portal to host the datasets, biomarkers, and benchmark results and to implement the computational methods for researchers to test their custom biomarkers. Our work provided valuable resources and a one-stop solution to facilitate ICB-related research.
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Yao J, Liang Z, Duan L, G Y, Liu J, An G. Construction of a novel immune response prediction signature to predict the efficacy of immune checkpoint inhibitors in clear cell renal cell carcinoma patients. Heliyon 2023; 9:e15925. [PMID: 37484396 PMCID: PMC10360603 DOI: 10.1016/j.heliyon.2023.e15925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 07/25/2023] Open
Abstract
Background Immune checkpoint inhibitor (ICI) treatment has enhanced survival outcomes in clear cell renal cell carcinoma (ccRCC) patients. Nevertheless, the effectiveness of immunotherapy in ccRCC patients is restricted and we intended to develop and characterize an immune response prediction signature (IRPS) to forecast the efficacy of immunotherapy. Methods RNA-seq expression profile and clinicopathologic characteristics of 539 kidney cancer and 72 patients with normal specimens, were downloaded from the Cancer Genome Atlas (TCGA) database, while the Gene Expression Omnibus (GEO) database was used as the validation set, which included 24 ccRCC samples. Utilization of the TCGA data and immune genes databases (ImmPort and the InnateDB), we explored through Weighted Gene Co-expression Network Analysis (WGCNA), along with Least Absolute Shrinkage and Selection Operator method (LASSO), and constructed an IRPS for kidney cancer patients. GSEA and CIBERSORT were performed to declare the molecular and immunologic mechanism underlying the predictive value of IRPS. The Human Protein Atlas (HPA) was deployed to verify the protein expressions of IRPS genes. Tumor immune dysfunction and exclusion (TIDE) score and immunophenoscore (IPS) were computed to determine the risk of immune escape and value the discrimination of IRPS. A ccRCC cohort with anti-PD-1 therapy was obtained as an external validation data set to verify the predictive value of IRPS. Results We constructed a 10 gene signature related to the prognosis and immune response of ccRCC patients. Considering the IRPS risk score, patients were split into high and low risk groups. Patients with high risk in the TCGA cohort tended towards advanced tumor stage and grade with poor prognosis (p < 0.001), which was validated in GEO database (p = 0.004). High-risk group tumors were related with lower PD-L1 expression, higher TMB, higher MSIsensor score, lower IPS, higher TIDE score, and enriched Treg cells, which might be the potential mechanism of immune dysfunction and exclusion. Patients in the IRPS low risk group had better PFS (HR:0.73; 95% CI: 0.54-1.0; P = 0.047). Conclusion A novel biomarker of IRPS was constructed to predict the benefit of immunotherapy, which might lead to more individualized prognoses and tailored therapy for kidney cancer patients.
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Aoki K, Yamasaki M, Umezono R, Hamamoto T, Kamachi Y. Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis. Cells 2024; 13:261. [PMID: 38334653 PMCID: PMC10854981 DOI: 10.3390/cells13030261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/28/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024] Open
Abstract
Successful genome editing depends on the cleavage efficiency of programmable nucleases (PNs) such as the CRISPR-Cas system. Various methods have been developed to assess the efficiency of PNs, most of which estimate the occurrence of indels caused by PN-induced double-strand breaks. In these methods, PN genomic target sites are amplified through PCR, and the resulting PCR products are subsequently analyzed using Sanger sequencing, high-throughput sequencing, or mismatch detection assays. Among these methods, Sanger sequencing of PCR products followed by indel analysis using online web tools has gained popularity due to its user-friendly nature. This approach estimates indel frequencies by computationally analyzing sequencing trace data. However, the accuracy of these computational tools remains uncertain. In this study, we compared the performance of four web tools, TIDE, ICE, DECODR, and SeqScreener, using artificial sequencing templates with predetermined indels. Our results demonstrated that these tools were able to estimate indel frequency with acceptable accuracy when the indels were simple and contained only a few base changes. However, the estimated values became more variable among the tools when the sequencing templates contained more complex indels or knock-in sequences. Moreover, although these tools effectively estimated the net indel sizes, their capability to deconvolute indel sequences exhibited variability with certain limitations. These findings underscore the importance of judiciously selecting and using an appropriate tool with caution, depending on the type of genome editing being performed.
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Zhang F, Zou M, Bai C, Zhu M. Prognostic signature based on S100 calcium-binding protein family members for lung adenocarcinoma and its clinical significance. Comput Methods Biomech Biomed Engin 2024:1-17. [PMID: 39012268 DOI: 10.1080/10255842.2024.2376668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The S100 family proteins (S100s) participate in multiple stages of tumorigenesis and are considered to have potential value as biomarkers for detecting and predicting various cancers. But the role of S100s in lung adenocarcinoma (LUAD) prognosis is elusive. Transcriptional data of LUAD patients were retrieved from TCGA, and relevant literature was extensively reviewed to collect S100 genes. Differential gene expression analysis was performed on the LUAD data, followed by intersection analysis between the differentially expressed genes (DEGs) and S100 genes. Unsupervised consensus clustering analysis identified two clusters. Significant variations in overall survival between the two clusters were shown by Kaplan-Meier analysis. DEGs between the two clusters were analyzed using Lasso regression and univariate/multivariate Cox regression analysis, leading to construction of an 11-gene prognostic signature. The signature exhibited stable and accurate predictive capability in TCGA and GEO datasets. Subsequently, we observed distinct immune cell infiltration, immunotherapy response, and tumor mutation characteristics in high and low-risk groups. Finally, small molecular compounds targeting prognostic genes were screened using CellMiner database, and molecular docking confirmed the binding of AMG-176, Estramustine, and TAK-632 with prognostic genes. In conclusion, we generated a prognostic signature with robust and reliable predictive ability, which may provide guidance for prognosis and treatment of LUAD.
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Lin F, Li H, Liu H, Shen J, Zheng L, Huang S, Chen Y. Identification of lysine lactylation (kla)-related lncRNA signatures using XGBoost to predict prognosis and immune microenvironment in breast cancer patients. Sci Rep 2024; 14:20432. [PMID: 39227722 PMCID: PMC11371909 DOI: 10.1038/s41598-024-71482-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
Breast cancer (BC) stands as a predominant global malignancy, significantly contributing to female mortality. Recently uncovered, histone lysine lactylation (kla) has assumed a crucial role in cancer progression. However, the correlation with lncRNAs remains ambiguous. Scrutinizing lncRNAs associated with Kla not only improves clinical breast cancer management but also establishes a groundwork for antitumor drug development. We procured breast tissue samples, encompassing both normal and cancerous specimens, from The Cancer Genome Atlas (TCGA) database. Utilizing Cox regression and XGBoost methods, we developed a prognostic model using identified kla-related lncRNAs. The model's predictive efficacy underwent validation across training, testing, and the overall cohort. Functional analysis concerning kla-related lncRNAs ensued. We identified and screened 8 kla-related lncRNAs to formulate the risk model. Pathway analysis disclosed the connection between immune-related pathways and the risk model of kla-related lncRNAs. Significantly, the risk scores exhibited a correlation with both immune cell infiltration and immune function, indicating a clear association. Noteworthy is the observation that patients with elevated risk scores demonstrated an increased tumor mutation burden (TMB) and decreased tumor immune dysfunction and exclusion (TIDE) scores, suggesting heightened responses to immune checkpoint blockade. Our study uncovers a potential link between Kla-related lncRNAs and BC, providing innovative therapeutic guidelines for BC management.
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Liu Y, Han T, Wu J, Zhou J, Guo J, Miao R, Xu Z, Xing Y, Bai Y, Hu D. SPOCK1, as a potential prognostic and therapeutic biomarker for lung adenocarcinoma, is associated with epithelial-mesenchymal transition and immune evasion. J Transl Med 2023; 21:909. [PMID: 38087364 PMCID: PMC10717042 DOI: 10.1186/s12967-023-04616-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/11/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The occurrence of epithelial-mesenchymal transition (EMT) and immune evasion is considered to contribute to poor prognosis in lung adenocarcinoma (LUAD). Therefore, this study aims to explore the key oncogenes that promote EMT and immune evasion and reveal the expression patterns, prognostic value, and potential biological functions. METHODS Firstly, we identified gene modules associated with EMT and Tumor Immune Dysfunction and Exclusion (TIDE) through weighted gene co-expression network analysis (WGCNA). Next, we utilized differential analysis and machine learning to identify the key genes and validate them. Moreover, we analyzed the correlation between key genes and tumor microenvironment remodeling, drug sensitivity, as well as mutation frequency. Furthermore, we explored and validated their malignant biological characteristics through in vitro experiments and clinical samples. Finally, potential drugs for LUAD were screened based on CMap and validated through experiments. RESULTS Firstly, WGCNA analysis revealed that red and green modules were highly correlated with EMT and TIDE. Among them, upregulated expression of SPOCK1 was observed in lung adenocarcinoma tissues and was associated with poor prognosis. Additionally, patients in the high SPOCK1 group showed more activation of malignant oncogenic pathways, higher infiltration of immunosuppressive components, and a higher frequency of mutations. The knockdown of SPOCK1 suppressed invasion and metastasis capabilities of lung adenocarcinoma cells, and the high expression of SPOCK1 was associated with low infiltration of CD8+ T cells. Therapeutic aspects, SPOCK1 can be a candidate indicator for drug sensitivity and CMap showed that VER-155008 was the drug candidate with the largest perturbation effect on the SPOCK1 expression profile. In vitro and in vivo experiments validated the cancer-inhibitory effect of VER-155008 in LUAD. CONCLUSION This study revealed through comprehensive bioinformatics analysis and experimental analysis that SPOCK1 can promote EMT and immune escape in LUAD, and it may serve as a promising candidate prognostic biomarker and therapeutic target for LUAD.
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Zhou J, Liu J, Yu Y, Nie H, Hong Y, Ning Y, Yang C, Lai J, Wang H, Tang X, Wang F, Zhao Q. Melanoma Cell Adhesion Molecule Plays a Pivotal Role in Proliferation, Migration, Tumor Immune Microenvironment, and Immunotherapy in Colorectal Cancer. Cancer Med 2025; 14:e70740. [PMID: 40042109 PMCID: PMC11880918 DOI: 10.1002/cam4.70740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 02/15/2025] [Accepted: 02/25/2025] [Indexed: 05/12/2025] Open
Abstract
INTRODUCTION MCAM, alternatively referred to as CD146, is an integral membrane glycoprotein belonging to the immunoglobulin superfamily. However, its importance in the tumorigenesis of colorectal cancer is still partially understood. Therefore, this study was designed to investigate the significance of MCAM in colorectal cancer. METHODS MCAM expression was analyzed by TCGA and GEO databases. qRT-PCR and IHC analysis were conducted to validate MCAM expression in patient tissues. The tumor-inhibiting ability of MCAM was further assessed by CCK-8 assay, colony formation assay, and wound-healing assay. qRT-PCR and WB analysis were conducted to evaluate the expression of EMT markers and MMP2/9. qRT-PCR analysis was utilized to detect the polarization status of macrophages. Kaplan-Meier curve, univariate, and multivariate cox analyses were employed to verify the ability of MCAM in prognosis prediction. TIDE scores were used to assess the impact of MCAM on immunotherapy. RESULTS The expression of MCAM was significantly downregulated in CRC, and low MCAM expression revealed poor prognosis in CRC patients. Moreover, MCAM overexpression inhibited the proliferation, migration, and invasive ability of CRC cells. Additionally, MCAM overexpression suppressed N-cadherin and MMP2/9 expression. Furthermore, MCAM impacted M1 macrophage polarization. MCAM is an independent predictor of CRC patient prognosis through Cox regression analysis. Lastly, TIDE score analysis indicated that elevated expression of MCAM increased immunotherapy efficacy. CONCLUSION The findings of this research suggest that MCAM impacts M1 macrophage polarization and enhances immunotherapy efficacy, underscoring its potential as a therapeutic target for colorectal cancer.
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