The Roles of Zinc Finger Proteins in Colorectal Cancer

DNA Methylation Biomarker Discovery for Colorectal Cancer Diagnosis Assistance Through Integrated Analysis

Objective

This study aimed to identify biomarkers for colorectal cancer (CRC) with representative gene functions and high classification accuracy in tissue and blood samples.

Methods

We integrated CRC DNA methylation profiles from The Cancer Genome Atlas and comorbidity patterns of CRC to select biomarker candidates. We clustered these candidates near the promoter regions into multiple functional groups based on their functional annotations. To validate the selected biomarkers, we applied 3 machine learning techniques to construct models and compare their prediction performances.

Results

The 10 screened genes showed significant methylation differences in both tissue and blood samples. Our test results showed that 3-gene combinations achieved outstanding classification performance. Selecting 3 representative biomarkers from different genetic functional clusters, the combination of ADHFE1, ADAMTS5, and MIR129-2 exhibited the best performance across the 3 prediction models, achieving a Matthews correlation coefficient > .85 and an F1-score of .9.

Conclusions

Using integrated DNA methylation analysis, we identified 3 CRC-related biomarkers with remarkable classification performance. These biomarkers can be used to design a practical clinical toolkit for CRC diagnosis assistance and may also serve as candidate biomarkers for further clinical experiments through liquid biopsies.

Increased ZNF83 is a potential prognostic biomarker and regulates oxidative stress-induced ferroptosis in clear cell renal cell carcinoma

While zinc finger proteins (ZFPs) are known to be crucial in various cellular activities such as gene expression regulation and energy metabolism, their specific roles in tumor progression are not well-documented. This study focuses on Zinc Finger Protein 83 (ZNF83) to explore its impact on clear cell renal cell carcinoma (ccRCC) and assess its viability as a prognostic biomarker. Public datasets were utilized to analyze ZNF83's expression and functions in ccRCC systematically. Further, in vitro and in vivo experiments were conducted to delve deeper into ZNF83's functional role. Techniques like electron microscopy for mitochondrial morphology and ROS level quantification were used to assess ferroptosis. RNA sequencing and metabolomic mass spectrometry were employed to understand ZNF83's role in oxidative stress modulation and ferroptosis resistance. Our findings demonstrated that ZNF83 overexpression significantly enhanced tumor cell survival and proliferation, while ZNF83 knockout suppressed these processes. Under oxidative stress or upon treatment with ferroptosis inducers, ZNF83 expression was markedly upregulated, and the protein predominantly localized to the cell nucleus. Notably, ZNF83 overexpression conferred resistance to ferroptosis, promoting tumor cell survival under ferroptosis-inducing conditions. Conversely, ZNF83 knockout sensitized cells to ferroptosis, increasing tumor cell death. RNA-seq and metabolomic analyses revealed that ZNF83 is intricately involved in the regulation of NRF2, a master regulator of the antioxidant response, and associated signaling pathways. ZNF83 represents a key ferroptosis regulator in ccRCC, serving as both a promising prognostic biomarker and therapeutic target. Targeting ZNF83 may improve treatment strategies for ccRCC patients. KEY MESSAGES: ZNF83 as a crucial regulator of tumor cell survival and proliferation in renal cancer, a novel discovery in the context of renal cancer progression. ZNF83 overexpression confers resistance to ferroptosis, enhancing tumor cell survival under oxidative stress or ferroptosis-inducing conditions. Utilizing both RNA sequencing and metabolomic mass spectrometry, we provide comprehensive insights into the molecular pathways, particularly NRF2-related, regulated by ZNF83 in ccRCC. ZNF83's potential as a novel prognostic biomarker for ccRCC is proposed, offering a new avenue for personalized treatment strategies and improving treatment outcomes for patients.

Integrating Tumor and Organoid DNA Methylation Profiles Reveals Robust Predictors of Chemotherapy Response in Rectal Cancer

Rectal cancer patients display heterogeneous responses to neoadjuvant treatment-including the intensive total neoadjuvant therapy (TNT)-and reliable biomarkers are lacking to guide which tumors will benefit most from these regimens. Here, we profiled DNA methylation in tumor tissue and matched patient-derived organoids (PDOs) from 18 rectal cancer cases (50 total samples), leveraging the Illumina MethylationEPIC array and quality control filters that retained 771,964 CpG sites. Analyses used linear models (for tissue-only or PDO-only) and a joint linear mixed-effects approach (accounting for patient-level random effects) to identify significant CpGs associated with log-transformed FOLFOX IC50. We found that PDOs faithfully recapitulate patient-tumor methylation patterns (Spearman's correlation >0.95 among replicate organoids), and the joint model uncovered 745 CpGs tied to FOLFOX sensitivity, many of which were missed in tissue-only analyses. Differentially methylated regions reinforced that broader epigenetic blocks near TSS or enhancer regions may modulate chemo-resistance, while pathway enrichment pinpointed focal adhesion, ECM-receptor interaction, calcium signaling, and folate metabolism as key processes. A methylation risk score derived from these CpGs significantly predicted progression-free survival in an independent colorectal cancer cohort (p=0.019), outperforming single-sample-based signatures. These findings suggest that combining methylation profiles from both tumors and PDOs can expose robust epigenetic drivers of therapy response, aiding the development of clinically actionable biomarkers for rectal cancer TNT.

snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses

Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, long-term monitoring for prognosis determination necessitates extended preservation of tissue samples using formalin-fixed and paraffin-embedded (FFPE) treatments, which can cause substantial RNA degradation, presenting challenges to single-cell or single-nucleus sequencing. In this study, employing snRandom-seq, a single-nucleus RNA sequencing (snRNA-seq) technology specifically for FFPE samples, we tested multiple lesion samples from 18 distinctive colorectal cancer liver metastasis cases with diverse prognostic outcomes that have been preserved for at least three years (mostly over five years). The process yielded expression data from 82,285 cells. The high-quality snRNA-seq data demonstrate the feasibility of single-nucleus sequencing in long-term preserved FFPE samples, offering potential insights into the heterogeneity between different prognoses of colorectal cancer liver metastases, and the relationship between the heterogeneity within different lesions of the same patient and prognosis.

Classification of colorectal cancer patients based on serum micronutrients: An exploratory investigation

BACKGROUND

Colorectal cancer (CRC) is a growing global health challenge with a multifactorial etiology encompassing genetic susceptibility, nutrition, and inflammation in the bowel.

OBJECTIVE

To examine micronutrient status in CRC patients undergoing CRC resection.

DESIGN

We performed a case-control study including 13 consecutive CRC patients and 10 healthy controls (CTRL) comparing the serum levels of 29 micronutrients, namely Copper, Zinc, Selenium, Chromium, Manganese, Carnitine, Choline, Inositol, Methylmalonic acid (MMA), Vitamin (Vit) B1, Vit B2, Vit B3, Vit B5, Vit B6, Vit C, Vit A, Vit D3, Vit E, Vit K1, Vit K2 and the amino acids Serine, Valine, Leucine, Isoleucine, Asparagine, Glutamine, Arginine, Citrulline and Cysteine.

RESULTS

After considering the effect of age and sex, copper, arginine, and cysteine were increased, while zinc, selenium, chromium, Vit B1, Vit K1, and Vit A were decreased in CRC patients in comparison with CTRL. Zinc levels perfectly predicted the diagnosis of CRC, and were associated with lymph nodes (pN), of the pTNM staging. Copper levels in serum were strongly associated with the pathological pTNM staging of CRC.

CONCLUSION

Though this is a preliminary study that needs confirmation with a larger longitudinal cohort, our results show that serum micronutrients are linked to tumor growth, likely caused by increased demand from tumor tissue associated with an aberrant cell proliferation and changes in the antioxidant function.

CD73 restrains mutant β-catenin oncogenic activity in endometrial carcinomas

Missense mutations in exon 3 of CTNNB1, the gene encoding β-catenin, are associated with poor outcomes in endometrial carcinomas (EC). Clinically, CTNNB1 mutation status has been difficult to use as a predictive biomarker as β-catenin oncogenic activity is modified by other factors, and these determinants are unknown. Here we reveal that CD73 restrains the oncogenic activity of exon 3 β-catenin mutants, and its loss associates with recurrence. Using 7 patient-specific mutants, with genetic deletion or ectopic expression of CD73, we show that CD73 loss increases β-catenin-TCF/LEF transcriptional activity. In cells lacking CD73, membrane levels of mutant β-catenin decreased which corresponded with increased levels of nuclear and chromatin-bound mutant β-catenin. These results suggest CD73 sequesters mutant β-catenin to the membrane to limit its oncogenic activity. Adenosine A1 receptor deletion phenocopied increased β-catenin-TCF/LEF activity seen with NT5E deletion, suggesting that the effect of CD73 loss on mutant β-catenin is mediated via attenuation of adenosine receptor signaling. RNA-seq analyses revealed that NT5E deletion alone drives pro-tumor Wnt/β-catenin gene expression and, with CD73 loss, β-catenin mutants dysregulate zinc-finger and non-coding RNA gene expression. We identify CD73 as a novel regulator of oncogenic β-catenin and help explain variability in patient outcomes in CTNNB1 mutant EC.

Exchangeable Copper Excess and Zinc Deficiency in the Serum of Patients with Colorectal Cancer

Copper (Cu) and Zinc (Zn) are altered in colorectal cancer (CRC) but their association with the clinical classification of the tumor has not been fully explored. To examine the association of Cu and Zn homeostasis in the onset and severity of CRC, we performed an exploratory case-control study comparing the serum levels for Cu, the exchangeable component of Cu in serum (CuExc), Zn, the ratio between them (CuExc:Zn), ceruloplasmin [Cp, concentration (iCp) and its activity (eCp), Cp specific activity (eCp:iCp)], and the Cu:Cp, assessed in 31 consecutive CRC patients before surgical resection to those obtained from 37 healthy controls (CTRL). Additionally, we correlated the analyte levels with the indices of the pathological tumor, node, and metastasis (TNM) staging, namely tumor (T), node (N), and metastasis (M), evaluated at the histopathological examination. We found that Cu, CuExc, CuExc:Zn, iCp, eCp, eCp:iCp, and Cu:Cp ratios increased while Zn decreased in CRC patients. In addition, correlation analyses showed that CuExc and Zn levels confirmed the CRC diagnosis. Specifically, CuExc:Zn further increased the discrimination between the individuals of the two groups, providing an area under the curve (ROC AUC) = 0.94. Elevated CuExc was the strongest factor associated with CRC resulting in 15-fold increased odds. These data were confirmed through a multivariable regression model revealing an effect of Zn and CuExc on the CRC risk, with the CuExc resulting in 11-fold increased odds of having the disease. We also found that most of the Cu biological variables analyzed were associated with T, while the CuExc was associated with M. The current pilot study demonstrates that excess labile Cu pool, Zn deficiency, and even further their combination in the CuExc:Zn provide information about CRC in terms of diagnosis, risk of having CRC, and CRC disease stage.

The Mechanism of Zinc Oxide in Alleviating Diarrhea in Piglets after Weaning: A Review from the Perspective of Intestinal Barrier Function

Weaning is one of the most challenging phases for piglets, and it is also the time when piglets are the most susceptible to diarrhea, which may result in significant economic losses for pig production. One of the dietary strategies for reducing post-weaning diarrhea (PWD) in piglets is to provide them with a pharmacological dose of zinc oxide (ZnO). However, excessive or long-term usage of high-dose ZnO has significant impacts on pig health and the ecological environment. Therefore, caution should be exercised when considering the use of high-dose ZnO for the prevention or treatment of PWD in piglets. In this paper, the significant role of zinc in animal health, the potential mode of action of ZnO in alleviating diarrhea, and the impact of innovative, highly efficient ZnO alternatives on the regulation of piglet diarrhea were reviewed to offer insights into the application of novel ZnO in pig production.

The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer

Epigenetic mechanisms play a pivotal role in controlling gene expression and cellular plasticity in both normal physiology and pathophysiological conditions. These mechanisms are particularly important in the regulation of stem cell self-renewal and differentiation, both in embryonic development and within adult tissues. A prime example of this finely tuned epigenetic control is observed in the gastrointestinal lining, where the small intestine undergoes renewal approximately every 3-5 days. How various epigenetic mechanisms modulate chromatin functions in intestinal stem cells (ISCs) is currently an active area of research. In this review, we discuss the main epigenetic mechanisms that control ISC differentiation under normal homeostasis. Furthermore, we explore the dysregulation of these mechanisms in the context of colorectal cancer (CRC) development. By outlining the main epigenetic mechanisms contributing to CRC, we highlight the recent therapeutics development and future directions for colorectal cancer research.

ZNF554 Inhibits Endometrial Cancer Progression via Regulating RBM5 and Inactivating WNT/β-Catenin Signaling Pathway

OBJECTIVE

Uterine corpus endometrial carcinoma (UCEC), a kind of gynecologic malignancy, poses a significant risk to women's health. The precise mechanism underlying the development of UCEC remains elusive. Zinc finger protein 554 (ZNF554), a member of the Krüppel-associated box domain zinc finger protein superfamily, was reported to be dysregulated in various illnesses, including malignant tumors. This study aimed to examine the involvement of ZNF554 in the development of UCEC.

METHODS

The expression of ZNF554 in UCEC tissues and cell lines were examined by qRT-PCR and Western blot assay. Cells with stably overexpressed or knocked-down ZNF554 were established through lentivirus infection. CCK-8, wound healing, and Transwell invasion assays were employed to assess cell proliferation, migration, and invasion. Propidium iodide (PI) staining combined with fluorescence-activated cell sorting (FACS) flow cytometer was utilized to detect cell cycle distribution. qRT-PCR and Western blotting were conducted to examine relative mRNA and protein levels. Chromatin immunoprecipitation assay and luciferase reporter assay were used to explore the regulatory role of ZNF554 in RNA binding motif 5 (RBM5).

RESULTS

The expression of ZNF554 was found to be reduced in both UCEC samples and cell lines. Decreased expression of ZNF554 was associated with higher tumor stage, decreased overall survival, and reduced disease-free survival in UCEC. ZNF554 overexpression suppressed cell proliferation, migration, and invasion, while also inducing cell cycle arrest. In contrast, a decrease in ZNF554 expression resulted in the opposite effect. Mechanistically, ZNF554 transcriptionally regulated RBM5, leading to the deactivation of the Wingless (WNT)/β-catenin signaling pathway. Moreover, the findings from rescue studies demonstrated that the inhibition of RBM5 negated the impact of ZNF554 overexpression on β-catenin and p-glycogen synthase kinase-3β (p-GSK-3β). Similarly, the deliberate activation of RBM5 reduced the increase in β-catenin and p-GSK-3β caused by the suppression of ZNF554. In vitro experiments showed that ZNF554 overexpression-induced decreases in cell proliferation and migration were counteracted by RBM5 knockdown. Additionally, when RBM5 was overexpressed, it hindered the improvements in cell proliferation and migration caused by reducing the ZNF554 levels.

CONCLUSION

ZNF554 functions as a tumor suppressor in UCEC. Furthermore, ZNF554 regulates UCEC progression through the RBM5/WNT/β-catenin signaling pathway. ZNF554 shows a promise as both a prognostic biomarker and a therapeutic target for UCEC.

De novo transcriptional analysis of the response to starvation stress in the white ridgetail prawn, Exopalaemon carinicauda

To study the mechanism of the biomolecular response in Exopalaemon carinicauda to starvation stress, we subjected muscle tissue RNA samples from four stress points, including 0 d(control group), 10 d, 20 d, and 30 d, to starvation stress on white ridgetail prawn with a body weight of 1.41 + 0.42 g, aquaculture water temperature of 23-25 °C, salinity of 26, dissolved oxygen ≥5 mg/L, and pH 8-8.5, Then performed de novo transcriptome assembly and gene expression analysis using BGISEQ-500 with a tag-based digital gene expression (DGE) system. By de novo assembling at the four times, we obtained 28,167, 21,115, 24,497, and 27,080 reads, respectively. The results showed that the stress at 10 d led to no significant difference in the expressed genes, while the stress at 20 d and 30 d showed a significant increase (or decrease) in the expression of 97 (276) and 143 (410) genes, respectively, which were involved in 8 different metabolic pathways. In addition, we detected 2647 unigene transcription factors. Eleven upregulated and sixteen downregulated genes from the different starvation stress groups were choose to verify the reliability of the transcriptome data, and the results showed that the expression trends of these genes were consistent with the results shown by the transcriptome. The analysis of the experimental data and our discussion of the response mechanism of white ridgetail prawn under starvation stress provides a foundation for further screening of the key genes of starvation stress and may help to elucidate their functions.