Correlation analysis of <i>RDM1</i> gene with immune infiltration and clinical prognosis of hepatocellular carcinoma

Qiu, Chen; Li, Zuyin; Cao, Wen-Jun; Cai, Xiaoni; Li, Ye; Zhang, Cheng; Ma, Yuefeng; Wang, Xiaoliang; Yang, Yanzhong

doi:10.1042/bsr20203978

Cited by 3 publications

(1 citation statement)

References 44 publications

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“…Moreover, knockdown of this gene reduced the proliferation of tumor cells, increased cell apoptosis, and induced cell cycle arrest ( Li et al, 2017 ; Xu et al, 2018 ; Chen et al, 2019 ; Tong et al, 2020 ). The expression of RDM1 is correlated with the degree of immune infiltration of immune cells, including macrophages and neutrophils, in a variety of cancer types ( Qui et al, 2021 ). A SNP located within 100 Kb of the RDM1 gene was associated with interdigital hyperplasia, and another was associated with sole hemorrhage in Holsteins ( Sousa Junior et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

The genetic architecture of complete blood counts in lactating Holstein dairy cows

Siberski-Cooper,

Mayes,

Gorden

et al. 2024

Front. Genet.

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Complete blood counts (CBCs) measure the abundance of individual immune cells, red blood cells, and related measures such as platelets in circulating blood. These measures can indicate the health status of an animal; thus, baseline circulating levels in a healthy animal may be related to the productive life, resilience, and production efficiency of cattle. The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained more than 1% of the genetic variance for at least one CBC trait, with 10 windows explaining more than 1% of the genetic variance for two or more traits. Multiple genes in the identified regions have functions related to immune response, cell differentiation, anemia, and disease. Positional candidate genes include RAD52 motif-containing protein 1 (RDM1), which is correlated with the degree of immune infiltration of immune cells, and C-X-C motif chemokine ligand 12 (CXCL12), which is critically involved in neutrophil bone marrow storage and release regulation and enhances neutrophil migration. Since animal health directly impacts feed intake, understanding the genetics of CBCs may be useful in identifying more disease-resilient and feed-efficient dairy cattle. Identification of genes responsible for variation in CBCs will also help identify the variability in how dairy cattle defend against illness and injury.

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Section: Discussionmentioning

confidence: 99%

The genetic architecture of complete blood counts in lactating Holstein dairy cows

Siberski-Cooper,

Mayes,

Gorden

et al. 2024

Front. Genet.

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m5C regulator-mediated methylation modification phenotypes characterized by distinct tumor microenvironment immune heterogenicity in colorectal cancer

Chen¹,

Li²,

Lin³

et al. 2023

Sci Rep

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The RNA 5-methylcytosine (m5C) modification has been demonstrated to be an important epigenetic regulator and to impact colorectal cancer (CRC) progression. However, the potential roles of m5C modification in immune cell infiltration in the CRC tumor microenvironment (TME) remain unknown. The m5C modification phenotypes were comprehensively evaluated based on 14 m5C regulators in a meta-CRC cohort of 1792 patients and systematically correlated with the m5C modification phenotypes, immune cell infiltration characteristics and known biological processes. The m5Cscore model was constructed by principal component analysis (PCA) algorithms to quantify the m5C modification phenotypes of individual CRC samples and was used to predict the immunotherapy response. We identified three m5C modification phenotypes associated with distinct clinical outcomes and biological processes among the 1792 meta-CRC patients. Three phenotypes with a highly consistent TME landscape and characteristics were revealed: immune excluded, immune desert and immune inflammation. The meta-CRC patients were divided into high and low m5Cscore subgroups based on the m5Cscore. The m5Cscore was confirmed to have a negative correlation with infiltrating immune cells and PD-L1 expression and a positive correlation with tumor mutation burden (TMB), mutation rate and microsatellite instability (MSI) score. Moreover, patients in the low m5Cscore group had better immunotherapy responses and significant durable survival benefits in independent anti-PD-1/L1 immunotherapy cohorts for the immune checkpoint inhibitor (ICI) therapeutic strategy. This study revealed that m5C modification plays a crucial role in TME composition and complexity. Comprehensive evaluation of the m5C modification phenotypes of individual patients will enhance our understanding of TME characteristics and promote the application of more appropriate and personalized treatment strategies.

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Transcriptomic analysis reveals prognostic molecular subtype and candidate risk model for pseudouridylation- related genes in hepatocellular carcinoma

Lan,

Wei,

Huang

et al. 2024

Preprint

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Growing studies have shown pseudouridylation can regulate translation and gene expression, but the molecular characteristics of pseudouridylation remain unknown in hepatocellular carcinoma (HCC). Based on public databases, we identified pseudouridylation-related molecular cluster and risk score model to evaluate the prognosis, clinical characteristic, molecular mechanisms, immune landscape of HCC. Polymerase Chain Reaction (PCR) was adopted to verify the expression of RDM1, CDCA3 and FLVCR1. We found that pseudouridylation-related genes (PRGs) mainly participate in regulation of transcription and translation. The prognostic PRGs can divide HCC sample into two subtypes, the cluster1 characterized with high AFP, poor differentiation, advanced tumor stage, large tumor size, frequent TP53 mutation, up-regulation of cell cycle and mitosis, and poor prognosis, which was similar to the proliferation type of HCC. On the contrary, the cluster2 presented good prognosis and increased infiltration of immune cells, which was partly similar to the non-proliferation HCC and may benefit from immunotherapy. Furthermore, the risk score model, constructed by RDM1, CDCA3 and FLVCR1, was demonstrated to be significantly related to prognosis, and be an independent prognostic factor. The overall survival (OS) and recurrence free survival (RFS) of high-risk group were worse than the low-risk. Receiver operating characteristic (ROC) curve revealed the model had a better predictive performance for 1- and 3- year survival with the maximum AUC reached 0.806. Functional enrichment analysis suggested that gene sets of cell cycle-, mitotic division-related biological processes and cell signaling pathways were upregulated in high-risk group, such as PLK1 pathway, FOXM1 pathway, P53 regulation pathway and so on. PCR experiment discovered the expression of RDM1, CDCA3 and FLVCR1 were obviously overexpressed in HCC tissues, which was consistent with public data. In conclusion, the prognostic PRGs related-molecular subtype and risk model may effectively forecast the prognosis and immune landscape of HCC.

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Correlation analysis of RDM1 gene with immune infiltration and clinical prognosis of hepatocellular carcinoma

Cited by 3 publications

References 44 publications

The genetic architecture of complete blood counts in lactating Holstein dairy cows

The genetic architecture of complete blood counts in lactating Holstein dairy cows

m5C regulator-mediated methylation modification phenotypes characterized by distinct tumor microenvironment immune heterogenicity in colorectal cancer

Transcriptomic analysis reveals prognostic molecular subtype and candidate risk model for pseudouridylation- related genes in hepatocellular carcinoma

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