Optical Imaging of Epigenetic Modifications in Cancer: A Systematic Review

Du, Yang; Zhang, Pei; Liu, Wei; Tian, Jie

doi:10.1007/s43657-021-00041-y

Cited by 10 publications

(7 citation statements)

References 121 publications

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“…This inefficient form of energy metabolism supplies the need for new proliferating cancer cells and enables the use of intermediate products to yield biomolecules, such as amino acids, and nucleotides ( 8 ). Previous studies revealed that amino acids could have impacts on cell proliferation, the tumor microenvironment, epigenetic modification, and drug resistance ( 9 – 14 ). Previous studies also revealed that amino acid aberrant metabolism was associated with tumor progression and immune infiltration in ccRCC and other cancers ( 15 – 18 ).…”

Section: Introductionmentioning

confidence: 99%

Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma

Chang

et al. 2022

Front. Oncol.

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BackgroundIncreasing evidence indicates that L-dopa decarboxylase (DDC), which mediates aberrant amino acid metabolism, is significantly associated with tumor progression. However, the impacts of DDC are not elucidated clearly in clear cell renal cell carcinoma (ccRCC). This study aimed to evaluate DDC prognostic value and potential mechanisms for ccRCC patients.MethodsTranscriptomic and proteomic expressions of and clinical data including 532 patients with ccRCC (The Cancer Genome Atlas RNA-seq data), 226 ccRCC samples (Gene Expression Omnibus), 101 ccRCC patients from the E-MTAB-1980 cohort, and 232 patients with ccRCC with proteogenomic data (Fudan University Shanghai Cancer Center) were downloaded and analyzed to investigate the prognostic implications of DDC expression. Cox regression analyses were implemented to explore the effect of DDC expression on the prognosis of pan-cancer. The "limma" package identified the differentially expressed genes (DEGs) between high DDC subgroups and low DDC groups. Functional enrichments were performed based DEGs between DDC subgroups. The differences of immune cell infiltrations and immune checkpoint genes between DDC subgroups were analyzed to identify potential influence on immune microenvironment.ResultsWe found significantly decreased DDC expression in ccRCC tissues compared with normal tissues from multiple independent cohorts based on multi-omics data. We also found that DDC expression was correlated with tumor grades and stages.The following findings revealed that lower DDC expression levels significantly correlated with shorter overall survival (P <0.001) of patients with ccRCC. Moreover, we found that DDC expression significantly correlated with an immunosuppressive tumor microenvironment, higher intra-tumoral heterogeneity, elevated expression of immune checkpoint CD274, and possibly mediated malignant behaviors of ccRCC cells via the PI3k/Akt signaling pathway.ConclusionThe present study is the first to our knowledge to indicate that decreased DDC expression is significantly associated with poor survival and an immune-suppressive tumor microenvironment in ccRCC. These findings suggest that DDC could serve as a biomarker for guiding molecular diagnosis and facilitating the development of novel individual therapeutic strategies for patients with advanced ccRCC.

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Section: Introductionmentioning

confidence: 99%

Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma

Chang

et al. 2022

Front. Oncol.

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Section: Mirnas and Epigenetics In Cllmentioning

confidence: 99%

“…In addition to genetic abnormalities, epigenetic factors can also play a crucial role in tumor formation. The difference between epigenetic and genetic factors is that the former alters gene expression without changing DNA sequences and can be reversibly inherited [136, 137]. Several important biological processes, including embryonic growth and cellular differentiation, are controlled by epigenetic factors [138].…”

Section: Introductionmentioning

confidence: 99%

MicroRNAs: Potential prognostic and theranostic biomarkers in chronic lymphocytic leukemia

Ali,

Mahla,

Reza

et al. 2024

eJHaem

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Small noncoding ribonucleic acids called microRNAs coordinate numerous critical physiological and biological processes such as cell division, proliferation, and death. These regulatory molecules interfere with the function of many genes by binding the 3'‐UTR region of target mRNAs to inhibit their translation or even degrade them. Given that a large proportion of miRNAs behave as either tumor suppressors or oncogenes, any genetic or epigenetic aberration changeing their structure and/or function could initiate tumor formation and development. An example of such cancers is chronic lymphocytic leukemia (CLL), the most prevalent adult leukemia in Western nations, which is caused by unregulated growth and buildup of defective cells in the peripheral blood and lymphoid organs. Genetic alterations at cellular and molecular levels play an important role in the occurrence and development of CLL. In this vein, it was noted that the development of this disease is noticeably affected by changes in the expression and function of miRNAs. Many studies on miRNAs have shown that these molecules are pivotal in the prognosis of different cancers, including CLL, and their epigenetic alterations (e.g., methylation) can predict disease progression and response to treatment. Furthermore, miRNAs are involved in the development of drug resistance in CLL, and targeting these molecules can be considered a new therapeutic approach for the treatment of this disease. MiRNA screening can offer important information on the etiology and development of CLL. Considering the importance of miRNAs in gene expression regulation, their application in the diagnosis, prognosis, and treatment of CLL is reviewed in this paper.

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“…In pursuit of early diagnosis and widespread implementation, obtaining blood samples proves to be a less invasive and more convenient alternative compared to tissue samples. Numerous cancer studies have revealed a significant association between cancer risk and DNA methylation in peripheral blood leukocytes, encompassing various types of tumors such as colorectal, bladder, gastric, breast, and head and neck cancers [ 7 – 12 ]. Recently, a diagnostic model for colorectal cancer (CRC) based on five methylation markers in peripheral blood mononuclear cells demonstrated the ability to identify colorectal patients earlier compared to conventional methods [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Blood leukocytes as a non-invasive diagnostic tool for thyroid nodules: a prospective cohort study

Wang,

Zhao,

et al. 2024

BMC Med

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Background Thyroid nodule (TN) patients in China are subject to overdiagnosis and overtreatment. The implementation of existing technologies such as thyroid ultrasonography has indeed contributed to the improved diagnostic accuracy of TNs. However, a significant issue persists, where many patients undergo unnecessary biopsies, and patients with malignant thyroid nodules (MTNs) are advised to undergo surgery therapy. Methods This study included a total of 293 patients diagnosed with TNs. Differential methylation haplotype blocks (MHBs) in blood leukocytes between MTNs and benign thyroid nodules (BTNs) were detected using reduced representation bisulfite sequencing (RRBS). Subsequently, an artificial intelligence blood leukocyte DNA methylation (BLDM) model was designed to optimize the management and treatment of patients with TNs for more effective outcomes. Results The DNA methylation profiles of peripheral blood leukocytes exhibited distinctions between MTNs and BTNs. The BLDM model we developed for diagnosing TNs achieved an area under the curve (AUC) of 0.858 in the validation cohort and 0.863 in the independent test cohort. Its specificity reached 90.91% and 88.68% in the validation and independent test cohorts, respectively, outperforming the specificity of ultrasonography (43.64% in the validation cohort and 47.17% in the independent test cohort), albeit with a slightly lower sensitivity (83.33% in the validation cohort and 82.86% in the independent test cohort) compared to ultrasonography (97.62% in the validation cohort and 100.00% in the independent test cohort). The BLDM model could correctly identify 89.83% patients whose nodules were suspected malignant by ultrasonography but finally histological benign. In micronodules, the model displayed higher specificity (93.33% in the validation cohort and 92.00% in the independent test cohort) and accuracy (88.24% in the validation cohort and 87.50% in the independent test cohort) for diagnosing TNs. This performance surpassed the specificity and accuracy observed with ultrasonography. A TN diagnostic and treatment framework that prioritizes patients is provided, with fine-needle aspiration (FNA) biopsy performed only on patients with indications of MTNs in both BLDM and ultrasonography results, thus avoiding unnecessary biopsies. Conclusions This is the first study to demonstrate the potential of non-invasive blood leukocytes in diagnosing TNs, thereby making TN diagnosis and treatment more efficient in China.

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Optical Imaging of Epigenetic Modifications in Cancer: A Systematic Review

Cited by 10 publications

References 121 publications

Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma

Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma

MicroRNAs: Potential prognostic and theranostic biomarkers in chronic lymphocytic leukemia

Blood leukocytes as a non-invasive diagnostic tool for thyroid nodules: a prospective cohort study

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