Journal: Oncotarget

Article Title: KIAA1114, a full-length protein encoded by the trophinin gene, is a novel surface marker for isolating tumor-initiating cells of multiple hepatocellular carcinoma subtypes

doi:

Figure Lengend Snippet: ( A and B ) Flow cytometric analysis of surface KIAA1114 expression in human CC cell lines (A) and AFP + and AFP − HCC cell lines (B) . (C) Immunoblot analysis of tissue lysates from normal liver (N), patient tumor (PT), and its adjacent normal tissue from the same donor (PN). β-actin served as an internal control.

Article Snippet: Human liver whole tissue lysate and paired primary tumor and normal tissues were purchased from Novus Biologicals.

Techniques: Expressing, Western Blot, Control

Journal: International Journal of Molecular Sciences

Article Title: MicroRNA Profiling of PRELI-Modulated Exosomes and Effects on Hepatic Cancer Stem Cells

doi: 10.3390/ijms252413299

Figure Lengend Snippet: Levels of AKT signaling molecules (phosphorylated AKT and phosphorylated mTORC1) in normal hepatocytes and LCSCs under various exosomes. (CE: control cellular exosome, UPE: upregulated PRELI cellular exosome, DPEs: downregulated PRELI cellular exosome) (* p < 0.05, ** p < 0.01,*** p < 0.001).

Article Snippet: Liver cancer stem cells (LCSCs) (sku: 36116-43; Celprogen, Torrance, CA, USA) and normal hepatocytes (NHs) (THLE-3; ATCC, Manassas, VA, USA) were cultured with Human Liver Cancer Stem Cell Media (Celprogen) and BEGM (Bronchial Epithelial Cell Growth Medium) (Lonza, Workingham, UK) using BEGM Bullet Kits (Lonza) at 37 °C, 5% CO 2 .

Techniques: Control

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Sources and modes of circulating tumor DNA in body fluids. (A) Mode of circulating tumor cell cfDNA entry into the bloodstream. The origin of ctDNA in the bloodstream is derived from CTC, exosomes secreted by tumor cells, apoptotic tumor cells and necrotic tumor cells, which contain methylated ctDNA. (B) Body fluids as a source of circulating cell‐free tumor DNA. Schematic illustration of various bodily fluids that may contain ctDNA, including blood, urine, CSF, saliva, and pleural effusions. The presence of ctDNA in different body fluids is influenced by the location of the primary tumor and metastatic lesions. It is possible to identify methylation alterations associated with the cancer by analyzing ctDNA obtained from these circulating tumor materials in the body fluids. Aberrant methylation generally occurs in the promoter region including hypermethylation and hypomethylation states.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Derivative Assay, Methylation

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Technologies and platforms for ctDNA methylation detection and sequencing. (A) Technologies for ctDNA methylation detection. cfMeDIP‐seq, cell‐free methylated DNA immunoprecipitation sequencing; MBD, methyl‐CpG‐binding domain; Methyl‐Seq, methylation sequencing; SeqCap, sequence capture; MS‐NaME, methylation specific nuclease‐assisted minor‐allele enrichment; MSP, methylation‐specific PCR; scWGBS, single‐cell WGBS; scRRBS, single‐cell RRBS; BSPP, bisulfite padlock probes; ELSA‐seq, enhanced linear fragment amplification sequencing; MRE‐seq, methylation restriction enzyme digestion followed by sequencing; HELP, HpaII‐tiny fragment enrichment by ligation‐mediated PCR; MSCC, methyl‐sensitive cut counting; MSAP, methylation‐sensitive amplified polymorphism. (B) Common base resolution methylation sequencing platforms. The required quantity varies according to the protocols.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Sequencing, DNA Immunoprecipitation Sequencing, Binding Assay, Amplification, Ligation

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Innovative approaches for ctDNA analysis: improved WGBS method, genome‐wide methylation amplification with digital PCR, and whole‐genome 5mC methylation sequencing. (A) An improved ctDNA–WGBS method. First, cfDNA was stably microextracted from plasma, and then as low as 1 ng of input DNA was utilized for methylation microlibrary construction. Then, machine learning algorithm was used to analyze the WGBS data, which could detect as low as five out of 1000 of the signal, finally, clinical multicenter validation was performed. (B) cfDNA was amplified by genome‐wide methylation followed by digital PCR. WGMA, Whole‐genome methylation amplification; ddPCR, digital droplet polymerase chain reaction. (C) Whole‐genome methylation sequencing of 5mC in ctDNA. ctDNA is extracted from plasma. After purification, the ctDNA is ligated with an adapter and subjected to bisulfite conversion. PCR amplification is then performed on the fragments, which are subsequently captured using beads. ⁵⁰

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Genome Wide, Methylation, Amplification, Digital PCR, Sequencing, Stable Transfection, Clinical Proteomics, Biomarker Discovery, Polymerase Chain Reaction, Purification

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Clinical application of ctDNA methylation in precision oncology. (A) Collection tube: ctDNA derived from apoptotic or necrotic tumor cells can be extracted from body fluids. The analysis of ctDNA enables the detection of alterations in DNA methylation patterns. Block diagram: shows the potential clinical applications of ctDNA methylation analysis in disease management throughout the progression of the condition. (B) Taking the latest clinical molecular subtype identification as an example, DNA methylation‐based classifier was used to classify SCLC based on plasma‐derived methylation data. Different SCLC subtypes have different DNA methylation, and the evolution of SCLC subtypes can be tracked by longitudinal evaluation through liquid biopsy.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Derivative Assay, DNA Methylation Assay, Blocking Assay, Clinical Proteomics

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Application of ctDNA methylation markers in early diagnosis and screening of cancer.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Biomarker Discovery, Diagnostic Assay, Clinical Proteomics, Marker, Control, Digital PCR

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Application of ctDNA methylation markers in recurrence and MRD monitoring of cancer.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Clinical Proteomics, DNA Sequencing, Multiplex Assay

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Application of ctDNA methylation markers in predicting cancer treatment response, prognosis, and assessing of tumor burden.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Clinical Proteomics, DNA Methylation Assay, DNA Sequencing, Marker, Concentration Assay, Methylation Sequencing, Multiplex Assay, Control

Journal: MedComm

Article Title: Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

doi: 10.1002/mco2.766

Figure Lengend Snippet: Summary of ongoing and completed trials utilizing ctDNA methylation detection.

Article Snippet: NCT05536089 , Observational , 2000 , Stage I/II CRC , Multilocus ctDNA methylation assay for relapse monitoring and chemotherapy evaluation , 5‐year DFS, ctDNA vs. CT/MRI , Singlera Genomics Inc. , .

Techniques: Methylation, Clinical Proteomics, Biomarker Discovery, Diagnostic Assay, Sequencing, Comparison, Adjuvant