Journal: Cells

Article Title: Multiplexed Digital PCR Reference Gene Measurement for Genomic and Cell-Free DNA Analysis

doi: 10.3390/cells14191544

Figure Lengend Snippet: Reference gene measurement and HER2 ratio analysis of breast carcinoma cell line-derived hgDNA. ( A ) Reference gene panel was tested using HER2+ gDNA and its matched lymphoblast gDNA (HER2− gDNA). Error bar for the individual genes show range. The error bar for the average shows the expanded measurement uncertainty.; ( B ) HER2 multiplex panel was tested using HER2+ gDNA and its matched lymphoblast gDNA (HER2−). Symbols in black represent HER2+ gDNA, and symbols in grey represent HER2− gDNA. Circle, square, triangle, diamond, hexagon, and down-pointing triangle represent HBB, RPPH1, RPS27A, DCK, PMM1 and the average respectively. Each symbol shows individual measurements.

Article Snippet: Commercially available human genomic DNA (gDNA) isolated from the HCC1954 breast carcinoma cell line with HER2 copy number gain (ATCC CRL-2338D) and paired healthy control gDNA (ATCC CRL-2339D) isolated from the HCC1954 BL EBV-transformed lymphoblastoid cell line (both ATCC, Manassas, VA, USA) were also digested prior to dPCR application as described above.

Techniques: Derivative Assay, Multiplex Assay

Journal: EXCLI Journal

Article Title: Mitochondrial DNA copy number instability in ERBB2-amplified breast cancer tumors

doi: 10.17179/excli2017-819

Figure Lengend Snippet: The association between ERBB2 (17q) and HER2 by likelihood-ratio chi2 (p<0.001)

Article Snippet: In order to analyse the ERBB2 gene copy number variation status GeneMarker ver 1.6 (softgenetics, USA) was used.

Techniques:

Journal: EXCLI Journal

Article Title: Mitochondrial DNA copy number instability in ERBB2-amplified breast cancer tumors

doi: 10.17179/excli2017-819

Figure Lengend Snippet: Possible factors affecting mitochondrial DNA content according to the ERBB2 status

Article Snippet: In order to analyse the ERBB2 gene copy number variation status GeneMarker ver 1.6 (softgenetics, USA) was used.

Techniques:

Journal: EXCLI Journal

Article Title: Mitochondrial DNA copy number instability in ERBB2-amplified breast cancer tumors

doi: 10.17179/excli2017-819

Figure Lengend Snippet: Schematic diagram of ERBB2 cellular signaling pathways known to regulate mitochondrial function. ERBB2 modulates several cellular functions by binding to other ligand bound EGF receptor which subsequently activates downstream signaling cascades including the MAP kinase, phosphatidylinositol-3-kinase (PI3-K) and calcium signaling pathways. It has been demonstrated that nuclear ERBB2 in the presence of unknown transcription factors activates the COX-2 gene. Translocation of ERBB2 to the mitochondria has also been observed in cancer cells and has been linked to decrease in ATP production and increase in cellular glycolysis.

Article Snippet: In order to analyse the ERBB2 gene copy number variation status GeneMarker ver 1.6 (softgenetics, USA) was used.

Techniques: Protein-Protein interactions, Binding Assay, Translocation Assay

Journal: Medicine

Article Title: Pathological complete response to neoadjuvant trastuzumab and pertuzumab therapy is related to human epidermal growth factor receptor 2 ( HER2 ) amplification level in HER2 -amplified breast cancer

doi: 10.1097/MD.0000000000023053

Figure Lengend Snippet: Fluorescence in situ hybridization (FISH) is shown for HER2 gene amplification on Thin-Prep specimens and on corresponding histologic sections ( HER2 : red signal, CEP17 : green signal). (A) A case with positive HER2 amplification status (DAPI counterstain; ×1000). (B) A case with negative HER2 amplification status (DAPI counterstain; ×1000). DAPI = 4′,6-diamidino-2-phenylin-dole.

Article Snippet: [ ] The National Surgical Adjuvant Breast and Bowel Project (NSABP) B-31 trial also did not find a relationship between HER2 copy number and therapeutic benefits.

Techniques: Fluorescence, In Situ Hybridization, Amplification

Journal: Medicine

Article Title: Pathological complete response to neoadjuvant trastuzumab and pertuzumab therapy is related to human epidermal growth factor receptor 2 ( HER2 ) amplification level in HER2 -amplified breast cancer

doi: 10.1097/MD.0000000000023053

Figure Lengend Snippet: Median (range) level of HER2 amplifications and pCR as defined by ypT0 N0, ypT0/is N0, ypT0/is.

Article Snippet: [ ] The National Surgical Adjuvant Breast and Bowel Project (NSABP) B-31 trial also did not find a relationship between HER2 copy number and therapeutic benefits.

Techniques:

Journal: Medicine

Article Title: Pathological complete response to neoadjuvant trastuzumab and pertuzumab therapy is related to human epidermal growth factor receptor 2 ( HER2 ) amplification level in HER2 -amplified breast cancer

doi: 10.1097/MD.0000000000023053

Figure Lengend Snippet: Average HER2 copy number in tumors from patient who did not (left box blot) or did (right box blot) experience pCR as defined by ypT0 ypN0 (A), ypT0/is ypN0 (B), ypT0/is (C). pCR = pathologic complete response.

Article Snippet: [ ] The National Surgical Adjuvant Breast and Bowel Project (NSABP) B-31 trial also did not find a relationship between HER2 copy number and therapeutic benefits.

Techniques:

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: A schematic illustration of the generation of cell lines with HER2 expression in vitro and preparation of HER2-low FFPE reference material. (A) Recombinant lentivirus packaged and tittered in HEK 293T cells. (B) In vitro transduction in MDA-MB-231 cells (C) Detection of GFP expression by flow fluorescence scan (D) Verification the monoclonal cells using droplet digital PCR. (E) FFPE samples derived from xenograft tumors.

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Expressing, In Vitro, Recombinant, Transduction, Fluorescence, Digital PCR, Derivative Assay

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: PCR assays primers used for certification values.

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Sequencing, Amplification

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: HER2 overexpression was generated in MDA-MB-231 cells using a lentivirus vector system. (A) After double restriction endonuclease Sph1 and Nhe1 digestion, electrophoresis showed two specific target bands of about 5kbp and 7kbp, line 1: Marker; line 2: Recombinant plasmid without enzyme digestion; line 3-5: Double digestion with three replicates. (B) The positive colonies of extracted plasmid were selected for PCR identification, and agarose gel electrophoresis showed a specific target band of about 3.7kbp. (C) The sequences were validated by sanger sequencing(Partial display. (D) MDA-MB-231 cells were transduced by lentivirus vector at five different multiplicity of infection (MOI 0, 5, 10, 20 and 50 virus particles per cell). GFP expression in cells was analyzed by flow cytometry 48 hours after lentivirus vector infection (×100).

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Over Expression, Generated, Plasmid Preparation, Electrophoresis, Marker, Recombinant, Agarose Gel Electrophoresis, Sequencing, Infection, Virus, Expressing, Flow Cytometry

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: Monoclonal cultured cells assigned by ddPCR. (A) Data was shown in the form of 2D amplitude of Bio-Rad droplet digital PCR. The number of microdroplet generated by all reactions was more than 10000, in accordance with Poisson distribution statistical principle, and the fluorescence of FAM (HER2) and VIC (CEP17) was clearly distinguished. і:Healthy human gDNA; ii: MDA-MB-231 WT cells; iii: HER2-low cells; iv: SK-BR-3 cells, (B) Data shown in the form of ratio (HER2/CEP17). The HER2/CEP17) ratios of healthy human genomic DNA, MDA-MB-231 cell line, HER2-low cells and SK-BR-3 cell line were 1.001 (0.982-1.026), 1.1638 (1.033-1.254), 1.693(1.632-1.775) 7.194 (6.066-7.872).

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Cell Culture, Digital PCR, Generated, Fluorescence

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: The cell slide evaluated that HER2-low cells can be detected by conventional detection methods. HE staining showed that the cell morphology was intact. IHC showed that MDA-MB-231 WT cell line had no staining and was negative. SK-BR-3 was brown-yellow, +++. HER2-low was moderately stained, denoted as ++. FISH showed that MDA-MB-231 WT cells had no amplification of HER2 (HER/CEP17 ratio was 1.057); the HER2 signal in SK-BR-3 was clustered and significantly amplified; HER2-low cells had no amplification of HER2 (HER/CEP17 ratio was 1.375).

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Staining, Amplification

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: The characteristics of the reference materials were evaluated for conformity with the real clinical specimens. The histopathological structure of the xenotransplantation was highly consistent with the real clinical specimens. The real clinical specimen was showed IHC 2+ and FISH negative. The results show that the candidate reference material fully meets the clinical needs of HER2-low (IHC 1+/2+ and FISH negative).

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques:

Journal: Frontiers in Oncology

Article Title: Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer

doi: 10.3389/fonc.2022.955943

Figure Lengend Snippet: Sample validation and homogeneity and stability assessment of the FFPE reference materials by ddPCR. (A) Sample validation by ddPCR of the FFPE reference materials. Data shown in the form of ratio (HER2/CEP17). (B) Homogeneity and stability assessment of the FFPE reference materials showing that no significant trends in the ratio are detectable within the detection limits of the assays. The mean values of all samples are consistent with their individual target values.

Article Snippet: For evaluating the performance of NGS in detecting HER2 copy number variation cell lines were used to extract genomic DNA (gDNA) at the National Institute of Standards and Technology , but it failed to meet the needs for monitoring the total testing process.

Techniques: Biomarker Discovery