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  • American Association for Cancer Research (AACR)  (4)
  • Ryu, Han Suk  (4)
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  • American Association for Cancer Research (AACR)  (4)
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  • 1
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 75, No. 9_Supplement ( 2015-05-01), p. P2-05-07-P2-05-07
    Abstract: Background/Purpose: Next-generation sequencing (NGS) is being incorporated rapidly into clinical practice. Fine-needle aspiration biopsy (FNAB) specimens have been used feasibly in molecular analysis including direct sequencing and microarrays. They are readily available and enriched in malignant cells, thus providing opportunities for genomic analysis for more clinical samples. In this study, we assessed the feasibility and sensitivity of FNAB for the detection of somatic mutations by NGS compared to bulk tissue. Methods: Bulk tissue and FNAB was sampled via skin superficial to the palpable tumor from surgically resected breast cancer specimen. DNA was extracted from the bulk tissues and FNAB samples obtained from twelve patients. Somatic mutations detected from whole exome sequencing (WES) by next-generation sequencing (NGS) (HiSeq 2500, Illumina) were analyzed for corresponding pairs of bulk tissue and FNAB. Verification of somatic mutations detected exclusively from FNAB and known to be clinically relevant to breast cancer was carried out by Sanger sequencing. Invasive tumor percentages of bulk tissues were evaluated using hematoxylin and eosin (H & E)-stained sections. Results: Average depth of coverage were 158.8x and 158.3x for bulk tissue and FNAB, respectively. Number of detected somatic mutations ranged from 2 to 153 (median 18.5) and 19 to 210 (median 39.5) for bulk tissue and FNAB, respectively. Ten specimens had more mutations detected exclusively from FNAB than from bulk tissue. Allele fractions plotting of corresponding pairs of bulk tissue and FNAB showed good, intermediate, and poor correlation in five, two, and five specimens, respectively. H & E-stained sections of bulk tissue from the five specimens with good correlation contained an invasive tumor percentage of 45 to 98%, whereas those from five specimens with poor correlation contained 0 to 25%. Three of the poorly correlated bulk tissues were judged to have 0% of invasive tumor. Among mutations detected exclusively from FNAB, eighteen different genes of interest in 22 foci were evaluated for both FNAB and corresponding bulk tissue by Sanger sequencing. In the results, three mutations (PIK3CA, TP53 x2) were verified in FNAB samples but not in the bulk tissue. Conclusion: WES was successfully carried out in all pairs of bulk tissue and FNAB from twelve breast cancer patients. In samples with high tumor content somatic mutation profiles showed high correlation between the two samples whereas samples with low tumor content failed to show correlation. The failure was mostly due to the scarcity of tumor portions in the bulk tissues, indicating that FNAB more reliably retained malignant tumor portion. This study suggests that FNAB is an easy and feasible method, and furthermore, provides a more reliable specimen for NGS analysis where somatic mutations could be identified for potential prognostic or therapeutic benefits. Citation Format: Han-Byoel Lee, Jisun Kim, Kyung-Min Lee, Je-Gun Joung, Hae-ock Lee, Min Kyoon Kim, Eunshin Lee, Jongjin Kim, Tae-Kyung Yoo, Yun-Gyoung Kim, Young Joon Kang, Han Suk Ryu, In-Ae Park, Hyeong-Gon Moon, Dong-Young Noh, Woong-Yang Park, Wonshik Han. Feasibility and sensitivity of fine-needle aspiration biopsies for the detection of somatic mutations using next-generation sequencing in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-07.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 84, No. 3_Supplement_1 ( 2024-02-01), p. A005-A005
    Abstract: The HER2 diagnostics is necessary for selection of patients harboring HER2 gene amplification or protein overexpression who will benefit from anti-HER2 therapies in breast cancer. However, HER2 testing is still challenging due to the subjective natures of immunohistochemistry (IHC) and in situ hybridization (ISH), standard methods for determining HER2 status. Thus, a new method is needed to accurately quantify HER2 levels. Here, we developed a clinically reliable HER2 testing method enabling ultra-fast detection of HER2 gene amplification with high accuracy by using the digital real-time PCR (drPCR) system, a potential new diagnostic platform with improved performance by integrating both real-time and digital PCR technologies. For drPCR-based HER2 copy number (CN) measurement, primer-probe sets specific to HER2 gene and a genomic region adjacent to chromosome 17 centromere (CEP17) were designed, and the optimal drPCR condition was determined in clinical breast tumor specimens. To test the clinical validity and standardize procedures of drPCR-based HER2 status evaluation, three independent breast cancer cohorts from different institutions were enrolled, which assigned as a training (SCHU hospital, n = 103) and two validation sets (SNU hospital, n = 170; CNUH hospital, n = 45), and the drPCR assay was compared with current standard HER2 testing methods. In the training cohort, the HER2/CEP17 ratio values from FISH and drPCR tests were highly correlated (r2 = 0.81; P & lt; 0.001), and the drPCR results displayed 98.1% concordance to HER2 status defined by IHC and/or FISH with 92.6% sensitivity and 100% specificity. Eight samples further verified by targeted NGS showed 100% concordance of dPCR to NGS. Consistently, two validation cohorts also showed high concordance of drPCR to IHC and/or ISH results (accuracy = 97.1% and 97.8% in SNU and CNUH cohorts, respectively). The optimal cutoff for HER2 positivity in the drPCR assay was set as a HER2/CEP17 ratio ≥ 1.9 with AUC of 0.963 based on the results from training cohort, and the same cut-off for drPCR was applicable to two independent validation cohorts, supporting the clinical validity of our drPCR-based HER2 assessment. In some discordant cases, low tumor purity (≤ 25%) was observed and microdissection partly improved the drPCR results. The discordance between drPCR and ISH results was also found in marginal HER2+ cases with HER2/CEP17 ratio 2-3, but these cases showed inter-observer variability when re-evaluating the ISH/IHC data due to intratumoral HER2 heterogeneity. Of note, in HER2 IHC3+ cases with negative drPCR results, re-evaluation of IHC using an artificial intelligence (AI)-based HER2 scoring system revised the HER2 IHC 3+ score to 2+, and ISH assessment also confirmed that these cases are indeed HER2-negative, proving the high accuracy of HER2 CN drPCR assay. In conclusion, given the advantages of drPCR-based HER2 assessment with high accuracy, sensitivity, and simplicity, the drPCR assay could be a complementary or alternative method to IHC and ISH to greatly improve current HER2 testing. Citation Format: Jin hyuk Chang, YoonSik Kim, Hee-Joo Choi, Soo Young Park, Ji-Hye Park, Hee-Young Won, Min Ji Song, Da Sol Kim, Hayeon Kim, Sohyeon Yang, Nam Hun Heo, Minsik Song, Seung-Shick Shin, Do Young Lee, Han Suk Ryu, Si-Hyong Jang, Jeong-Yeon Lee. Ultra-rapid and precise measurement of HER2 copy number alteration by next-generation digital PCR capable of real-time analysis in patients with breast cancer: A multicenter retrospective study [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A005.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2024
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 4739-4739
    Abstract: Purpose Defects of DNA damage repair are known to be associated with the efficacy of anthracycline or platinum-based chemotherapy as well as poly[ADP-ribose] polymerase (PARP) inhibitors (PARPi) and PD-1/PD-L1 checkpoint inhibitors. Since multiple proteins are involved in DNA-damage response (DDR) and operate collectively, our main aim was to better understand the expression of proteins in DDR machinery and their integrated prognostic value in the different subtypes of breast cancer. Methods A total of 419 consecutive breast cancer patients who underwent curative resection in 2008 were enrolled in the study. Tissue microarray has been constructed, and NBS1, BRCA1, BRCA2, ATM and p53 expression were determined by immunohistochemistry. Results All patients were female, with a median age of 47 years; 280 (67%) had luminal A, 36 (9%) had luminal B, 37 (9%) had HER2-enriched, and 56 (13%) had triple-negative breast cancer (TNBC). Loss of NBS1, BRCA1, BRCA2, and ATM expression was observed in 6.7%, 33.7%, 89.9%, and 30.8% of breast cancer patients, respectively, and abnormal p53 expression was observed in 39.3% of patients. Loss of NBS1, BRCA1, ATM and abnormal p53 expression was associated with significantly lower disease-free survival (DFS) rates, respectively. “Abnormal DDR protein expression”, defined as loss of any one of NBS1, BRCA1, ATM and/or abnormal p53 expression, was observed in 258 of 399 evaluable cases (64.7%) and was significantly associated with higher tumor grade, larger tumor size, and ER- and/or PR-negative status. Majority of patients with luminal B (31/36, 86.1%), HER2-enriched (34/35, 94.4%), and TNBC (46/53, 86.8%) subtype showed abnormal DDR protein expression. In comparison, 136/264 patients (53.8%) with luminal A subtype had abnormal DDR protein expression. Abnormal DDR protein expression was associated with significantly lower 5-year DFS rate than those in patients with normal DDR protein expression in all patients (95.6% vs. 84.8%, p = 0.001), as well as in luminal A subgroup (97.4% vs. 89.0%, p = 0.011). In multivariate analysis, abnormal DDR protein expression remained as an independent predictor of shorter DFS for luminal A subtype tumors (hazard ratio 3.14; 95% confidence interval, 1.16 – 8.47, p = 0.024). Conclusion We demonstrated differential expression of proteins in DDR machinery according to breast cancer subtypes and its prognostic implication. Most of luminal B and HER2-enriched tumors has abnormal DDR expression as frequently as triple negative tumors. Less but significant proportion of luminal A tumors also shows abnormal DDR protein expression, which is an independent poor prognostic factor. Citation Format: Koung Jin Suh, Han Suk Ryu, Kyung-Hun Lee, Hyojin Kim, Ahrum Min, Tae-Yong Kim, Hyeong-Gon Moon, Sae-Won Han, Do-Youn Oh, Wonshik Han, In Ae Park, Dong-Young Noh, Seock-Ah Im. Prognostic impact of abnormal DNA damage response protein expression in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4739. doi:10.1158/1538-7445.AM2017-4739
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 4
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 79, No. 7 ( 2019-04-01), p. 1520-1534
    Abstract: Various miRNAs play critical roles in the development and progression of solid tumors. In this study, we describe the role of miR-204-5p in limiting growth and progression of breast cancer. In breast cancer tissues, miR-204-5p was significantly downregulated compared with normal breast tissues, and its expression levels were associated with increased survival outcome in patients with breast cancer. Overexpression of miR-204-5p inhibited viability, proliferation, and migration capacity in human and murine breast cancer cells. In addition, miR-204-5p overexpression resulted in a significant alteration in metabolic properties of cancer cells and suppression of tumor growth and metastasis in mouse breast cancer models. The association between miR-204-5p expression and clinical outcomes of patients with breast cancer showed a nonlinear pattern that was reproduced in experimental assays of cancer cell behavior and metastatic capacities. Transcriptome and proteomic analysis revealed that various cancer-related pathways including PI3K/Akt and tumor–immune interactions were significantly associated with miR-204-5p expression. PIK3CB, a major regulator of PI3K/Akt pathway, was a direct target for miR-204-5p, and the association between PIK3CB-related PI3K/Akt signaling and miR-204-5p was most evident in the basal subtype. The sensitivity of breast cancer cells to various anticancer drugs including PIK3CB inhibitors was significantly affected by miR-204-5p expression. In addition, miR-204-5p regulated expression of key cytokines in tumor cells and reprogrammed the immune microenvironment by shifting myeloid and lymphocyte populations. These data demonstrate both cell-autonomous and non-cell–autonomous impacts of tumor suppressor miR-204-5p in breast cancer progression and metastasis. Significance: This study demonstrates that regulation of PI3K/Akt signaling by miR-204-5p suppresses tumor metastasis and immune cell reprogramming in breast cancer.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2019
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    detail.hit.zdb_id: 410466-3
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