Development of a media cell-free DNA direct digital PCR method for cell viability estimation.

BACKGROUND: Accurate estimation of cell viability is crucial in various applications such as cytotoxicity testing and routine cell culture on both industrial and laboratory scales. For this, the real-time monitoring of cell status would be beneficial. Conventional cell-based assays for cell viability have limitations in sensitivity and time-effectiveness. Analysis of cell-free DNA (cfDNA) in (culture) media is a good alternative as cfDNA release are a well-known phenomenon during cell death. RESULTS: We demonstrate a direct digital PCR (dPCR) method to estimate cell viability by analyzing cfDNA in media during induced cell death. After validating the duplex dPCR method for short and long amplicons of the SMAD4 and RPP30 loci, we determined that a media volume of 2 µL is feasible to measure the target DNA copy number with minimal negative effects on amplification. dPCR inhibition was evident with a higher media volume per reaction targeting long amplicons. Next, we applied our dPCR method using media cfDNA and other conventional methods to the monitoring of camptothecin (CPT)-induced cell death. Copy numbers increased significantly after 4 h of CPT treatment, showing a fold change of approximately 4-6 compared to the controls. Cell-based assays such as the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay and annexin V/7-AAD assay also indicated increased cell death at 4 h, but the trypan blue exclusion assay did not. SIGNIFICANCE: The developed media cfDNA direct dPCR method allows for efficient measurements of the degree of cell viability. Unlike other conventional cell-based assays, our method has advantages of no loss of cultured cells and the ability to implement online analysis. Accurate and sensitive media cfDNA analysis using dPCR can be adopted in various applications such as determining cytotoxicity levels in large-scale bioreactors or screening for effective anticancer drugs.

Impact of immunohistochemistry staining conditions on the incidence of human epidermal growth factor receptor 2 (HER2)-low breast cancer.

We investigated frequencies of HER2-low breast cancer (BC) (immunohistochemistry [IHC] 1+ or 2+ without gene amplification) before and after IHC conditions were modified in order to understand the impact of IHC staining conditions on frequencies of HER2-low BC. Primary BC cases diagnosed at the Yeungnam University Hospital (YUH, n = 728) or Keimyung University Dongsan Hospital (KUDH, n = 290) in 2022 were reviewed, and data on HER2 status and IHC conditions were collected (cohort 1). Both institutions used the 4B5 antibody for HER2 IHC but had different staining protocols. After modifications of the IHC conditions at both institutions, primary BC cases (YUH, n = 324 and KUDH, n = 135) diagnosed from April to July 2023 (cohort 2) were reviewed to assess any changes in the frequency of HER2 status. In cohort 1, of the 728 cases diagnosed at YUH, 556 (76.4%) were HER2-zero, 76 (10.4%) were HER2-low, and 96 (13.2%) were HER2-positive, and of the 290 cases diagnosed at KUDH, 135 (46.6%) were HER2-zero, 82 (28.3%) were HER2-low, and 73 (25.2%) were HER2-positive. Modifications in HER2 IHC staining conditions dramatically increased the frequencies of HER2-low BC in cohort 2 (YUH 38.9% and KUDH 49.6%), but they did not result in significant changes in the HER2-positive rates (YUH 15.4% and KUDH 25.2%) compared to cohort 1. In conclusion, minor modifications in HER2 IHC staining conditions significantly affected the frequency of HER2-low BC but had little impact on the HER2-positivity rate. Each pathology laboratory should verify IHC conditions using control slides (including 1+) to enable the accurate identification of HER2-low BC.

A Nationwide Study on HER2-low Breast Cancer in South Korea: Its Incidence of 2022 Real World Data and the Importance of Immunohistochemical Staining Protocols.

Purpose: Notable effectiveness of trastuzumab deruxtecan (T-DXd) in patients with HER2-low advanced breast cancer (BC) has focused pathologists' attention. We studied the incidence and clinicopathologic characteristics of HER2-low BC, and the effects of immunohistochemistry (IHC) associated factors on HER2 IHC results. Materials and Methods: The Breast Pathology Study Group of the Korean Society of Pathologists conducted a nationwide study using real-world data on HER2 status generated between January 2022 and December 2022. Information on HER2 IHC protocols at each participating institution was also collected. Results: Total 11,416 patients from twenty-five institutions included in this study. Of these patients, 40.7% (range: 6.0%-76.3%) were classified as HER2-zero, 41.7% (range: 10.5%-69.1%) as HER2-low, and 17.5% (range: 6.7%-34.0%) as HER2-positive. HER2-low tumors were associated with positive ER and PR statuses (p<0.001 and p<0.001, respectively). Antigen retrieval times (≥ 36 min vs. < 36 min) and antibody incubation times (≥ 12 min vs. < 12 min) affected on the frequency of HER2 IHC 1+ BC at institutions using the PATHWAY HER2 (4B5) IHC assay and BenchMark XT or Ultra staining instruments. Furthermore, discordant results between core needle biopsy (CNB) and subsequent resection specimen HER2 statuses were observed in 24.1% (787/3259) of the patients. Conclusion: The overall incidence of HER2-low BC in South Korea concurs with those reported in previously published studies. Significant inter-institutional differences in HER2 IHC protocols were observed, and it may have impact on HER2-low status. Thus, we recommend standardizing HER2 IHC conditions to ensure precise patient selection for targeted therapy.

Optimization of duplex digital PCR for the measurement of SARS-CoV-2 RNA.

Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations. In particular, the formation of heterodimers among assays greatly interfered with qPCR results, but only minimally with dPCR results. In dPCR, existing heterodimers lowered the PCR efficiency, producing a dampened fluorescent signal in positive partitions. This can be corrected by adjusting the PCR cycling conditions, after which dPCR shows the capability of measuring the expected copy number. In addition, we present a process to improve the existing RdRp assay by correcting the primer sequences and matching the melting temperature, ultimately producing highly sensitive and robust assays. The results of this study can reduce the cost and time of SARS-CoV-2 diagnosis while increasing accuracy. Furthermore, our results suggest that dPCR is a reliable method for the accurate measurement of nucleic acid targets.

Digital PCR for the characterization of reference materials.

Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.

Methotrexate-Induced Accelerated Nodulosis in a Patient with Systemic Lupus Erythematosus.

Methotrexate (MTX)-induced accelerated nodulosis (MIAN) reportedly occurs in patients with rheumatic arthritis receiving MTX therapy. However, it has also been reported in patients with other autoinflammatory conditions, such as systemic lupus erythematosus (SLE). A 38-year-old woman diagnosed with SLE presented with multiple movable, firm, flesh-colored nodules on both hands that had developed 3 years ago. She was taking oral medications, specifically hydroxychloroquine, azathioprine, and MTX. Histopathological examination revealed palisaded granulomatous inflammation, surrounded by histiocytes and lymphocytes, along the dermis to the subcutaneous fat layer. Fibrinoid degeneration was observed at the center of the granulomatous inflammation, and dermal mucin deposition was not observed. The patient was diagnosed with MIAN, and therefore discontinuation of MTX was recommended. Subsequently, the lesions almost completely disappeared with no signs of recurrence. MIAN exhibits clinicopathological features similar to those of rheumatoid nodules; therefore, it can be easily misdiagnosed. Herein, we report a case of MIAN in a patient with SLE to contribute to the accurate diagnosis and appropriate management.

Intradermal Low-Fat Spindle Cell Lipoma: A Case Report.

Spindle cell lipoma is a rare benign neoplasm that features a mixture of evenly aligned spindle cells, mature adipocytes, and ropey collagen. Most cases of spindle cell lipoma are found in the subcutaneous tissue, and intradermal spindle cell lipoma is rarely reported. We present a case of intradermal spindle cell lipoma in a 46-year-old female who presented with a 0.7-cm flesh-colored and dome-shaped nodule on the right temple that had developed 6 years ago. This mass was excised, and upon histopathologic examination, an unencapsulated lesion was located in the dermis, which consisted of bland spindle cells, scanty mature adipocytes, rare lipoblasts, and ropey collagen bundles with prominent basophilic myxoid stroma. Immunohistochemical staining showed diffuse positivity for CD34, negativity for the S-100 protein, and loss of retinoblastoma protein expression. Based on these features, intradermal low-fat spindle cell lipoma was diagnosed. No evidence of local recurrence was observed 4 months after excision. Intradermal low-fat spindle cell lipomas are extremely rare and can easily be mistaken for tumors that have similar clinical and histopathological findings. Herein, we report a globally rare case of an intradermal low-fat spindle cell lipoma.

Superficial CD34-Positive Fibroblastic Tumor: Two Case Reports.

Superficial CD34-positive fibroblastic tumor (SCPFT) is a recently described disease entity characterized by marked nuclear pleomorphism, low mitotic count, and diffuse CD34 positivity. It is a rare, distinctive, low-grade fibroblastic neoplasm. To date, only 44 cases have been reported in the English-language literature. Herein, we report two cases of SCPFT involving a 48-year-old male and a 22-year-old male with superficial tumors on the right and left thighs, respectively. Excision was performed in both cases. Histologically, both tumors showed spindle-to-epithelioid cells arranged in fascicular or sheet-like patterns. Most cells displayed granular or eosinophilic glassy cytoplasm, marked nuclear pleomorphism, and a low mitotic rate. On immunohistochemical staining, tumor cells were diffusely positive for CD34 and negative for S100 protein, smooth muscle actin, and desmin. After wide excision, neither patient experienced recurrence or metastasis after 16 months and 11 months of clinical follow-up, respectively. To the best of our knowledge, these are the first two cases of SCPFT reported in Korea. We believe these case reports would contribute to the clinicopathological understanding of SCPFT and assist clinicians in differentiating this tumor from other superficial soft tissue neoplasms.

Prediction of Oncotype DX Recurrence Score Using Clinicopathological Variables in Estrogen Receptor-Positive/Human Epidermal Growth Factor Receptor 2-Negative Breast Cancer.

PURPOSE: Oncotype DX (ODX) is a well-validated multigene assay that is increasingly used in Korean clinical practice. This study aimed to develop a clinicopathological prediction (CPP) model for the ODX recurrence scores (RSs). METHODS: A total of 297 patients (study group, n = 175; external validation group, n = 122) with estrogen receptor-positive, human epidermal growth factor receptor 2 (HER2)-negative, T1-3N0-1M0 breast cancer, and available ODX test results were included in the study. Risk categorization as determined by ODX RSs concurred with the TAILORx study (low-risk, RS ≤ 25; high-risk, RS > 25). Univariate and multivariate logistic regression analyses were used to assess the relationships between clinicopathological variables and risk stratified by the ODX RSs. A CPP model was constructed based on regression coefficients (ß values) for clinicopathological variables significant by multivariate regression analysis. RESULTS: Progesterone receptor (PR) negativity, high Ki-67 index, and nuclear grade (NG) 3 independently predicted high-risk RS, and these variables were used to construct the CPP model. The C-index, which represented the discriminatory ability of our CPP model for predicting a high-risk RS, was 0.915 (95% confidence interval [CI], 0.859-0.971). When the CPP model was applied to the external validation group, the C-index was 0.926 (95% CI, 0.873-0.978). CONCLUSION: Our CPP model based on PR, Ki-67 index, and NG could aid in the selection of patients with breast cancer requiring an ODX test.

Characteristics and Prognosis of Estrogen Receptor Low-Positive Breast Cancer.

PURPOSE: The updated American Society of Clinical Oncology/College of American Pathologists guideline for estrogen receptor (ER) testing recommends that breast cancer with ER expression in 1-10% of tumor cells should be reported as ER-low positive (ERlow), although limited data are available on the overall benefits of endocrine therapy. We investigated the clinicopathological characteristics and clinical outcomes of ERlow breast cancer and to compare them with those of ER-negative (ERneg) and ER-high (> 10% of tumor cells, ERhigh) breast cancers. METHODS: Consecutive patients with invasive breast cancer who underwent curative surgery between November 2007 and December 2014 were included. Clinicopathological characteristics and disease-free survival (DFS) of ERlow tumors were compared with those of ERneg and ERhigh tumors. RESULTS: Of the 2,309 cases included, 46 (2%), 643 (27.8%), and 1,620 (70.2%) were ERlow, ERneg, and ERhigh, respectively. ERlow tumors were associated with no special type of histology (p = 0.011), advanced pT (p = 0.017), pN (p = 0.009) and anatomic stages (p < 0.001), high grade (p < 0.001), negative/low progesterone receptor (PR) status (p < 0.001), human epidermal growth factor receptor 2 positivity (p < 0.001), high Ki-67 (p < 0.001), and recurrence (p = 0.006) compared to ERhigh tumors. DFS was significantly dependent on ER status, and ERlow tumors showed poorer DFS than ERhigh tumors (p = 0.001), however, there was no significant survival difference between ERlow and ERneg tumors. Furthermore, DFS in ERhigh patients was affected by hormone therapy (p < 0.001), while it was not affected in ERlow patients. CONCLUSION: Patients with ERlow breast cancer have clinicopathological characteristics that differ from those with ERhigh tumors. Although this study was limited by the small sample size of the ERlow group, no benefit from hormone therapy was observed in the ERlow group compared with the ERhigh group.