bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-328 A Novel Pathway of Akt-Dependent PARP1 Activation Through the Nuclear Localization of EPRS1
Authors: Zin I , China A , Gogonea V , Fox P 
Published: October 2024

Abstract

Background
Glutamyl-prolyl-tRNA synthetase (EPRS1) is the only bifunctional aminoacyl-tRNA synthetase (aaRS) and is essential for interpreting the genetic code. EPRS1, along with seven other aaRSs, forms the multi-tRNA synthetase complex (MSC). EPRS1 consists of two catalytic domains, GluRS and ProRS, connected by a linker region. Several aaRSs within the MSC, including EPRS1, can dissociate from the MSC in response to specific stimuli. This dissociation enables non-canonical activities distinct from their primary role in protein synthesis. Breast cancer cells harboring a loss-of-function mutation in phosphatase and tensin homolog (PTEN) are known to have more activity in the serine/threonine kinase Akt. Poly-(ADP)-ribose polymerase 1 (PARP1), plays a vital role in DNA damage repair (DDR). PARP1 deposits one or more ADP-Ribose moieties onto damaged DNA or other proteins in a process referred to as PARylation. We hope to connect Akt activation and PARP1 activity through the nuclear localization and noncanonical function of EPRS1. We hypothesize, that when Akt is activated, either through the loss of PTEN function or through stimuli such as heat shock or H2O2 treatment, will stimulate the nuclear localization of EPRS1 and modulate PARP1 activity.

Methods
To test our hypothesis, we evaluate Akt activation, EPRS1 localization, and PARP1 activity. Using pharmacological activators and inhibitors of Akt, we test if inhibitors and activators alone are sufficient to cause the nuclear localization of EPRS1. Biochemically, we isolate nuclear and cytosolic fractions used in various western blot analysis. We use a variety of assays for PARP1 activity and DDR that include immobilized histones, calculating IC50s of PARP1 inhibitors, comet assay, and confocal microscopy. To ascertain the connection between PARP1 and EPRS1 we use LC-MS/MS analysis and immunoprecipitation.

Results
We show, in both patient-derived and cultured breast cancer cells, elevated levels of EPRS1 not only in the cytoplasm, but also within the nucleus. We find that nuclear localization EPRS1 is facilitated by a nuclear localization sequence (NLS) located within the linker region of the protein. Breast cancer cells harboring a loss-of-function in PTEN exhibit higher levels of EPRS1 in the nucleus compared to PTEN-positive cells. In EPRS1 knockdown cells, there is diminished expression of multiple tumor-related transcription factors, DNA-damage repair, tumor cell survival, and PARP1 auto-PARylation. We demonstrate that nuclear EPRS1 binds to and shares an interactome with PARP1.

Conclusions
EPRS1-mediated regulation of PARP1 activity provides a new mechanistic link between PTEN loss in breast cancer cells, PARP1 activation, and cell survival and tumor growth. Targeting the non-canonical activity of EPRS1, without inhibiting canonical tRNA ligase activity, might provide a new therapeutic approach in breast and other forms of cancer, potentially supplementing existing cancer therapeutics.
B-332 Use of urinary volatile organic compounds in monitoring prostate cancer after radical prostatectomy
Authors: Badmos S , Lee W 
Published: October 2024

Abstract

Background
Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous cancer among males and the second cause of cancer-related deaths. PCa treatment involves different methods, and most common is radical prostatectomy (RP), which entails removal of prostate-gland from men who have been diagnosed with PCa. Prostatic-specific-antigen (PSA) has been used for detection of recurrent disease for years. After its introduction as biochemical recurrence (BCR) marker, men with distinct diseases were treated similarly. Overtime, it has been observed that PSA relapse presents several meanings according to clinicopathological features, like Gleason score, PSA-doubling-time, clinical stage, surgical margin status. Despite this, PSA remains main tool to assess disease progression after RP. RP remains primary treatment for localized PCa and has been performed for years with excellent oncologic control. However, approximately 20-40% of patients with clinically localized PCa will present biochemical-recurrence (BCR) after RP, while some with recurrent-metastasis. The study aims to investigate potential volatile organic compounds (VOCs) associated with men who have undergone RP but still abhor the disease.

Methods
Urine samples were collected from 110 male adults with biopsy-proven PCa-positive results before and after RP. VOCs in urine were extracted by stir-bar-sorptive-extraction and analyzed using thermal-desorption with gas chromatography-mass spectrometry. Metabolomics and machine-learning tools used to develop and evaluate models for PCa diagnosis before and after RP.

Results
PLS-DA and VIP loading plots identified potential VOC panels that could be used to differentiate PCa patients before and after RP and those with BCR and recurrent metastasis. Furthermore, logistic-regression results with validation provide a promising diagnostic model for PCa diagnosis after RP.

Conclusions
This novel method using urinary VOCs was developed to fill gaps in PCa monitoring after RP. These research findings could aid and fast-track the provision of rapid point of care to the treated PCa patients who still abhor the disease.
B-333 Optimizing AFP Cutoffs for Hepatocellular Carcinoma Screening: Insights from the National Cancer Screening Program in Korea
Authors: Choi Y , Kim S , Kim H , Jeong H , Lee H , Lee W , Chun S 
Published: October 2024

Abstract

Background
The incidence rate and mortality rate of liver cancer were 11.6 (ranked 8th among cancers) and 10.7 (4th) per 100,000 individuals respectively globally in 2020, whereas in Korea, they were higher at 29.5 (7th) and 20.6 (2nd) per 100,000 individuals. The National Cancer Screening Program (NCSP) in Korea conducts biannual concurrent liver ultrasound and serum alpha-fetoprotein (AFP) measurement for hepatocellular carcinoma (HCC) surveillance in high-risk groups, including those with chronic hepatitis B and C, and liver cirrhosis. The effectiveness of surveillance is impacted by varying AFP cutoffs; however, within the NCSP, different cutoffs are being used, and it is not clear which cutoffs are being employed. Harmonization of AFP test results by major reagent manufacturers have been achieved, enabling the adoption of a uniform threshold. This study aims to assess the variation of AFP cutoffs among institutions within the NCSP and suggest a unified and optimal AFP threshold.

Methods
This study examined HCC screening results from the NCSP between 2018 and 2020, investigating unit and cutoff usage for AFP test across institutions each year (number of institutions were 4452 for 2018, 4754 for 2019, and 4847 for 2020). To determine the optimal AFP cutoff for HCC screening, datasets comprised unique patient results from 2018 to 2020 (number of patients = 819,644). Receiver operating characteristic (ROC) curve analyses were conducted for determine best AFP cutoffs. Cancer diagnosis was defined by billing records indicating HCC within one year post-screening.

Results
More than 96% of institutions used ng/mL as a unit of AFP test. Among institutions using ng/mL, the most frequently used AFP cutoff was 7 ng/mL, with frequency percentages of 75.7%, 72.2%, and 62.2% in 2018, 2019, 2020, respectively. The percentiles (1st, 10th, 90th, 99th) of AFP cutoff usage for the years 2018, 2019, and 2020 were (7, 7, 8.8, 15), (7, 7, 8.9, 15), and (7, 7, 9, 15) respectively. The AUC of ROC was 0.824 and some cut-off points with their sensitivity and specificity values were as follows: 5 ng/mL (0.648, 0.874); 10 (0.457, 0.976); 20 (0.327, 0.993); 40 (0.246, 0.997); 100 (0.169, 0.998); 200 (0.123, 0.999); 400 (0.084, 1).

Conclusions
Different cutoffs observed across institutions in NCSP. Our study cautiously suggests that the optimal AFP value for screening HCC in NCSP may range from 10 to 20 ng/mL, considering sensitivity and specificity when AFP is combined with ultrasound in regions with a high prevalence of HCC. For a more suitable AFP cutoff recommendation, additional analyses based on ultrasound findings and underlying diseases should be considered.
B-340 Evaluation of the Analytical Performance of Three Major Immunoglobulins Assays on the Atellica CI Analyzer
Authors: Carter R H , Gupta P , Tyler C , Micklitsch C , Arrode-Bruses G , Snyder J 
Published: October 2024

Abstract

Background
The Atellica® CI Analyzer is an automated, high-throughput integrated chemistry and immunoassay analyzer utilizing both Atellica® CH and Atellica® IM Assays. This study evaluated the analytical performance of the the Atellica CH Immunoglobulin A_2 (IgA_2), Immunoglobulin G_2 (IgG_2), and Immunoglobulin M_2 (IgM_2) Assays on the Atellica CI Analyzer.

Methods
Precision studies were performed according to CLSI EP05-A3 using native and contrived human serum samples. One aliquot of each sample was tested in duplicate in two runs per day ≥2 hours apart on each analyzer for ≥20 days. Precision was evaluated using three reagent lots on one system. Method comparison studies were performed using three reagent lots according to CLSI EP09c. Individual native and contrived human serum samples were analyzed using the Atellica CH IgA_2, IgG_2, and IgM_2 Assays on the Atellica CH Analyzer and the Atellica CI Analyzer. LoB and LoD were determined as described in CLSI EP17-A2.

Results
Representative precision and method comparison results for each assay are listed in the table. For the three assays tested, repeatability and within-lab %CVs were &lt;1.8% and &lt;3.9%, respectively. Slopes determined by the Deming linear regression model were approximately equal to 1. Detection capability for the Atellica CH IgA_2 Assay on the Atellica CI Analyzer was estimated at 1.6 mg/dL (0.02 g/L) and 3.6 mg/dL (0.04 g/L) for LoB, and LoD. For the Atellica CH IgG_2 Assay, LoB and LoD were determined at 7 mg/dL (0.07 g/L) and 21 mg/dL (0.21 g/L). For the Atellica CH IgM_2 Assay, LoB and LoD were determined at 5.0 mg/dL (0.05 g/L) and 8.0 mg/dL (0.08 g/L).

Conclusions
Evaluation of the Atellica CH IgA_2, IgG_2, and IgM_2 Assays using the Atellica CI Analyzer demonstrated good precision and equivalent performance compared to the same assays on the Atellica CH Analyzer.
B-347 Analytical Performance Evaluation of the High Sensitivity PSA Assay and the Free PSAII Assay on the Atellica IM Analyzer
Authors: Olson Nissen K , Ngbokoli M , Snyder J , Pagano M , Owusu A , Patibandla S 
Published: October 2024

Abstract

Background
Measurement of serum prostate specific antigen (PSA) levels may be used in prostate cancer (PC) screening, but elevated PSA levels also are observed in patients with other etiologies such as benign prostatic hypertrophy. Studies suggest that measuring PSA with or before digital rectal examination (DRE) provides a better method of detecting PC than DRE alone. The free prostate specific antigen (fPSA) assay is an aid for distinguishing PC from benign prostate conditions in men 50 years or older with PSA values 4.0-10.0 ng/mL (µg/L) and DRE findings nonsuspicious for PC. The goal of this study was to evaluate the analytical performance of the high sensitivity PSA (hsPSA)* and free PSA (fPSAII)* assays on the Atellica® IM Analyzer.

Methods
Detection capability studies were performed per CLSI EP17-A2. Precision testing was performed per CLSI EP05-A3 with native human serum and QC samples, 3 reagent lots, 1 analyzer, 2 runs/day, 2 replicates/run for 20 days. For Atellica® hsPSA and fPSAII assays a multi-site reproducibility study was conducted per CLSI EP-05 A3 using native and contrived serum samples, 3 reagent lots, and 3 different sites and analyzers; samples were assayed in triplicate for five days, two runs/day ∼2 hours apart. Linearity testing was performed per CLSI EP06-A on a dilution series made from a high PSA sample (native human male serum pool) and a low sample (native human female serum), 4 replicates, 3 reagent lots, and 1 analyzer. Specimen equivalency was determined by Weighted Deming regression model per CLSI EP09c-ed3.

Results
Results are presented in the table.

Conclusions
The Atellica IM hsPSA assay and fPSAII assays detection capability, precision, linearity, and specimen equivalency were acceptable.
*CAUTION: Investigational Device. Not available for sale. Future availability cannot be guaranteed. The results are preliminary and were achieved in unique setting with no expected timeline for completion.
B-348 Performance of the Atellica IM Analyzer’s HighSensitivity PSA Assay as an Aid for Monitoring Prostate Cancer Recurrence
Authors: Olson Nissen K , Snyder J , Pagano M , Owusu A , Grosett M , Birmingham N , Christenson R , deFilippi C 
Published: October 2024

Abstract

Background
Prostate specific antigen (PSA) is a suitable marker for monitoring men with prostate cancer (PC), and for detecting recurrence after therapy in conjunction with other diagnostic measures. Studies were performed to evaluate performance of the Atellica® IM High-Sensitivity PSA assay (hsPSA)* versus the Atellica® IM PSA assay in patients undergoing management (monitoring) of PC.

Methods
A total of 868 serum samples from 170 subjects with PC (92 [54%] subjects had a radical prostatectomy (RP) before enrollment) were collected at 7 sites across the United States. Subjects had baseline and &gt;2 follow-up visits during treatment (average 5.106 visits, SD=1.414). Samples were tested using the Atellica IM hsPSA assay and the commercially available Atellica IM PSA assay (comparative method). For RP and non-RP combined, 644 paired samples for each assay were tested. Subjects were designated “No Progression” (responding, stable, and no evidence of disease subjects) or “Progression” at each visit based on clinical classification.

Results
In this study the Atellica IM hsPSA assay demonstrated equivalent performance as commercial Atellica IM PSA in predicting disease status (table). The PPA between the assays was 95.5% and the NPA was 98.9%. Concordance to clinician classification was similar for both assays (∼80% PPA and 90% NPA).

Conclusions
Preliminary results demonstrated equivalent performance of the Atellica IM hsPSA assay as the commercially available Atellica IM PSA assay in terms of predicting disease status. This hsPSA assay can detect very low levels of PSA, which is particularly important for the monitoring of RP patients.
*CAUTION: Investigational Device. Not available for sale. Future availability cannot be guaranteed. The results are preliminary and were achieved in unique setting with no expected timeline for completion.
B-351 Genotoxic Producing Escherichia coli Protects and Promotes Breast Adenocarcinoma
Authors: Heaton L , Figard S D , Garcia R A 
Published: October 2024

Abstract

Background
Recent studies have linked certain colibactin producing subphylas of E. coli to colorectal cancer. The bacterium synthesizes colibactin via the pks genomic island containing a series of clbA to clbS genes. The genotoxin causes inter-strand DNA cross-links, which lead to double strand breaks and promotion of colorectal adenocarcinoma. The published studies have prioritized the colorectal regions of the body where E. coli is commonly found, but none have identified the same genotoxic relationship with other types of adenocarcinoma. In this study, we evaluate DNA damage and cellular changes of mammary breast tissue based on high and low levels of colibactin producing E. coli exposure. The goal is to evaluate if colibactin can affect cells in the mammary breast tissue promoting breast adenocarcinoma growth.

Methods
Two cell lines were acquired from ATCC: primary mammary epithelial cells (PCS-600-010) and MCF-7 breast adenocarcinoma cells (HTB-22). Both cell lines were split into six culture flasks and maintained until ∼80% confluence was reached using the ATCC cell culture protocols. Once all the flasks had reached the target confluence, they were divided into exposure groups of high and low concentrations of colibactin producing E. coli, a group of non-colibactin producing E. coli, a group exposed only to phosphate buffered saline, and a control group with no exposure. Cellular morphology was observed using light microscopy before, after exposure, and every 5 minutes up to 15 minutes. E. coli and colibactin DNA concentrations were quantified using quantitative polymerase chain reaction. Genomic DNA was extracted from each group of cells. The DNA from each group was whole genome sequenced and analyzed for genomic variation.

Results
The normal cells exposed to E. coli showed immediate lysing and continued to lyse after a 5 minute incubation; however, the adenocarcinoma positive cells showed no lysing up to 30 minutes incubation. Sequencing results show genomic variation between the groups and specific break points associated with the E. coli exposed groups.

Conclusions
Our results show that the presence of E. coli with mammary breast tissue can destroy normal tissue, promote lysis resistance, and allow adenocarcinoma cells to continue to grow. The colibactin producing E. coli does cause double stranded breaks and can lead to cell death. This new information points out a critical need to monitor the microbiome and infection levels of people at risk or in early stages of cancer to prevent adenocarcinoma growth and destruction of normal tissue. This study indicates that colibactin producing E. coli may play a larger role in tissue damage and promotion of other types of cancer. More research is needed to elucidate the molecular pathway and mechanisms of colibactin, which will lead to new diagnostics or therapeutics that monitor E. coli levels or inhibit colibactin’s toxic effects.
B-356 Siemens CYFRA 21-1: an assay for measurement of cytokeratin fragment 21-1
Authors: Cline D J , Khokhar S , Benina N , Thorne G 
Published: October 2024

Abstract

Background
Cytokeratins are structural proteins forming the subunits of epithelial intermediary filaments. The soluble fragment of cytokeratin 19, cytokeratin fragment 21-1 (CYFRA 21-1), can be found in the blood of lung cancer patients, primarily those with non-small cell lung cancer (NSCLC). CYFRA 21-1 is the preferred biomarker in the management of NSCLC, particularly squamous cell and large cell carcinoma subtypes. An assay for CYFRA 21-1 on Siemens ADVIA Centaur® XPT and Siemens Atellica® IM (Siemens CYFRA) is being developed and analytical performance is being presented.

Methods
The Siemens CYFRA 21-1 assay (in development) is a one-step chemiluminescent microparticle immunoassay (CMIA) for the quantitative determination of CYFRA 21-1 in human serum and plasma. The specimen is incubated with paramagnetic microparticles coated with the monoclonal antibody (mAb) BM19.21 and acridinium-labeled mAb KS19.1 conjugate on the Siemens ADVIA Centaur XPT System and Siemens Atellica IM System. After incubation and washing, Acid and Base reagents are added. The resulting relative light units (RLUs) are directly proportional to the amount of CYFRA 21-1 in the sample allowing for the quantitative determination of CYFRA 21-1 in the specimen.

Results
The following performance were determined using 3 unique lots of reagents and calibrators with the calibration range for the assay being 0.00 to 100.00 ng/mL. For the ADVIA Centaur XPT and Atellica IM systems were shown to be equivalent within 4%. The limit of blank (LoB), limit of detection (LoD), and limit of quantitation at 20% CV (LoQ) were determined and met the goal of ≤ 1.00 ng/mL. Linearity according to CLSI EP06 Ed2 was demonstrated for a range of 0.66 through 100.00 ng/mL. A Precision study of 2 controls and 5 panels spanning the range of the assay demonstrated a total %CV ≤ 8% at all levels. In the sample tube type study, a matrix comparison of 61 matched serum and plasma samples were evaluated. Passing-Bablock slopes of &lt; 5% and r &gt; 0.99 were observed when evaluating samples within the measurement range for plasma (LiHep, LiHep separator, K2EDTA and K3EDTA) tubes and serum separator tubes (SST) compared to the Red Top serum samples. Six endogenous substances were evaluated for interference in the CYFRA 21-1 assay. The average percent difference between test and control samples for all endogenous interferents was &lt; 10%. Percent difference in the presence of 20 potentially interfering drugs was ≤ 4.0%.

Conclusions
The Siemens CYFRA 21-1 assay currently in development is a sensitive and precise assay for the quantitative determination of CYFRA 21-1 in human serum and plasma.
B-357 Siemens CA 72-4: an assay for measurement of Tumor Associated Glycoprotein (TAG) 72
Authors: Cline D J , Glass E , Benina N , Thorne G 
Published: October 2024

Abstract

Background
The tumor associated glycoprotein (TAG) 72, also known as CA 72-4 is a mucin protein of high molecular weight. CA 72-4 is found on the surface of many cancer cells, including stomach (gastric), ovary, breast, colon and pancreatic cells. CA 72-4 is currently one of the primary markers for the diagnosis of gastric cancer and monitoring the course and efficacy of gastric cancer. In ovarian cancer, it has a higher sensitivity for mucin- type ovarian cancer, and its combination with CA125 for detection can significantly improve the clinical sensitivity. In colorectal cancer, CA 72-4 combined with CEA detection was also found to significantly improve the sensitivity of the initial diagnosis. An assay for CA 72-4 on Siemens Atellica IM (Siemens CA 72-4) is being developed and analytical performance is being presented.

Methods
The Siemens CA 72-4 assay (in development) is a one-step chemiluminescent microparticle immunoassay (CMIA) for the quantitative determination of CA 72-4 in human serum and plasma. The specimen is incubated with paramagnetic microparticles coated with the monoclonal antibody (mAb) B72.3 and acridinium-labeled mAb CC49 conjugate on the Siemens Atellica IM® System. After incubation and washing, Acid and Base reagents are added. The resulting relative light units (RLUs) are directly proportional to the amount of CA 72-4 in the sample allowing for the quantitative determination of CA 72-4 in the specimen.

Results
The following performance were determined using 3 unique lots of reagents and calibrators with the calibration range for the assay being 0.00 to 200.00 U/mL. The limit of blank (LoB), limit of detection (LoD), and limit of quantitation at 20% CV (LoQ) were determined and met the goal of ≤ 1.00 U/mL. Linearity according to CLSI EP06 Ed2 was demonstrated for a range of 1.00 through 200.00 U/mL. A Precision study of 2 controls and 5 panels spanning the range of the assay demonstrated a total %CV ≤ 6% for samples ≥ 5.00 U/mL and ≤ 0.25 SD for samples &lt;5.00 U/mL. In the sample tube type study, a matrix comparison of 23 matched serum and plasma samples were evaluated. Passing-Bablock slopes of &lt; 8% and r &gt; 0.99 were observed when evaluating samples within the measurement range for plasma (LiHep, LiHep separator, K2EDTA and K3EDTA) tubes and serum separator tubes (SST) compared to the Red Top serum samples. Five endogenous substances were evaluated for interference in the CA 72-4 assay. The average percent difference between test and control samples for all endogenous interferents was &lt; 10%. Percent difference in the presence of 28 potentially interfering drugs was ≤ 4.0%.

Conclusions
The Siemens CA 72-4 assay currently in development is a sensitive and precise assay for the quantitative determination of CA 72-4 in human serum and plasma.