Marker Of Disease Research Articles

The Relationship Between Physical Activity and Non-Modifiable Risk Factors on Alzheimer's Disease and Brain Health Markers: A UK Biobank Study.

Modifiable (physical activity) and non-modifiable (sex and genotype) risk factors interact to affect Alzheimer's disease (AD) risk. Further investigation is necessary to understand if these factors influence brain volume and cognition. The study aimed to assess the effect of physical activity, APOE genotype, and sex on AD risk, brain volume, and cognition. UK Biobank data from 2006 to 2023 was accessed. Physical activity was measured by accelerometers, and International Physical Activity Questionnaire. Outcomes were AD incidence; brain volume (ventricular cerebrospinal fluid and total brain); and cognition (executive function, memory, visuospatial ability, processing speed, and reaction time). Logistic and linear regression models were conducted. 69,060 participants met inclusion criteria (mean age: 62.28 years, SD: 7.84; 54.64% female). Higher self-reported (OR = 0.63, 95% CI [0.40, 1.00], p = 0.047) and accelerometer-assessed (OR = 0.96 [0.93, 0.98], p = 0.002) physical activity was associated with lower disease incidence. Smaller ventricular cerebrospinal fluid volume (β= - 65.43 [- 109.68, - 17.40], p = 0.007), and larger total brain volume (β= 4398.46 [165.11, 8631.82], p < 0.001) was associated with increased accelerometer-assessed and self-reported physical activity respectively. Both brain volume analyses were moderated by sex. Increased accelerometer-assessed physical activity levels were associated with faster reaction time (β= - 0.43 [- 0.68, - 0.18], p = 0.001); though poorer visuospatial ability (β= - 0.06 [- 0.09, - 0.03], p < 0.001), and executive function (β= 0.49 [0.31, 0.66], p < 0.001; β= 0.27 [0.10, 0.45], p = 0.002) was related to self-reported physical activity levels. Higher levels of physical activity reduce AD risk independently of non-modifiable risk factors. Moderation of sex on brain volume highlighted the importance of incorporating non-modifiable risk factors in analysis.

High-density lipoprotein functionality in cholesterol efflux in early childhood is related to the content ratio of triglyceride to cholesterol

Cholesterol efflux capacity (CEC), commonly measured as a useful risk marker of atherosclerotic cardiovascular disease, depends on high-density lipoprotein (HDL) functionality and its concentration. We defined the relative HDL functionality in cholesterol efflux, not influenced by HDL concentration, as the ratio of measured CEC to standardized CEC (stCEC) based on HDL-cholesterol (HDL-C) of each individual using the curve regression equation obtained from the correlation. HDL-C, CEC, and CEC/stCEC levels in the < 28-day-old participants (neonates) were significantly low compared to those of the ≥ 28-day-old participants, indicating that the low CEC levels in the neonates depend on not only lower HDL-C but also lower HDL functionality. The low level of CEC/stCEC was remarkable in neonates born at < 34 weeks of gestation and did not improved to the reference level (1.000) until the infantile period. The relatively low or high CEC/stCEC ratios in neonates and infants were associated with lower or higher HDL-TG and HDL-TG/HDL-C ratio, respectively. However, no apparent effect of HDL-TG and HDL-TG/HDL-C ratio on CEC/stCEC was observed in the ≥ 1-year-old participants, indicating that HDL functionality in cholesterol efflux could be associated with the various HDL particles with various lipid compositions, but not just with HDL-TG and HDL-TG/HDL-C ratio.

A simplified approach to define cervical vertebral levels in spinal cord MRI studies.

Spinal cord (SC) cross-sectional areas (CSAs) assessed with MRI have proven to be extremely valuable imaging markers in several diseases. Among the challenges is the delineation of vertebral levels to determine level-dependent changes in cord atrophy. With this study, we aimed to (1) test the hypothesis that there is proportionality in the position of the first six intervertebral discs and the length of the upper portion of the SC and (2) show that a proportionality approach can simplify the CSA assessment across vertebrae offering good reliability. Forty-six volunteers underwent standard T2-weighted and T1-weighted cervical SC MRI acquisitions. The distance between the obex and the intervertebral discs (from C2-C3 to T1-T2) was measured on the T2-weighted acquisitions of the entire cohort. In a test-retest experiment on 12 subjects, the % disc position values were used to define vertebral levels, and a comparison was performed with manual vertebrae assignment in terms of mean CSA and its coefficient of variation. The mean upper cord length for the cohort was 144.0±13.1mm. The discs' level % position in the upper cord was found to be fairly consistent, with standard deviations of 0.8%-1.7%. The mean vertebral CSA obtained with the proportionality method was substantially equivalent to the manual approach in terms of mean CSA values and test-retest reliability. With this study, we propose a proportionality method for the assignment of cervical SC vertebral levels that can simplify the processing of MRI datasets in the context of CSA measurements.

6934 Nutritional Factors and Endothelial Dysfunction in Women with Functional Hypothalamic Amenorrhea

Abstract Disclosure: E.R. Uddenberg: None. N. Safwan: None. G. Cook-Wiens: None. O. Obrutu: None. M. Saadedine: None. M.D. Hurtado: None. S. Faubion: None. M.D. Pisarska: None. S.L. Berga: None. J.E. Manson: None. C.N. Bairey Merz: None. C.L. Shufelt: None. Background: Functional hypothalamic amenorrhea (FHA) occurs in women of reproductive age and is a common form of secondary amenorrhea that results in hypoestrogenemia and hypercortisolemia. The underlying cause of FHA is due to a mismatch between energetic intake and expenditure that often manifests as disordered eating, excessive exercise, and psychosocial stress. Previous research identified that 1 in 3 women with FHA had endothelial dysfunction, a preclinical marker for cardiovascular disease. We sought to evaluate the nutrition content in young women with FHA compared to eumenorrheic controls and further assess the relationship to endothelial dysfunction. Methods: We enrolled 30 women with FHA and 29 eumenorrheic controls, not on hormones. FHA was defined as ≥3 consecutive months of amenorrhea, estradiol &amp;lt;50 pg/mL, FSH&amp;lt;10 mIU/L, and LH&amp;lt;10 mIU/L, and exclusion of polycystic ovary syndrome, hyperprolactinemia, thyroid dysfunction, and pregnancy. Eumenorrheic controls had monthly menses with ovulation (progesterone ≥4 ng/mL). Vascular function was measured using EndoPAT 2000 (Itamar® Medical Ltd) to calculate the reactive hyperemic index (RHI). An RHI ≤1.67 indicates endothelial dysfunction. Nutritional intake was collected using a 3-day food diary and analyzed using ESHA Research Food Processor® Nutrition Analysis. Percent (%) recommendation values for nutrition content comparison were calculated based on height, weight, and age. Statistical analysis included Analysis of Variance and Kruskal Wallis test with nonparametric variables reported as median [IQR]. Results: The mean age and BMI of FHA and controls were 26.4 ± 6.2 yrs and 30.3 ± 3.7 yrs (p=0.008), and 21.6 ± 6.2 and 21.8 ± 2.0 kg/m2 (p=0.16), respectively. The median months of FHA amenorrhea was 12 months [5.0, 34.0]. After adjusting for age, there was no difference in caloric intakes in women with FHA compared to controls (1783.9 [1465, 2011] kcal vs. 1731.9 [1578, 1982] kcal, p=0.73); however FHA has higher intake of grams of protein (84.2 [74, 112] g vs. 74 [59, 92] g, p=0.0036), and higher grams of dietary fiber (30.1 [22, 43] g vs. 17.3 [15, 23] g, p=0.0037), respectively. In women with FHA, endothelial dysfunction was associated with a higher % recommended calories (p=0.0098), calories from fat (p=0.02), grams of saturated fat (p=0.03), and grams of carbohydrates (p=0.049). Conclusions: Our results demonstrate that women with FHA consumed similar daily calories, although more grams of protein and dietary fiber than controls. In women with FHA, higher calories, calories from fat, grams of saturated fat and carbohydrates were associated with endothelial dysfunction. Future studies should aim to identify other factors related to endothelial dysfunction among women with FHA and whether some FHA phenotypes are associated with more endothelial dysfunction than others. Presentation: 6/1/2024

6934 Nutritional Factors and Endothelial Dysfunction in Women with Functional Hypothalamic Amenorrhea

Abstract Disclosure: E.R. Uddenberg: None. N. Safwan: None. G. Cook-Wiens: None. O. Obrutu: None. M. Saadedine: None. M.D. Hurtado: None. S. Faubion: None. M.D. Pisarska: None. S.L. Berga: None. J.E. Manson: None. C.N. Bairey Merz: None. C.L. Shufelt: None. Background: Functional hypothalamic amenorrhea (FHA) occurs in women of reproductive age and is a common form of secondary amenorrhea that results in hypoestrogenemia and hypercortisolemia. The underlying cause of FHA is due to a mismatch between energetic intake and expenditure that often manifests as disordered eating, excessive exercise, and psychosocial stress. Previous research identified that 1 in 3 women with FHA had endothelial dysfunction, a preclinical marker for cardiovascular disease. We sought to evaluate the nutrition content in young women with FHA compared to eumenorrheic controls and further assess the relationship to endothelial dysfunction. Methods: We enrolled 30 women with FHA and 29 eumenorrheic controls, not on hormones. FHA was defined as ≥3 consecutive months of amenorrhea, estradiol &amp;lt;50 pg/mL, FSH&amp;lt;10 mIU/L, and LH&amp;lt;10 mIU/L, and exclusion of polycystic ovary syndrome, hyperprolactinemia, thyroid dysfunction, and pregnancy. Eumenorrheic controls had monthly menses with ovulation (progesterone ≥4 ng/mL). Vascular function was measured using EndoPAT 2000 (Itamar® Medical Ltd) to calculate the reactive hyperemic index (RHI). An RHI ≤1.67 indicates endothelial dysfunction. Nutritional intake was collected using a 3-day food diary and analyzed using ESHA Research Food Processor® Nutrition Analysis. Percent (%) recommendation values for nutrition content comparison were calculated based on height, weight, and age. Statistical analysis included Analysis of Variance and Kruskal Wallis test with nonparametric variables reported as median [IQR]. Results: The mean age and BMI of FHA and controls were 26.4 ± 6.2 yrs and 30.3 ± 3.7 yrs (p=0.008), and 21.6 ± 6.2 and 21.8 ± 2.0 kg/m2 (p=0.16), respectively. The median months of FHA amenorrhea was 12 months [5.0, 34.0]. After adjusting for age, there was no difference in caloric intakes in women with FHA compared to controls (1783.9 [1465, 2011] kcal vs. 1731.9 [1578, 1982] kcal, p=0.73); however FHA has higher intake of grams of protein (84.2 [74, 112] g vs. 74 [59, 92] g, p=0.0036), and higher grams of dietary fiber (30.1 [22, 43] g vs. 17.3 [15, 23] g, p=0.0037), respectively. In women with FHA, endothelial dysfunction was associated with a higher % recommended calories (p=0.0098), calories from fat (p=0.02), grams of saturated fat (p=0.03), and grams of carbohydrates (p=0.049). Conclusions: Our results demonstrate that women with FHA consumed similar daily calories, although more grams of protein and dietary fiber than controls. In women with FHA, higher calories, calories from fat, grams of saturated fat and carbohydrates were associated with endothelial dysfunction. Future studies should aim to identify other factors related to endothelial dysfunction among women with FHA and whether some FHA phenotypes are associated with more endothelial dysfunction than others. Presentation: 6/1/2024

Urinary cyclophilin A as an early marker of chronic kidney disease with underlying type 2 diabetes

Cyclophilin A (CypA) is a novel renal inflammation biomarker, with levels altered in various diseases, particularly in patients with diabetes mellitus (DM) and kidney damage. This study aimed to investigate the correlation between urinary cyclophilin A (uCypA) and chronic kidney disease (CKD) conditions with and without type 2 diabetes mellitus (T2DM) using an in-house enzyme-linked immunoassay (ELISA) method. A uCypA strip-test prototype was also developed. An indirect ELISA was performed to determine the uCypA levels. A 0.48 µg/mL uCypA cutoff differentiated healthy patients from those with early-stage CKD (stages I and II). The uCypA levels were significantly increased in patients with progression of renal deterioration, especially in the T2DM with late-stage CKD group, compared to the control group. Fasting blood sugar (FBS), estimated glomerular filtration rate (eGFR), albumin/creatinine ratio, and metformin use were associated with uCypA levels. Multinomial logistic regression analysis revealed an association between uCypA levels and T2DM diagnosed for over five years and early-stage CKD. This finding shows that uCypA could be used as a biomarker for distinguishing early-stage CKD as well as T2DM complications, which is beneficial for patients to be aware of their health status and change their behavior to slow kidney deterioration.

Large expansion of plasma commensal viruses is associated with SIV pathogenesis in Macaca leonina.

Human immunodeficiency virus-1 (HIV-1) infection disrupts the homeostatic equilibrium between the host and commensal microbes. However, the dynamic changes of plasma commensal viruses and their role in HIV/simian immunodeficiency virus (SIV) pathogenesis are rarely reported. Here, we investigated the longitudinal changes of plasma virome, inflammation levels, and disease markers using an SIV-infected Macaca leonina model. Large expansions of plasma Anelloviridae, Parvoviridae, Circoviridae and other commensal viruses, and elevated levels of inflammation and D-dimer were observed since the chronic phase of SIV infection. Anelloviridae abundance appears to correlate positively with the CD4+ T cell count but negatively with SIV load especially at the acute phase, whereas other commensal viruses' abundances show opposite correlations with the two disease markers. Antiretroviral therapy slightly reduces but does not substantially reverse the expansion of commensal viruses. Furthermore, 1387 primate anellovirus open reading frame 1 sequences of more than 1500 nucleotides were annotated. The data reveal different roles of commensal viruses in SIV pathogenesis.

Altered anthropometrics and HA1c levels, but not dyslipidemia, are associated with elevated hs-CRP levels in middle-aged adults: A population-based analysis.

Population-based studies of cardiovascular disease markers, such as hs-CRP, are crucial. However, studies exploring the effect of metabolic indices on hs-CRP while controlling for confounding variables adequately in middle-aged adults are limited. Using Wave 5 data from the National Longitudinal Study of Adolescent Health (Add Health), we examined the impact of various metabolic indices on hs-CRP in adults aged 32-42, controlling for eight allergic and infectious factors that may elevate hs-CRP levels. We used multiple linear regression analysis to determine which factors predict hs-CRP levels after log transformation of the dependent variable. The total number of participants was N = 1839 (weighted N = 1390763), with a mean age of 38.1 (SD = 2.0) and 46.4% having obesity. Among the controlled variables, recent surgery was the only confounder to significantly predict increased hs-CRP levels (P = 0.029, exponentiated estimate (EE) = 1.61; 95% Cl: [1.31-1.91]). Notably, current smoking and altered LDL or TG levels did not show a significant association with hs-CRP levels (P > 0.05). However, a significant increase in hs-CRP levels was observed in females compared to males (P < 0.001, EE = 1.43; 95%Cl: [1.35-1.51]). Similar findings were noted for diabetic HbA1c levels (P = 0.001, EE = 1.6; 95%CL: [1.42-1.78]), high waist circumference (P = 0.015, EE = 1.25; 95%CL: [1.15-1.35]), and grade 3 obesity (P = 0.006, EE = 7.62; 95%CL: [2.86-12.38]). Although not statistically significant, hs-CRP levels exhibited a gradual increase with rising BMI after controlling for other variables. These findings will improve the clinical application of hs-CRP in predicting coronary artery disease, especially in younger adults.

Interactive effect of diabetes mellitus and subclinical MRI markers of cerebrovascular disease on cognitive decline and incident dementia: a memory-clinic study

BackgroundCognitive impairment is an increasingly recognized comorbidity of diabetes, yet the mechanisms underlying this association remain poorly understood. This knowledge gap has contributed to conflicting findings regarding the impact of diabetes on long-term cognitive outcomes in older adults. The presence of cerebrovascular disease (CeVD) may potentially modify this relationship. However, interactive effect between diabetes and subclinical MRI markers of CeVD on cognitive trajectories and incident dementia remains unexplored.MethodsA total of 654 participants underwent brain MRI at baseline, from whom 614 with at least one follow-up were selected for longitudinal analysis. Cognitive tests were performed annually up to 5 years. CeVD markers of interest were lacunes, white matter hyperintensities (WMHs), cerebral microbleeds (CMBs), cortical microinfarcts (CMIs), intracranial stenosis (ICS), and cortical infarcts. Blood-based Alzheimer biomarkers, including p-tau181 and p-tau181/Aβ42 ratio, were used as indicators of Alzheimer pathology.ResultsAt baseline, diabetes was associated with lower cognitive performance and higher burden of CeVD, but not p-tau181 or p-tau181/Aβ42 ratio. Longitudinally, we found an interactive effect of diabetes and WMHs, rather than an independent effect of diabetes, on cognitive decline and dementia risk. Subgroup analyses showed association of diabetes with cognitive outcomes was stronger in participants with high WMHs load but non-significant in those with low WMHs load. Moreover, these associations remained unchanged after adjusting for blood-based Alzheimer biomarkers.ConclusionsThe effect of diabetes on cognitive decline is contingent upon the presence of WMHs and independent of Alzheimer’s pathology. This finding raises the possibility of utilizing WMHs as an imaging biomarker to identify diabetic subgroup at greater risk of developing cognitive impairment. Furthermore, therapeutic interventions targeting WMHs may prevent cognitive deterioration in older adults with diabetes.

Identification of DNA methylation markers for age and Bovine Respiratory Disease in dairy cattle: A pilot study based on Reduced Representation Bisulfite Sequencing

Methylation profiles of animals are known to differ by age and disease status. Bovine respiratory disease (BRD), a complex infectious disease, primarily affects calves and has significant impact on animal welfare and the cattle industry, due to production losses, increased veterinary costs as well as animal losses. BRD susceptibility is multifactorial, influenced by both environmental and genetic factors. We have performed a pilot study to investigate the epigenetic profile of BRD susceptibility in six calves (three healthy versus three diagnosed with BRD) and age-related methylation differences between healthy calves and adult dairy cows (three calves versus four adult cows) using Reduced Representation Bisulfite Sequencing (RRBS). We identified 2537 genes within differentially methylated regions between calves and adults. Functional analysis revealed enrichment of developmental pathways including cell fate commitment and tissue morphogenesis. Between healthy and BRD affected calves, 964 genes were identified within differentially methylated regions. Immune and vasculature regulatory pathways were enriched and key candidates in BRD susceptibility involved in complement cascade regulation, vasoconstriction and respiratory cilia structure and function were identified. Further studies with a greater sample size are needed to validate these findings and formulate integration into breeding programmes aiming to increase animal longevity and disease resistance.

A-214 Evaluate LDL-C using NIH equation 2, Friedewald equation, and direct homogeneous measurement

Abstract Background It is essential to accurately assess Low-density lipoprotein cholesterol (LDL-C) levels, a key marker for cardiovascular disease often used for treatment recommendations. The Friedewald equation has been used for many years to calculate plasma LDL-C levels, but it has limitations. Therefore, before implementing the NIH equation, we compared LDL-C results from NIH Equation 2 to the Friedewald formula and then to Atellica direct homogeneous assay LDL-C results. Methods A retrospective study of 1200 randomly selected patients out of 53,258 data points pulled from the laboratory information (LIS) system between November 2021 and October 2023. The study evaluated triglycerides, LDL-C, total cholesterol, and HDL-C measurements. The LDL-C calculated using NIH equation 2 has been set in the LIS as a non-reportable test component since November 1, 2021. The results obtained from NIH equation 2 and Friedewald equation were compared. LDL-C levels were measured using an Atellica direct homogeneous assay for an additional 75 specimens. Deming regression analysis compared measured and calculated LDL-C using both formulae. Results The LDL-C calculated using the Friedewald equation has a mean of 106.1 mg/dL and SD 40.1 mg/dL, while the NIH equation has a mean of 108.5 mg/dL and SD 39.9 mg/dL. The average difference between both equations is 2.5 mg/dL, and there is a significant difference between both calculations using paired t-tests (p-value&amp;lt;0.0001). We first compared the calculated LDL-C derived from the Friedewald formula to the NIH equation 2. The regression analysis equation for the Friedewald formula was y = -2.7 + 1.001 X (r = 0.99). When the Triglyceride values &amp;lt;150 mg/dL (N=879), the average difference is 1.3, and the regression equation is -0.45+1.01X(r=0.99). However, when the Triglyceride value &amp;gt;= 150 mg/dL (N=321), the average bias is 5.4 mg/dL, and the regression equation is -11.2+1.05X(r=0.99). The Friedewald formula was compared to the measured LDL-C in 75 specimens; the regression analysis for the Friedewald formula was y = -19.6 + 1.06 X (r = 0.91, p-value &amp;lt;0.0001). The 75 measured LDL-C results were also compared with the NIH formula. The regression analysis of NIH LDL-C with measured LDL-C was y = -5.6 + 0.981 x (r = 0.90, p-value = 0.0002). Both formulae showed a linear relationship against measured LDL-C. The NIH formula outperformed the Friedewald formula; bias difference -7.8(-6.8%) compared to the Friedwald equation bias -12.9(-12.0%). If the NIH equation had been used during this period, an additional 1,116 patients would have had LDL-C results. This is because the Friedewald equation should not be used if the triglyceride value is above 400 mg/dL. Out of the additional patients, 513 (46%) had a high LDL (&amp;gt;100 mg/dL). Conclusions The NIH formula performed better than the Friedewald formula, with a less negative bias when both calculations were compared to direct homogenous measurement. The average difference between the two formulas showed the lowest value when triglyceride &amp;lt; 150 mg/dL. Moving to NIH equation 2 will benefit our population as we had 2% of our patients in the past two years have triglyceride &amp;gt;400 mg/dL.

B-038 A Novel Ultrasensitive Single-Molecule Counting Technology for Quantitation of Low Abundance Biomarkers

Abstract Background There is a need for sensitive, robust, and scalable analytical methods for accurate, early detection of disease using less invasive sampling methods. Often, smaller volumes and low marker concentrations present challenges to achieving sufficient sensitivity and accuracy with traditional immunoassay methods. This is particularly the case for measuring markers for Alzheimer's and other neurological diseases in blood, where levels are typically at much lower concentrations than in CSF. Here we introduce a novel ultrasensitive technology for flow-based single molecule detection in an optofluidic chip. We have developed an Ultrasensitive Detection Module (UDM) device and optofluidic cartridge that enable easy integration of this technology into existing immunoassay systems. UDM sensitivity data is shown for three prototype biomarker assays in comparison to the Lumipulse G1200 (Fujirebio Inc., Japan). We also present analytical validation data for three Alzheimer’s Disease plasma biomarker assays developed on a fully automated benchtop analyzer with integrated UDM detector. Methods Ultrasensitive detection is achieved by integrated low-loss waveguide in an optofluidic chip that enables maximal excitation of fluorescent molecules traveling through a narrow fluidic channel. The resulting high-intensity emission is detected as a single digital event, enabling individual molecules to be counted without need for amplification. Fluorescence-based immunoassays were developed for detection with the UDM using high performance monoclonal antibodies and reagents (Fujirebio Inc., Japan). Capture antibodies were immobilized on magnetic particles and detection antibodies conjugated to a fluorescent reporter construct (“reporter-Ab”). Multiple incubation and wash steps were followed by dissociation of immune complexes and separation of reporter-Ab from magnetic particles. Released reporter-Ab molecules were injected into the UDM device for digital detection. Signal to noise performance was evaluated in the UDM using reporter construct alone (no assay), as well as for prototype PSA, IL-6, and TSH assays, to establish baseline performance for analytical sensitivity. Plasma assays for pTau181, Aβ1-40, and Aβ1-42 were developed and optimized for the automated benchtop analyzer and validated for analytical sensitivity (LOD/LOQ), linearity, parallelism, precision and repeatability using clinical samples. Results Detection signal-to-noise testing of the reporter construct alone (no immunoassay) demonstrated up to 1000-fold higher sensitivity than the Lumipulse G1200. Prototype assays for PSA, TSH, and IL-6 showed up to 118-fold, 36-fold, and 80-fold higher signal to noise ratio, respectively, when compared to the Lumipulse G1200. Plasma assays for pTau181, Aβ1-40, and Aβ1-42 showed preliminary LLOQs calculated at 0.03 pg/mL, 0.17 pg/mL and 0.37 pg/mL, respectively. Conclusions We have developed a new single molecule counting platform able to detect neurological biomarkers at sub-pg/ml levels in plasma, with the potential to provide sensitive and accurate diagnostic testing of low abundance biomarkers in blood. Such technologies can create new clinical value through higher detection sensitivity and accuracy in areas like Alzheimer’s and other neurological diseases, supporting clinical research and translation to clinical practice.

B-119 Comparative performance of GPT-4 and CNV-ETLAI in extracting copy number variations from medical journals: Bridging the gap between large language models and specialized NLP tools in genomic data interpretation

Abstract Background Copy Number Variations (CNVs) are critical genetic markers in diversity and disease, yet their accurate extraction from medical literature remains challenging due to the complexity of genetic data. While specialized NLP models like CNV-ETLAI have been developed for this task, the advent of Large Language Models (LLMs) such as GPT-4 presents a potential alternative with broader applicability. This study evaluates the efficacy of GPT-4 against CNV-ETLAI in extracting CNVs from medical journal articles, aiming to enhance genetic research and clinical decision-making. Methods We configured GPT-4 to process and interpret medical journal PDFs, designing custom prompts for CNV information extraction. The performance of GPT-4 was benchmarked against CNV-ETLAI using a dataset of 146 true positive CNVs extracted from 23 journal articles. Performance metrics focused on accuracy in extracting CNVs from both text and tables, recognizing the importance of structured data interpretation in genomic analysis. Results CNV-ETLAI demonstrated superior accuracy, achieving a 98% success rate in CNV extraction, compared to GPT-4’s 49%. Specifically, CNV-ETLAI outperformed GPT-4 in table extraction accuracy (99% vs. 41.2%) and context extraction accuracy (96% vs. 63.2%). Despite GPT-4's lower performance, its capacity for improvement and adaptability was noted, indicating potential future applicability in medical data extraction. Conclusions The study highlights CNV-ETLAI's current superiority in extracting CNVs from medical texts, particularly in interpreting structured data like tables. However, the adaptability and potential for growth in LLMs like GPT-4 suggest they could soon become valuable tools for medical data extraction, offering a more versatile and powerful solution across a broader range of applications. The promise of LLMs, despite their current limitations, underscores the need for continued research and development in AI technologies for genomic data interpretation.

B-249 Assessing Targeted Mass Spectrometry Assay Performance for Putative Biomarker Proteins on a New Hybrid Nominal Mass Instrument

Abstract Background The development of targeted mass spectrometry-based proteomics assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to highly multi-analyte clinical studies. Targeted assays are currently unable to scale to thousands of peptide targets from hundreds of proteins, requiring extensive refinement down assays for the minimum useful analytes. Large parallel reaction monitoring (PRM) assays are now possible with a new hybrid nominal-mass instrument. The scale of assay is achievable with this instrument by using real-time alignment, while being sensitive and fast enough to handle many concurrent targets. To assess the performance of this new instrument we constructed a large scale PRM assay for proposed neurodegenerative disease marker proteins, and an assay for proteins associated with amyloid tissue typing. Methods To evaluate the performance of this instrument on proteins of interest in cerebrospinal fluid, we performed an analysis on a pool from individuals diagnosed as Alzheimer’s, Parkinson’s, or cognitively normal. A calibration curve of cerebrospinal fluid diluted into chicken serum at 14 dilutions and individual human cerebrospinal fluid were digested with a protein aggregation and capture based digestion protocol. CSF peptides were separated by 60 minute gradient on C18 IonOpticks column, and amyloid tissue peptides separated by 30 minute gradient on C18 PepMap column with a Vanquish Neo UHPLC and analyzed by data-independent acquisition (DIA) and PRM with a new hybrid nominal mass instrument designed for targeted tandem mass spectrometry (tMS2). Scheduled methods were generated using a Skyline external tool, transitions were refined to minimize interference and maximize the LLOQ. DIA data was searched, and data extracted and analyzed in Skyline. PRM data was extracted and quantified with Skyline; CSF calibration curve LLOQ is calculated by bilinear fit. Results For the large scale cerebrospinal fluid (CSF) assay the selection of protein targets was based on literature from neurodegenerative disease cohort studies. We target 1065 peptides from 104 proteins, including proteins currently measured by ELISA in clinical research, e.g.: APP, TAU, and APOE. Sensitivity and reproducibility of the assay is assessed using figures of merit from replicate matched-matrix calibration curves. Over 80% of proteins have at least one peptide with a LLOQ below 30% dilution in the matched matrix, and of all targeted peptides over 55% had a LLOQ below 30% dilution. To demonstrate the application of the real-time alignment on the new instrument we constructed an assay for samples where not every analyte is shared. An assay for amyloidosis associated proteins was constructed for a total of 180 peptides mapping to 52 proteins. This includes 11 proteins most commonly associated with amyloid deposition; APCS, APOA4, APOE, CLU, LECT2, IGKC, IGLC2/4/7, SAA1, TTR, and VTN. From the preliminary set of 12 previously typed samples we observe peptide abundances consistent with the assigned type. Conclusions This novel instrument provides a new approach for building large targeted mass spectrometry assays. We demonstrate the ability of the real-time alignment to adjust scheduled retention time windows, ensuring that chromatographic shifts do not lead to a loss of peptide detection and quantification.

Choice of blood collection methods influences extracellular vesicles counts and miRNA profiling.

Circulating RNAs have been investigated systematically for over 20years, both as constituents of circulating extracellular vesicles (EVs) or, more recently, non-EV RNA carriers, such as exomeres and supermeres. The high level of variability and low reproducibility rate of EV/extracellular RNA (exRNA) results generated even on the same biofluids promoted several efforts to limit pre-analytical variability by standardizing sample collection and sample preparation, along with instrument validation, setup and calibration. Anticoagulants (ACs) are often chosen based on the initial goal of the study and not necessarily for the later EV and/or exRNA analyses. We show the effects of blood collection on EV size, abundance, and antigenic composition, as well on the miRNAs. Our focus of this work was on the effect of ACs on the number and antigenic composition of circulating EVs and on a set of circulating miRNA species, which were shown to be relevant as disease markers in several cancers and Alzheimer's disease. Results show that while the number of plasma EVs, their relative size, and post-fluorescence labeling profile varied with each AC, their overall antigenic composition, with few exceptions, did not change significantly. However, the number of EVs expressing platelet and platelet-activation markers increased in serum samples. For overall miRNA expression levels, EDTA was a better AC, although this may have been associated with stimulation of cells in the blood collection tube. Citrate and serum rendered better results for a set of miRNAs that were described as circulating markers for Alzheimer's disease, colon, and papillary thyroid cancers.

Effect of SGLT2 Inhibitor Therapy on Urinary Podocyte Markers in Diabetic Kidney Disease

Effect of SGLT2 Inhibitor Therapy on Urinary Podocyte Markers in Diabetic Kidney Disease

Involvement of pentraxin-3 in the development of hypertension but not left ventricular hypertrophy in male spontaneously hypertensive rats.

Hypertension drives the development of concentric left ventricular hypertrophy (LVH). However, the relative contribution of pentraxin-3 (PTX-3), a novel marker for inflammatory cardiovascular disease, in the hypertrophic response to pressure overload has not been adequately elucidated. We investigated the role of PTX-3 in the development of LVH in spontaneously hypertensive rats (SHR), untreated and treated with either captopril (an ACE inhibitor) or hydralazine (a non-specific vasodilator). Three-month-old SHR received either 20 mg/kg/day hydralazine (SHR + H, n = 6), 40 mg/kg/day captopril (SHR + C, n = 6), or plain gelatine cubes (untreated SHR, n = 7) orally for 4 months. Wistar Kyoto rats (WKY, n = 7) were used as the normotensive controls. Blood pressure (BP) was measured using the tail-cuff method. Cardiac geometry and function were determined using M-mode echocardiography. Circulating concentrations of inflammatory markers were measured in plasma by ELISA. LV fibrosis and cardiomyocyte width were assessed by histology. Relative mRNA expression of PTX-3 was determined in the LV by RT-PCR. Untreated SHR exhibited greater systolic BP and relative wall thickness (RWT) compared to WKY. Captopril and hydralazine normalized BP but only captopril reversed RWT in SHR. Circulating PTX-3 and VCAM-1 levels were elevated in untreated SHR and reduced with captopril and hydralazine. Circulating PTX-3 was positively associated with systolic BP but lacked independent relations with indices of LVH. LV relative mRNA expression of PTX-3 was similar between the groups. PTX-3 may not be involved in the development of LVH in SHR, but plausibly reflects the localized inflammatory milieu associated with hypertension.

Exploring the Effects of Low-Energy Diets on Risk Factors and Markers of Kidney Disease: Findings from the Slowing Kidney Disease with Weight-Loss Feasibility Study

Exploring the Effects of Low-Energy Diets on Risk Factors and Markers of Kidney Disease: Findings from the Slowing Kidney Disease with Weight-Loss Feasibility Study

Pediatric Pain

ABSTRACT OBJECTIVE This article reviews pain disorders encountered in pediatric neurology practice and provides current information regarding the assessment and treatment of pediatric chronic pain. LATEST DEVELOPMENTS Data about pediatric pain management remain sparse, owing to a dearth of controlled trials and longitudinal studies in these patients. However, the field of pain management and understanding of central and peripheral pain processing has expanded to allow more effective treatment of a broad group of children and adolescents with pain associated with neurologic disease. Neuroimaging visualizes sensory and nonsensory systems, and genetic markers of sensitivity and disease may guide specific therapy. The concept of central sensitization in chronic pain disorders has supported the development of multidisciplinary paradigms for the comprehensive care of these patients. ESSENTIAL POINTS Pain involves sensory activation and central nervous system modulation in pediatric patients. Pediatric neurologists should be prepared to define, investigate, and treat pain disorders in this complex patient population. Appropriate interventions during childhood may attenuate or prevent chronic pain later in life. Current interventions include behavioral, physical, and pharmacologic approaches, as well as potential noninvasive tools for neuromodulation. Research is progressing in sensory measurement, neuroimaging, genetics, and neuroinflammation to guide future targeted therapies.

Effect of mitochondrial translocator protein TSPO on LPS-induced cardiac dysfunction

IntroductionSepsis-induced cardiac dysfunction is one of the most serious complications of sepsis. The mitochondrial translocator protein (TSPO), a mitochondrial outer membrane protein, is widely used as a diagnostic marker of inflammation-related diseases and can also lead to the release of inflammatory components. However, whether TSPO has a therapeutic effect on sepsis-induced cardiac dysfunction is unclear. ObjectivesThe aim of this study is to investigate the involvement of TSPO in the pathogenesis of sepsis-induced cardiac dysfunction and elucidate its underlying mechanism, as well as develop therapeutic strategies targeting TSPO for the prevention and treatment of sepsis-induced cardiac dysfunction. MethodsThe sepsis-induced cardiac dysfunction model was established by intraperitoneal injection of lipopolysaccharide (LPS) in C57BL/6 mice (LPS-induced cardiac dysfunction, LICD). TSPO knockout mice were constructed,and the effects of TSPO was detected by survival rate, echocardiography, HE staining, mitochondrial electron microscopy, TUNEL staining. TSPO-binding proteins were identified by co-immunoprecipitation and mass spectrometry. The mechanisms underlying between TSPO and voltage-dependent anion channel (VDAC) was studied through western blot and immunofluorescence. Proteolysis-Targeting Chimeras (PROTAC) technology was used to construct TSPO-PROTAC molecules that can degrade TSPO. ResultsOur present study found that LPS increased cardiac TSPO expression. Knockout of TSPO in C57BL/6 mice with LICD attenuated the cardiac pathology, mitochondrial dysfunction, and apoptosis of cardiomyocytes and significantly improved cardiac function and survival rate. Co-immunoprecipitation and mass spectrometry identified VDAC as a TSPO binding protein.Down-regulation of TSPO reduced PKA-mediated VDAC phosphorylation and VDAC oligomerization, ameliorated mitochondrial function, and reduced cardiomyocyte apoptosis. The study has clinical translational potential, because administration of TSPO-PROTAC to degrade TSPO improved cardiac function in mice with LICD. ConclusionThis study elucidated the effect of TSPO in LICD, providing a new therapeutic strategy to down-regulate TSPO by administration of TSPO-PROTAC for the prevention and treatment of LICD.