Markers Of Disease Progression Research Articles

Human T-cell lymphotropic virus type 1 (HTLV-1) grip on T-cells: investigating the viral tapestry of activation

IntroductionHuman T-cell Lymphotropic virus type 1 (HTLV-1) belongs to retroviridae which is connected to two major diseases, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and Adult T-cell leukemia/lymphoma (ATLL). This study aims to investigate the mRNA expressions of key proteins correlated to T-cell activation in asymptomatic carriers (ACs) HTLV-1 infected patients, shedding light on early molecular events and T-cell activation following HTLV-1 infection.Material and MethodsThe study involved 40 participants, including 20 ACs and 20 healthy subjects. Blood samples were collected, ELISA assessment for screening and confirmation with PCR for Trans-activating transcriptional regulatory protein (Tax) and HTLV-1 basic leucine zipper factor (HBZ) of the HTLV-1 were done. mRNA expressions of C-terminal Src kinase (CSK), Glycogen Synthase Kinase-3 Beta (GSK3β), Mitogen-Activated Protein Kinase 14 (MAP3K14 or NIK), Phospholipase C Gamma-1 (PLCG1), Protein Tyrosine Phosphatase non-Receptor Type 6 (PTPN6) and Mitogen-Activated Protein Kinase Kinase Kinase-7 (SLP-76) and Mitogen-Activated Protein Kinase14 (MAP3K7 or TAK1) were assayed using RT-qPCR. Statistical analyses were performed using PRISM and SPSS software.ResultsWhile there were no significant upregulation in CSK and PTPN6 in ACs compared to healthy individuals, expression levels of GSK3β, MAP3K14, PLCG1, SLP-76, and TAK1 were significantly higher in ACs compared to healthy subjects which directly contributes to T-cell activation in the HTLV-1 ACs.ConclusionHTLV-1 infection induces differential mRNA expressions in key proteins associated with T-cell activation. mRNAs related to T-cell activation showed significant upregulation compared to PTPN6 and CSK which contributed to T-cell regulation. Understanding these early molecular events in ACs may provide potential markers for disease progression and identify therapeutic targets for controlling viral replication and mitigating associated diseases. The study contributes novel insights to the limited literature on T-cell activation and HTLV-1 pathogenesis.

Caspases compromise SLU7 and UPF1 stability and NMD activity during hepatocarcinogenesis

Background & AimsThe homeostasis of the cellular transcriptome depends on transcription and splicing mechanisms. Moreover, the fidelity of gene expression, essential to preserve cellular identity and function is secured by different quality control mechanisms including nonsense-mediated RNA decay (NMD). In this context, alternative splicing is coupled to NMD, and several alterations in these mechanisms leading to the accumulation of aberrant gene isoforms have been involved in human disease including cancer. MethodsRNAseq, Westen blot, qPCR, co-IP in multiple silenced culture cell lines (replicates n≥4), primary hepatocytes and samples of animal models (Jo2, APAP, Mdr2-/- mice, n≥3). ResultsHere we describe that in animal models of liver injury and in human HCC (TCGA, NT =50 vs HCC =374), the process of NMD is inhibited. Moreover, we demonstrate that the splicing factor SLU7 interacts with and preserves the levels of the NMD effector UPF1, and that SLU7 is required for a correct NMD. Our previous findings demonstrated that SLU7 expression is reduced in the diseased liver, contributing to hepatocellular de-differentiation and genome instability during disease progression. However, little was known about the mechanisms underlying SLU7 downregulation. Here we provide evidence showing that caspases activated during liver damage would be responsible of the cleavage and degradation of SLU7. ConclusionsHere we identify the downregulation of UPF1 and the inhibition of NMD as a new molecular pathway contributing to the malignant reshaping of the liver transcriptome. Moreover, and importantly, we uncover caspases activation as the mechanism responsible for the downregulation of SLU7 expression during liver disease progression, which is a new link between apoptosis an hepatocarcinogenesis. Impact and implicationsThe mechanisms involved in the reshaping of hepatocellular transcriptome driving the progressive loss of cell identity and function in liver disease are not completely understood. In this context, we provide evidence on the impairment of a key mRNA surveillance mechanism known as nonsense-mediated mRNA decay (NMD). Mechanistically, we uncover a novel role for the splicing factor SLU7 in the regulation of NMD, including its ability to interact and preserve the levels the key NMD factor UPF1. Moreover, we demonstrate that the activation of caspases during liver damage mediates SLU7 and UPF1 proteins degradation and NMD inhibition. Our findings identify potential new markers of liver disease progression, and SLU7 as a novel therapeutic target to prevent the functional decay of the chronically injured organ.

Mineralocorticoid receptor antagonists and reno-protection: What's the evidence & where do they fit? A guide for non-specialists.

The role of aldosterone has yet to be well appreciated in chronic kidney disease (CKD). Two variables define CKD: an estimated glomerular filtration rate of <60 ml/min/1.73 m2 and a spot urine albumin-creatinine ratio of >30 mg/g. Both are needed for an accurate diagnosis. The presence of CKD at this level is associated with an elevated risk of cardiovascular death and a greater risk of CKD progression to kidney failure and subsequent dialysis. This paper presents an overview of aldosterone's importance in CKD and its contribution to the inflammatory processes involved in CKD development. Data on outcomes, both surrogate and hard, related to outcomes on CKD progression will also be discussed in the context of mineralocorticoid blockade. Based on recent epidemiological data as well as data examining markers of diabetic kidney disease progression, it is clear that use of both renin-angiotensin system inhibitors and aldosterone receptor antagonists have a significant role in altering the natural history of kidney disease progression itself, as well as reducing the risk of cardiovascular events that generally accompany long-standing kidney disease. This paper will discuss these issues and the management of consequent hyperkalaemia when both steroidal and non-steroidal mineralocorticoid receptor antagonists are used in detail.

Frontal QRST Angle as a Marker of Arrhythmogenesis and Disease Progression in Dogs with Myxomatous Mitral Valve Disease

Frontal QRST Angle as a Marker of Arrhythmogenesis and Disease Progression in Dogs with Myxomatous Mitral Valve Disease

Elevated Exposure to Air Pollutants Accelerates Primary Glomerular Disease Progression

IntroductionEnvironmental contributors to kidney disease progression remain elusive. We explored how residential air pollution impacts disease progression in patients with primary glomerulopathies. MethodsNephrotic Syndrome Study Network (NEPTUNE) and CureGlomerulonephropathy (CureGN) participants with residential census tract data and ≥2 years of follow-up were included. Using Cox proportional hazards models, the associations per doubling in annual average baseline concentrations of total particulate matter with diameter ≤ 2.5 μm (PM2.5) and its components, black carbon, and sulfate, with time to ≥40% decline in estimated glomerular filtration rate (eGFR) or kidney failure were estimated. Serum tumor necrosis factor levels and kidney tissue transcriptomic inflammatory pathway activation scores were used as molecular markers of disease progression. ResultsPM2.5, black carbon, and sulfate exposures were comparable in NEPTUNE (n=228) and CureGN (n=697). In both cohorts, participants from areas with higher levels of pollutants had lower eGFR, were older and more likely self-reported racial and ethnic minorities. In a fully adjusted model combining both cohorts, kidney disease progression was associated with PM2.5 (adjusted HR 1.55 [95% CI:1.00, 2.38], p=0.0489) and black carbon (adjusted HR 1.43 [95% CI:0.98, 2.07], p=0.0608) exposure. Sulfate and PM2.5 exposure were positively correlated with serum tumor necrosis factor (TNF) (p=0.003) and interleukin-1β levels (p=0.03), respectively. Sulfate exposure was also directly associated with transcriptional activation of the TNF and JAK-STAT signaling pathways in kidneys (r=0.55-0.67, p-value <0.01). ConclusionElevated exposure to select air pollutants is associated with increased risk of disease progression and systemic inflammation in patients with primary glomerulopathies (word count: 248).

HYPERTENSIVE NEPHROPATHY: TRANSCRIPTOMICS OF KIDNEY BIOPSIES PREDICTS LONG TERM OUTCOME AND IDENTIFIES THERAPEUTIC TARGETS

Objective: Hypertensive nephropathy (HN) represents a major cause of chronic kidney disease, but it is incompletely understood why some patients show disease progression. Our project aim is to identify potential markers of disease progression and novel therapeutic targets. Design and method: Adult patients (n=43; n=16 females, mean age 53 years) with biopsy-verified HN were categorized as ’early’ (estimated glomerular filtration rate (eGFR) &gt;45 ml/min/1.73m2) or ’late’ disease (eGFR &lt;45 ml/min/1.73m2) at the time of biopsy. Patients were further divided into “stable” (eGFR decline &lt;3 ml/min/year) or “progressive” (eGFR decline &gt;3 ml/min/year or start of renal replacement therapy) after median follow-up of 10 years (5-22). TruSeq Exome sequencing was executed after RNA extraction (miRNeasy FFPE kit, Qiagen) at Novogene, Cambridge, UK. Quality control and data analysis was performed using R Studio (v4.2.0) and QIAGEN Ingenuity Pathway Analysis. Results: We analyzed the following subgroups of HN patients: early stable (ES, n=11), early progressive (EP, n=11), late stable (LS, n=9) and late progressive (LP, n=12). Differentially expressed genes (DEG, fold change (FC) &gt;1.5 and p-value &lt; 0.05) were identified, with n=265 in ES vs. EP, and n=674 in LS vs. LP. Principal component analysis (PCA) showed separation of ES vs. EP and LS vs. LP, as depicted in Figure 1A and B. K-nearest neighbour (KNN) analysis of DEG identified a 6-gene classifier in LS vs. LP (19/21 samples correctly classified), while IER5L and CNTNAP5 were the top 2-gene classifier in ES vs. EP (20/21 samples). These classifiers, as well as other DEGs such as PER1, YB1, TIMP3, ADAMTS4, IGFBP5 and EGF could represent novel targets to inhibit disease progression. Differentially regulated pathways were associated with regulation of TP53 activity and circadian rhythm involving melatonin metabolism in ES vs. EP, and metabolic processes related to water-soluble vitamins, glutathione and sphingolipids in LS vs. LP. Conclusions: Transcriptomic profiling from diagnostic kidney biopsies with HN can distinguish future disease progression from non-progression and may identify novel therapeutic targets.

Bioactive adrenomedullin as a marker of congestion and disease progression in patients with a systemic right ventricle

BackgroundAdults with a systemic right ventricle (sRV) are at a high risk for heart failure (HF) hospitalization and mortality. Bioactive adrenomedullin (bio-ADM) has been proposed as a marker of congestion and prognosis in patients with cardiovascular disease. We aimed to evaluate the association between bio-ADM and mortality and HF events in sRV patients. MethodsPlasma bio-ADM was measured by a novel immunoassay in plasma of 85 sRV patients. A composite endpoint of all-cause mortality and HF events was used as outcome. HF events were defined as onset or progression of HF signs or symptoms requiring hospitalization, initiation or intensification of therapy. Multivariable Cox regression analyses were performed to evaluate the association between bio-ADM and outcome. ResultsThe mean age of the patients was 37 ± 9 years and 65% were male. Patients with higher plasma bio-ADM concentrations were more often treated with diuretics (p = 0.007), possibly because of signs and/or symptoms of congestion. During a median follow-up of 10.2 years, 33.7% of the patients reached the endpoint. After adjustment for age and N-terminal pro B-type natriuretic peptide (NT-pro BNP), higher bio-ADM levels were associated with a higher risk of the composite endpoint (hazard ratio: 2.09 [95%-confidence interval: 1.15–3.78]). Bio-ADM improved risk prediction when added to NT-proBNP and age (C-statistic improved from 0.748 to 0.776 [p = 0.03]). ConclusionsBio-ADM can be considered as a marker of congestion and independent predictor of death and HF events in adult patients with a sRV. Moreover, in terms of risk prediction, it has added value to NT-proBNP.

Could the motor unit number index be an early prognostic biomarker for amyotrophic lateral sclerosis?

ObjectiveTo evaluate the associations between motor unit number index (MUNIX) and disease progression and prognosis in amyotrophic lateral sclerosis (ALS) in a large-scale longitudinal study. MethodsMUNIX was performed at the patient's first visit, at 3, 6, and 12 months in 4 muscles. MUNIX data from the patients were compared with those from 38 age-matched healthy controls. Clinical data included the revised ALS functional rating scale (ALSFRS-R), the forced vital capacity (FVC), and the survival of the patients. ResultsEighty-two patients were included at baseline, 62 were evaluated at three months, 48 at six months, and 33 at twelve months. MUNIX score was lower in ALS patients compared to controls. At baseline, MUNIX was correlated with ALSFRS-R and FVC. Motor unit size index (MUSIX) was correlated with patient survival. Longitudinal analyses showed that MUNIX decline was greater than ALSFRS-R decline at each evaluation. A baseline MUNIX score greater than 378 predicted survival over the 12-month period with a sensitivity of 82% and a specificity of 56%. ConclusionsThis longitudinal study suggests that MUNIX could be an early quantitative marker of disease progression and prognosis in ALS. SignificanceMUNIX might be considered as potential indicator for monitoring disease progression.

Expression of HLA-DR and KLRG1 enhances the cytotoxic potential and cytokine secretion capacity of CD3+ T cells in tuberculosis patients

BackgroundHuman T cells play an important role in immunity against tuberculosis (TB) infection. Activating receptor HLA-DR and inhibitory receptor KLRG1 are critical regulators of T cell function during viral infection and tumorigenesis, but they have been less studied in TB infection. MethodsIn this study, we explored the relationship between CD3+ T cell expression of HLA-DR and KLRG1 receptors and function against TB infection. Flow cytometry was conducted to assess the immunomodulatory effects of HLA-DR and KLRG1 receptors on CD3+ T cells in patients with different TB infection status. ResultsWe found activating receptors HLA-DR, NKG2C, CD57 and NKP46, and inhibitory receptors KLRG1 and KIR on CD3+ T cells in different TB infection status showed different distribution patterns; the cytotoxic potential and cytokine secretion capacity of CD3+ T cells after Mtb-specific antigen stimulation were significantly enhanced in TB infection groups. Further studies revealed HLA-DR+ T and KLRG1+ T cells expressed higher activating and inhibitory receptors than the negative population. In addition, the expression of cytotoxic potential and cytokine secretion capacity of HLA-DR+ T and KLRG1+ T cells was significantly higher than that of HLA-DR- T and KLRG1- T cells. ConclusionsExpression of HLA-DR and KLRG1 enhances the cytotoxic potential and cytokine secretion capacity of CD3+ T cells in TB patients, suggesting CD3+ T cells expressing HLA-DR and KLRG1 are important effector cell phenotypes involved in the host anti-TB infection. HLA-DR and KLRG1 expressed by CD3+ T cells may be potential predictive markers of TB disease progression and clinical immune assessment.

Syndecans, Exostosins and Sulfotransferases as Potential Synovial Inflammation Moderators in Patients with Hip Osteoarthritis.

The gradual deterioration of articular cartilage was thought to be the central event in osteoarthritis (OA), but recent studies demonstrated the importance of low-grade synovitis in the progression of OA. The Syndecan (SDC) family of membrane proteoglycans is known to be involved in the regulation of inflammation, but there is limited evidence considering the role of syndecans in OA synovitis. Our study aimed to investigate the hip OA synovial membrane expression patterns of SDC1, SDC2 and SDC4, as well as exostosins and sulfotransferases (enzymes involved in the polymerisation and modification of syndecans' heparan sulphate chains). Synovial membrane samples of patients with OA (24) were divided into two groups according to their Krenn synovitis score severity. The immunohistochemical expressions of SDC1, SDC2, SDC4, EXT1, EXT2, NDST1 and NDST2 in synovial intima and subintima were then analysed and compared with the control group (patients with femoral neck fracture). According to our study, the immunoexpression of SDC1, NDST1 and EXT2 is significantly increased in the intimal cells of OA synovial membrane in patients with lower histological synovitis scores and SDC4 in patients with higher synovitis scores, in comparison with non-OA controls. The difference in the expression of SDC2 among the OA and non-OA groups was insignificant. SDC1, SDC4, NDST1 and EXT2 seem to be involved as inflammation moderators in low-grade OA synovitis and, therefore, should be further investigated as potential markers of disease progression and therapeutic goals.

NFL and GFAP in (pre)symptomatic RVCL-S carriers: a monogenic cerebral small vessel disease

BackgroundNeurofilament light chain (NfL) and glial fibrillary acidic protein (GFAP) have emerged as biomarkers for cerebral small vessel disease (SVD). We investigated their role in a hereditary SVD model, retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S).MethodsNfL and GFAP levels of 17 pre-symptomatic, 22 symptomatic RVCL-S mutation carriers and 69 controls were measured using a Simoa assay. We assessed the association of serum and cerebrospinal fluid (CSF) levels of NfL and GFAP with RVCL-S symptomatology and neuropsychological functioning.ResultsSerum and CSF NfL levels were higher in symptomatic RVCL-S compared to controls ≥ 45 years (33.5 pg/mL vs. 9.2 pg/mL, p < 0.01; 8.5*102 pg/mL vs. 3.9*102 pg/mL, p < 0.01, respectively). Serum NfL levels were higher in symptomatic RVCL-S than pre-symptomatic carriers (33.5 pg/mL vs. 5.9 pg/mL, p = 0.02). Pre-symptomatic RVCL-S carriers had increased CSF NfL levels compared to controls < 45 years (5.2*102 pg/mL vs. 1.9*102 pg/mL, p < 0.01). No differences were found in GFAP levels across groups, but in RVCL-S carriers higher serum levels of both NfL and GFAP were linked to poorer global cognitive functioning (β[95%CI] = − 2.86 [− 5.58 to − 0.13], p = 0.04 and β[95%CI] = − 6.85 [− 11.54 to − 2.15], p = 0.01, respectively) and prolonged psychomotor test times (β[95%CI] = 6.71 [0.78–12.65], p = 0.03 and β[95%CI] = 13.84 [3.09–24.60], p = 0.01).DiscussionHigher levels of serum NfL and GFAP are associated with worse cognitive functioning in RVCL-S carriers and may serve as marker for disease progression. CSF NfL levels may serve as early marker as pre-symptomatic RVCL-S patients already show differences compared to young controls.

Alpha Calcitonin Gene-related Peptide, Neuropeptide Y, and Substance P as Biomarkers for Diagnosis and Disease Activity and Severity in Multiple Sclerosis.

Alpha calcitonin gene-related peptide (aCGRP), neuropeptide Y (NPY), and substance P (SP) are neuropeptides that have emerged recently as potent immunomodulatory factors with potential as novel biomarkers and therapeutic targets in multiple sclerosis (MS). The study aimed to detect serum levels of aCGRP, NPY, and SP in MS patients versus healthy controls and their association with disease activity and severity. Serum levels were measured in MS patients and age and sex-matched healthy controls using ELISA. We included 67 MS patients: 61 relapsing-remitting MS (RR-MS) and 6 progressive MS (PR-MS), and 67 healthy controls. Serum NPY level was found to be lower in MS patients than in healthy controls (p < 0.001). Serum aCGRP level was higher in PR-MS compared to RR-MS (p = 0.007) and healthy controls (p = 0.001), and it positively correlated with EDSS (r = 0.270, p = 0.028). Serum NPY level was significantly higher in RR-MS and PR-MS than in healthy controls (p < 0.001 and p = 0.001, respectively), and it was lower in patients with mild or moderate/severe disease than in healthy controls (p < 0.001). Significant inverse correlations were found between SP level and MS disease duration (r = -0.279, p = 0.022) and duration of current DMT (r = -0.315, p = 0.042). Lower serum levels of NPY were revealed in MS patients compared to healthy controls. Since serum levels of aCGRP are significantly associated with disease activity and severity, it is a potential disease progression marker.

ASSOCIATION OF SERUM URIC ACID WITH DIABETES MELLITUS TYPE-2: A NARRATIVE REVIEW

Diabetes mellitus type 2 (T2DM) is a disease which imposes a great burden on the health resources of the emerging and developing world. It is a global pandemic which leads to chronic complications. Serum uric acid (SUA) is a biomarker that could be of value in detection of early complications and better prognosis in diabetic patients. SUA serves both as a causal factor and disease progression marker in DM, having a causal relationship with diabetic complications. This narrative review aims to determine the association between SUA and T2DM. Research articles from the year 2005 to 2023 were selected for this review. Literature search was conducted from PubMed and Google Scholar which resulted in short listing of 15 articles. It also reflects upon the diabetic complications associated with Hyperuricemia (HUA) and focuses on the health implications of HUA in T2DM patients. SUA and T2DM were negatively associated in 8 research studies and positively associated in 6 studies in which one revealed a partial association, one was prevalent in the female gender only, and one was negatively associated in uncontrolled DM. Another study was associated with both hypouricemia and HUA. Pak J Physiol 2024;20(1):52-7

Stratifying Disease Progression in Patients With Cardiac ATTR Amyloidosis

BackgroundTransthyretin cardiac amyloidosis (ATTR-CA) is a progressive cardiomyopathy. The clinical course varies among individuals and there are no established measures to assess disease progression. ObjectivesThe goal of this study was to assess the prognostic importance of an increase in N-terminal pro–B-type natriuretic peptide (NT-proBNP) and outpatient diuretic intensification (ODI) as markers of disease progression in a large cohort of patients with ATTR-CA. MethodsWe evaluated landmark survival analysis based on worsening of NT-proBNP and requirement for ODI between time of diagnosis and a 1-year visit, and subsequent mortality in 2,275 patients with ATTR-CA from 7 specialist centers. The variables were developed in the National Amyloidosis Centre (NAC) cohort (n = 1,598) and validated in the external cohort from the remaining centers (n = 677). ResultsBetween baseline and 1-year visits, 551 (34.5%) NAC patients and 204 (30.1%) patients in the external validation cohort experienced NT-proBNP progression (NT-proBNP increase >700 ng/L and >30%), which was associated with mortality (NAC cohort: HR: 1.82; 95% CI: 1.57-2.10; P < 0.001; validation cohort: HR: 1.75; 95% CI: 1.32-2.33; P < 0.001). At 1 year, 451 (28.2%) NAC patients and 301 (44.5%) patients in the external validation cohort experienced ODI, which was associated with mortality (NAC cohort: HR: 1.88; 95% CI: 1.62-2.18; P < 0.001; validation cohort: HR: 2.05; 95% CI: 1.53-2.74; P < 0.001). When compared with patients with a stable NT-proBNP and stable diuretic dose, a higher risk of mortality was observed in those experiencing either NT-proBNP progression or ODI (NAC cohort: HR: 1.93; 95% CI: 1.65-2.27; P < 0.001; validation cohort: HR: 1.94; 95% CI: 1.36-2.77; P < 0.001), and those experiencing both NT-proBNP progression and ODI (NAC cohort: HR: 2.98; 95% CI: 2.42-3.67; P < 0.001; validation cohort: HR: 3.23; 95% CI: 2.17-4.79; P < 0.001). ConclusionsNT-proBNP progression and ODI are frequent and consistently associated with an increased risk of mortality. Combining both variables produces a simple, universally applicable model that detects disease progression in ATTR-CA.

Abstract 3710: Determining the efficacy of blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy

Abstract Cancer becomes lethal as it spreads from the primary site to the rest of the body. Circulating tumor cells (CTCs) are considered a marker of disease progression and have been associated with decreased overall survival. Blood filtration is one such method of removing cancer cells from circulation to improve patient prognosis. This study utilizes the liquid biopsy to assess the efficacy of a proprietary filtration device on the blood of patients with pancreatic ductal adenocarcinoma (PDAC) using the third generation high-definition single cell assay (HDSCA3.0) workflow. Blood samples were collected and analyzed to characterize the CTCs and other rare cells present before and after filtration. Examination of 6 paired portal (PoVB) samples demonstrated a statistically significant decrease in total rare cells, total CK+ cells, and epi.CTCs across all patients due to filtration of the blood. Furthermore, analysis of 2 paired peripheral blood (PB) samples showed a decrease in total rare cells, total CK+ cells, and specific phenotypes of rare cells upon filtration. These preliminary results demonstrate initial proof of concept that this filtration device can remove CTCs from the circulation, which may be used as a potential therapeutic device for PDAC patient care. Citation Format: Divya D. Suresh, George Courcoubetis, Emmeline Lin, Jeremy Mason, Nicholas Nissen, Srinivas Gaddam, Simon Lo, Stephen Pandol, Peter Kuhn, Stephanie Shishido. Determining the efficacy of blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3710.

Chronic Viral Infection Compromises the Quality of Circulating Mucosal-Associated Invariant T Cells and Follicular T Helper Cells via Expression of Inhibitory Receptors.

Chronic viral infection results in impaired immune responses rendering viral persistence. Here, we compared the quality of T-cell responses among chronic hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV)-infected individuals by examining the levels of expression of selected immune activation and exhaustion molecules on circulating MAIT cells and Tfh cells. Cytokines were measured using a commercial Bio-plex Pro Human Cytokine Grp I Panel 17-plex kit (BioRad, Hercules, CA, USA). Inflammation was assessed by measuring an array of plasma cytokines, and phenotypic alterations in CD4+ T cells including circulating Tfh cells, CD8+ T cells, and TCR iVα7.2+ MAIT cells in chronic HBV, HCV, and HIV-infected patients and healthy controls. The cells were characterized based on markers pertaining to immune activation (CD69, ICOS, and CD27) proliferation (Ki67), cytokine production (TNF-α, IFN-γ) and exhaustion (PD-1). The cytokine levels and T cell phenotypes together with cell markers were correlated with surrogate markers of disease progression. The activation marker CD69 was significantly increased in CD4+hi T cells, while CD8+ MAIT cells producing IFN-γ were significantly increased in chronic HBV, HCV and HIV infections. Six cell phenotypes, viz., TNF-α+CD4+lo T cells, CD69+CD8+ T cells, CD69+CD4+ MAIT cells, PD-1+CD4+hi T cells, PD-1+CD8+ T cells, and Ki67+CD4+ MAIT cells, were independently associated with decelerating the plasma viral load (PVL). TNF-α levels showed a positive correlation with increase in cytokine levels and decrease in PVL. Chronic viral infection negatively impacts the quality of peripheral MAIT cells and Tfh cells via differential expression of both activating and inhibitory receptors.

Abstract 2390: Longitudinal assessment of circulating tumor DNA in patients with advanced colorectal cancer: A proposed general statistical framework and visualization tool

Abstract Background: Understanding how ctDNA levels change over time can act as a surrogate marker for disease progression. Since ctDNA evolution is complicated—exhibiting variability within and between patients—we propose a rigorous and flexible statistical framework that comprehensively represents these types of time-varying biomarkers. We propose employing a hierarchal random effects cubic spline model due to its advantages over traditional longitudinal modeling approaches such as the former’s ability to incorporate patient characteristics and create patient-specific results. Visualization of individual patient trajectories may provide clinical utility in precision oncology settings. Methods: 167 patients with CRC were selected from GuardantINFORM, a real-world database linking genomic and claims data. All patients received chemotherapy and had at least three serial liquid biopsy tests completed via Guardant360. To meet model assumptions, ctDNA levels, measured by maximum variant allele frequency on each test, were transformed into logits. Due to the model’s hierarchal structure, an unconditional cubic spline model was fit first, producing an estimated response pattern for the cohort. Next, as patient-level results are of interest, the unconditional model was built upon by fitting a conditional model that incorporated covariates consisting of demographic, health status, and mortality information, which provided numerous patient-level response patterns. The best fitting conditional model was guided by Akaike’s information criteria. Results: Since model parameter estimates are uninterpretable, and because numerous patient-level projections are generated (each covariate value combination produces a unique projection), an R-Shiny application was developed to visually present and compare results in an intuitive interactive fashion. Additionally, to enhance the understanding of patient response patterns, velocity plots, which provides the instantaneous rate of change in ctDNA levels at different time points, are also provided. Conclusions: We demonstrate that the proposed method can successfully be applied to genomic data to describe and explore complex patient-level temporal ctDNA patterns while accounting for the impact of covariate values have on these patterns. We implemented the proposed methodology as a visualization tool that can be used in a wide variety of settings, ranging from hypothesis testing in clinical trials to patient monitoring. Results from the model can further our basic conceptualization of ctDNA dynamics and enhance our ability to integrate these results into targeted, patient centric, clinical decision-making. Citation Format: Christopher R. Pretz, Jiemin Liao, Leylah Drusbosky, Amar Das. Longitudinal assessment of circulating tumor DNA in patients with advanced colorectal cancer: A proposed general statistical framework and visualization tool [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2390.

Transcriptome-Wide 5-Methylcytosine Profiling of lncRNAs in the Mouse Cerebral Ischemia Model.

An increasing body of research has demonstrated the significant role of long non-coding RNAs (lncRNAs) in the pathogenesis of stroke. They can actively contribute to the disease's progression either by directly participating in its pathogenesis or by acting as mediators through competing endogenous RNA (ceRNA) mechanisms. Concurrently, epigenetics plays a pivotal role in the pathological mechanisms underlying stroke. Epigenetic factors serve as valuable markers for disease progression, diagnostic biomarkers, and novel therapeutic targets. One of the most prevalent epigenetic modifications is 5-methylcytosine (m5C). However, the specific profiles of 5-methylcytosine in lncRNAs associated with stroke remain to be solved. Within the scope of this research, we performed a thorough transcriptome-wide analysis of m5C methylation within lncRNAs by methylated RNA immunoprecipitation sequencing (MeRIP-Seq), within a mouse stroke model induced by middle cerebral artery occlusion. Our findings reveal substantial disparities in both the quantity and distribution of m5C within the mouse stroke model compared to normal mice. This suggests a potential linkage between stroke and lncRNA m5C modifications, offering valuable insights into the mechanisms of stroke pathogenesis and the development of new drug targets.

Salmonella-driven intestinal edema in mice is characterized by tensed fibronectin fibers.

Intestinal edema is a common manifestation of numerous gastrointestinal diseases and is characterized by the accumulation of fluid in the interstitial space of the intestinal wall. Technical advances in laser capture microdissection and low-biomass proteomics now allow us to specifically characterize the intestinal edema proteome. Using advanced proteomics, we identify peptides derived from antimicrobial factors with high signal intensity, but also highlight major contributions from the blood clotting system, extracellular matrix (ECM) and protease-protease inhibitor networks. The ECM is a complex fibrillar network of macromolecules that provides structural and mechanical support to the intestinal tissue. One abundant component of the ECM observed in Salmonella-driven intestinal edema is the glycoprotein fibronectin, recognized for its structure-function interplay regulated by mechanical forces. Using mechanosensitive staining of fibronectin fibers reveals that they are tensed in the edema, despite the high abundance of proteases able to cleave fibronectin. In contrast, fibronectin fibers increasingly relax in other cecal tissue areas as the infection progresses. Co-staining for fibrin(ogen) indicates the formation of a provisional matrix in the edema, similar to what is observed in response to skin injury, while collagen staining reveals a sparse and disrupted collagen fiber network. These observations plus the absence of low tensional fibronectin fibers and the additional finding of a high number of protease inhibitors in the edema proteome could indicate a critical role of stretched fibronectin fibers in maintaining tissue integrity in the severely inflamed cecum. Understanding these processes may also provide valuable functional diagnostic markers of intestinal disease progression in the future.

Longitudinal serum chloride as a marker for poor prognosis in severely ill COVID-19 patients: A joint model approach

Coronavirus Disease 2019 (COVID-19) has been responsible for an international health crisis that demanded incredible efforts from the scientific community to understand the disease, its risk factors, and consequences. In this work, we seek to investigate the role of serum chloride and main Strong Ion Difference (mSID) on the survival of severely ill COVID-19 patients treated in the Intensive Care Unit (ICU). Electrolyte measurements were taken daily from each patient from their admission to death or discharge. ICU survival time was measured in days from admission, and discharged patients were considered censored. The longitudinal trajectories of chloride and mSID were associated with patients’ survival times using joint models for longitudinal and time-to-event data. A total of 58 COVID-19 patients were enrolled, and 21 died during hospitalization. Older patients had lower concentrations of chloride overall, and both chloride and mSID increased over time for patients on average. Age was a significant risk factor for ICU mortality, along with the slope of estimated longitudinal trajectory of chloride. Patients with decreasing chloride levels during ICU stay had increased hazard of death. This results of this study suggest that acquired hypochloremia may be an important marker of disease progression and risk of death in patients with severe COVID-19. As such, chloride should be further validated as longitudinal marker for monitoring prognosis during the course of ICU stay. Neither the current values or the slope of the trajectory of mSID were associated with mortality in this sample. The association between the longitudinal trajectory’s slope and ICU mortality is important to understand the dynamics of the disease on a patient level, and could only be quantified by using the joint model framework.