Stages Of Disease Progression Research Articles

Global burden of colorectal cancer: epidemiology, risk factors

A few decades ago, colorectal cancer (CRC) was diagnosed much less frequently. It is currently the fourth and in some countries the third most lethal cancer in the world, with about one million deaths each year. Most colon tumors develop as a result of a multistep process involving a number of histological, morphological and genetic changes, the frequency of detection of which increases with the age of the patient. Timely screening aimed at identifying and removing precancerous neoplasms in the early stages can lead to a significant reduction in the incidence of CRC. Despite this, the currently diagnosed rate of CRC in everyday clinical practice is relatively low, however, it is predicted that with personalized, based on anamnesis, screening for CRC, the frequency of its detection will increase significantly. The practitioner needs to be aware of the risk factors leading to CRC and the various stages of disease progression in order to recommend appropriate screening strategies. The use of a surveys that includes risk factors in the collection of anamnesis will reduce economic costs and not miss a cohort of patients who need a detailed examination. The purpose of the review is to present current data on the epidemiology of CRC and risk factors contributing to the occurrence of CRC. A literature review of articles (original studies and reviews) published between 2016 and February 2022 on the study of risk factors for CRC was performed. The methods of bibliographic, informational and semantic search of sources in the databases of Google PubMed, Scopus were used. The article discusses in detail the epidemiology and highlights the modified and non-modified risk factors for CRC, including within different age categories. Data on early CRC in young people are presented in detail and carry clinical and molecular features, as well as the role of the hereditary factor in development.

Cortical diffusivity associates with early neuronal damage

AbstractBackgroundDiffusion weighted imaging can provide a marker a microstructural damage which cannot be detected by conventional structural MRI. Changes in cortical diffusivity may be a value marker of neuronal breakdown, which predates macrostructural damage. We aimed to evaluate the efficacy of cortical diffusivity in predicting the extent of metabolic changes in different stages of Alzheimer’s disease progression.Method90 participants diagnosed with mild to moderate Alzheimer’s disease were recruited at Imperial College London. A median split was conducted to categorise participants into ‘Early’ (MMSE ≥ 25, n = 42) and ‘Late’ stage of AD groups (MMSE < 25, n = 48) to reflect different stages of disease progression. All participants underwent [18F]fluorodeoxyglucose imaging with arterial input, t1‐weighted MRI images and diffusion weighted images were also acquired. Spectral analysis was conducted to calculate the cerebral metabolic rate of glucose (CMRglc). CMRglc and mean diffusivity maps were spatially normalised to MNI space and individualised grey matter object maps were created for all participants. Linear regression was conducted between CMRglc and mean diffusivity maps. Mean diffusivity and CMRglc values within the temporal lobe were extracted to confirm voxelwise results.ResultIn this cohort, voxel‐wise statistics revealed a significant relationship between cortical diffusivity and reduced CMRglc, particularly in our ‘early’ stage AD group. Most notable correlations were located within temporal lobe regions. Regional analysis revealed that increased temporal lobe mean diffusivity was strongly correlated with decreased CMRglc in ‘early’ AD participants (r=‐0.525, p<0.001, 95% CI: ‐0.263 to ‐0.715). We found evidence of a weaker correlation in the ‘late’ AD group between increased diffusivity and CMRglc reductions within the temporal lobe (r=‐0.322, p=0.026, 95% CI: ‐0.042 to ‐0.555).ConclusionCortical mean diffusivity is a valuable predictor of early neuronal damage measured by cerebral glucose metabolism in Alzheimer’s disease. This association was strongest in earlier stages of the disease trajectory, as such, we establish that cortical mean diffusivity as an early biomarker in Alzheimer’s disease which reflects early changes in tissue integrity and cell/organelle breakdown.

Novel peptide‐driven global proteomics platform to identify unique peptide profiles linked to Alzheimer’s disease

AbstractBackgroundThere is a growing need for new biomarker signature(s) to further improve the predictive values of currently used markers for Alzheimer’s disease (AD) staging, monitoring, and prognostic prediction of disease progression. Most AD biomarker discovery studies have not focused on peptide level alterations despite unquestionable importance of abnormal proteolysis in AD. Here we present a peptide‐focused unbiased global proteomics platform to identify unique peptide profiles associated with amyloid pathology in cognitively impaired subjects.MethodWe used the mass spectrometry (MS) data from a recently published multi‐cohort study (PRIDE archive PXD016278) using cerebrospinal fluid (CSF) from cognitively impaired AD (classified based on t‐tau > 400 ng/l, Aβ1–42 <550 ng/l and Aβ1–42/Aβ1–40 ratio <0.065) and non‐AD control participants. Data from the Sweden cohort was used for “discovery” and Magdeburg and Kiel cohort for “validation”. RAW MS files were analyzed using a novel platform integrating a de novo‐based workflow with comprehensive project‐specific hybrid spectral libraries to enable the identification of non‐tryptic and microbial peptides missed in traditional proteomics workflows. Raw intensities were quantile normalized and log transformed to reduce technical variation and ensure distribution symmetry. Differentially expressed peptides were identified via analysis of covariance after adjusting for age and gender, at 20% false discovery rate.Result1199 peptides identified as significant for amyloid positivity in discovery cohort were confirmed in an independent validation cohort. Most of the confirmed peptides demonstrate strong separation of amyloid (+) and amyloid (‐) subjects; 270 out of 1199 peptides had area under receiver operating characteristic curve (ROC‐AUC) over 90%, and 975 peptides had ROC‐AUC over 80%. Interestingly, 64.4% of CSF proteins identified as significant for amyloid positivity were altered only at the peptide‐level, including recently reported markers of AD progression such as VGF and PTPRN, underscoring the importance of tracking peptide‐based alterations in biomarker discovery.ConclusionOur unbiased peptide‐focused global proteomics platform has yielded a unique profile of over 1000 novel peptide signatures linked to amyloid pathology. Further evaluation is ongoing to study the pathways and interactions associated with these unique peptide profiles, and their potential utility for disease staging, monitoring, and progression.

Smoking Gun? Effect of smoking history on cognition in AD and MCI

AbstractBackgroundMany lifestyle factors have been associated with lower rates of cognitive decline in AD and MCI patients, however the effect of tobacco smoking remains unclear. This study examined how longitudinal cognitive performance in AD and MCI patients varied for those with versus without smoking history.MethodThe study included all 126 patients from the Ontario Neurodegenerative Disease Research Initiative (ONDRI) AD/MCI cohort. The patients were divided into those with a history of cigarette smoking (n = 67) vs without (n = 59), defined as greater than two years of daily smoking. To measure longitudinal cognition, MoCA scores were taken three times with one year elapsing between assessments.ResultLinear mixed effects models were performed, with MoCA score as the dependent variable. Time point, smoking history, sex, education, age, clinical diagnosis (AD vs MCI) and number of languages spoken were fixed effects and subject was a random effect. The presence of smoking history had a significant effect on MoCA score (χ2(1) = 4.5, p = 0.034), improving the average score by 1.37 points ± 0.66 (standard errors). A strong interaction was also found between smoking history and time point (χ2(1) = 8.2, p = 0.0042), as the positive effect of smoking history on MoCA score increased with time. No other significant interactions were found.ConclusionOur findings indicate that smoking history may improve longitudinal cognition in AD and MCI patients. It is unclear whether smoking history is simply a mediating variable for another protective factor, or whether these results arise from cigarette smoking itself affecting some stage of disease progression. Smoking has been consistently associated with a lower risk of developing Parkinson’s disease (PD), however the mechanism for such protection remains unclear. Further research into any association between smoking history and longitudinal cognition in AD and MCI might indicate whether a similar protective association is found in AD and MCI as exists in PD. However, it must be remembered that smoking is associated with many serious diseases, particularly lung cancer, and remains one of the biggest causes of preventable death worldwide.

Expression and Significance of PD-1, PD-L1 and CTLA-4 in the Bone Marrow of Patients with Multiple Myeloma

To study the expression and significance of PD-1, PD-L1 and CTLA-4 tumor-associated antigens in multiple myeloma. Bone marrow specimens from 122 patients with multiple myeloma were collected and divided into new-onset group (NDMM), complete remission group (CRMM) and relapsed and refractory group (RRMM) according to the disease progression stage. The proportion of CD4+ T lymphocytes, CD8+ T lymphocytes, Treg cells and plasma cells in the specimens and the expressions of PD-1, PD-L1 and CTLA-4 were detected by multi-parameter flow cytometry. There was no significant difference in the proportion of CD8+T and Treg cells among the three groups (P>0.05), while the proportions of CD4+T cells and PC in NDMM group were significantly higher than those in the CRMM group (P<0.05), the ratios of CD4+ to CD8+T in the NDMM and RRMM groups were significantly higher than those in the CRMM group (P<0.05). The expressions of PD-1, PD-L1 and CTLA-4 in CD8+ T cells was no significant difference among NDMM, CRMM and RRMM groups (P>0.05). While the expressions of PD-1, PD-L1 and CTLA-4 in CD4+ T cells and PC in the NDMM group were significantly lower than that in the CRMM group (P<0.05). There was significantly difference among the three groups in the expression of PD-1 in Treg cells, of which the NDMM group was significantly lower than that of the CRMM group (all P<0.05). The expressions of PD-1 and CTLA-4 in PC were significantly higher than those in CD8+ T, CD4+ T and Treg cells (P<0.05), the expression of PD-L1 in CD8+ T cells was significantly higher than that in CD4+ T and Treg cells (P<0.05). There is a correlation between the immune status of multiple myeloma and the expressions of PD-1, PD-L1 and CTLA-4 in plasma cells and lymphocyte subsets in vivo.

Simulating the impact of photoreceptor loss and inner retinal network changes on electrical activity of the retina

Objective. A major reason for poor visual outcomes provided by existing retinal prostheses is the limited knowledge of the impact of photoreceptor loss on retinal remodelling and its subsequent impact on neural responses to electrical stimulation. Computational network models of the neural retina assist in the understanding of normal retinal function but can be also useful for investigating diseased retinal responses to electrical stimulation. Approach. We developed and validated a biophysically detailed discrete neuronal network model of the retina in the software package NEURON. The model includes rod and cone photoreceptors, ON and OFF bipolar cell pathways, amacrine and horizontal cells and finally, ON and OFF retinal ganglion cells with detailed network connectivity and neural intrinsic properties. By accurately controlling the network parameters, we simulated the impact of varying levels of degeneration on retinal electrical function. Main results. Our model was able to reproduce characteristic monophasic and biphasic oscillatory patterns seen in ON and OFF neurons during retinal degeneration (RD). Oscillatory activity occurred at 3 Hz with partial photoreceptor loss and at 6 Hz when all photoreceptor input to the retina was removed. Oscillations were found to gradually weaken, then disappear when synapses and gap junctions were destroyed in the inner retina. Without requiring any changes to intrinsic cellular properties of individual inner retinal neurons, our results suggest that changes in connectivity alone were sufficient to give rise to neural oscillations during photoreceptor degeneration, and significant network connectivity destruction in the inner retina terminated the oscillations. Significance. Our results provide a platform for further understanding physiological retinal changes with progressive photoreceptor and inner RD. Furthermore, our model can be used to guide future stimulation strategies for retinal prostheses to benefit patients at different stages of disease progression, particularly in the early and mid-stages of RD.

2.5D mass spectrometry imaging of N-glycans in esophageal adenocarcinoma and precursor lesions

Glycosylation plays an important role in the progression of esophageal adenocarcinoma (EAC). Being able to image these glycosylation changes directly in endoscopic resection specimens could provide useful insights into the molecular mechanisms of the disease progression and potential markers for EAC staging. For this purpose, both 3D and 2.5D matrix-assisted laser/desorption ionization (MALDI) mass spectrometry imaging (MSI) have been employed in this study to investigate glycosidase-cleaved N-glycans in a total of 24 formalin-fixed paraffin-embedded esophageal local excision specimens spanning all stages of disease progression, namely from non-dysplastic Barrett’s esophagus to metastatic EAC. 3D-MSI was first used to estimate the number of sections needed to sufficiently cover the molecular heterogeneity of each stage of progression. This analysis showed that a total of four sections out of 20 were sufficient. This subset of four sections was measured for all remaining specimens and is called 2.5D-MSI. Subsequent analyses of the 2.5D-MSI datasets revealed significant elevations of five high-mannose N-glycans (Man3, Man4, Man6, Man7, and Man8) in EAC and three complex (Hex6HexNAc5, Hex6HexNAc5NeuAc1, Hex7HexNAc6) N-glycans in metastatic EAC as compared to previous stages of the disease. The augmented levels of these glycans in EAC could be explained by publically available gene expression data of enzymes involved in glycan synthesis and processing. As the role of glycosylation is gaining more interest in MSI and cancer research, our results show the added value of combining localized N-glycan levels, as provided by MSI, with gene expression to gain a deeper understanding of the mechanisms behind N-glycan changes. This gives evidence at multiple levels that specific N-glycosylation plays an important role during progression of dysplasia to EAC and could play a role in patient surveillance.

The rate of chronic kidney disease progression in advanced stages and the dynamics of the uremic syndrome parameters

Background. The current practice of patients with advanced CKD stages management is not optimal, as it leads to the risk of an emergency dialysis start with an unfavorable prognosis, does not utilize all the possibilities of nephroprotective therapy and does not provide optimal correction of the most important uremic syndromes before starting dialysis, which worsens the per spectives of long-term patient-oriented dialysis treatment. THE AIM. The obtained features of the standard practice will provide the possibility to assemble group carefully matched with intensive management group to compare outcomes in future prospective study and to assess the significance of the proposed program components of the intensive management of patients with advanced stages of chronic kidney disease in the "transition center". PATIENTS AND METHODS. A group with regular (at least 6 visits per year) follow-up of 540 patients with baseline CKD3B was retrospectively formed from the city nephrology center database (which included 7696 patients with CKD3 and higher) and was traced to the need for renal replacement therapy or to death. As part of the follow-up, patients underwent regular clinical and laboratory evaluation and received nephroprotective therapy, which were recorded in the database. RESULTS. The dynamics of an accelerating decrease in eGFR (according to CKD-EPICr) from median of -2.76 (-3.26÷-2.36) to -4.34 (-5.01÷-3.46) and further to -6.01 (-7.11÷-5.23) ml/min/1.73 m2/ year for the stages of CKD3B→CKD4→CKD5 in parallel with the dynamics of blood levels of hemoglobin (and iron), phosphate (and calcium), albumin, as well as proteinuria is described – factors that turned out to be significant in the multiple regression model with a dependent variable – the rate of eGFR reduction (the significance of the model F=2.864; p=0.015). CONCLUSION. The obtained detailed description of the progression of CKD in a typical regional population under standard management conditions will provide the possiblity to form a group from a cohort of regular monitoring in a nephrocenter, carefully compared with an intensive management group in the prototype of a transition center based on a large inpatient dialysis center to assess the significance of the components of the proposed control and interventions program.

Systemic Delivery of a Monoclonal Antibody to Immunologically Block Myostatin in the A17 Mouse Model of OPMD.

Oculopharyngeal muscular dystrophy (OPMD) is a late-onset rare muscle disease affecting approximately 1 in 80,000 individuals worldwide. However, it can affect as much as 1:600 individuals in some populations due to a strong founder effect. The muscle pathology is characterized by progressive eyelid drooping (ptosis), swallowing difficulties (dysphagia), and limb weakness at later stages of disease progression. The genetic defect is associated with significant fibrotic deposition and atrophy in affected muscles. No treatments are available to cure the disease. Only surgical techniques to correct ptosis and swallowing are currently possible, though they carry a risk of recurrence. Myostatin is a negative regulator of muscle growth, and several strategies to downregulate its expression have been developed with the aim of improving muscle mass and strength in muscular pathologies. We recently showed that weekly systemic treatment of the A17 murine model of OPMD with a monoclonal antibody for myostatin improves body and muscle mass, increases muscle strength, and reduces muscle fibrosis. Here, we describe the methodology for repeated intraperitoneal delivery of myostatin antibody in the murine model. Furthermore, we detail the most relevant analyses to assess histopathological and functional improvements of this treatment in this mouse model.

A novel small molecule glycolysis inhibitor WZ35 exerts anti-cancer effect via metabolic reprogramming

BackgroundLiver cancer is the fifth leading cause of cancer death worldwide, but early diagnosis and treatment of liver cancer remains a clinical challenge. How to screen and diagnose liver cancer early and prolong the survival rate is still the focus of researchers.MethodsCell experiments were used to detect the effect of WZ35 on the colony formation ability and proliferation activity of hepatoma cells, nude mouse experiment to observe the in vivo anticancer activity and toxic side effects of WZ35; metabolomics analysis, glucose metabolism experiment and Seahorse analysis of liver cancer cells treated with WZ35; cell experiments combined with bioinformatics analysis to explore the mechanism of WZ35-mediated metabolic reprogramming to exert anticancer activity; tissue microarray and case analysis to evaluate the clinical significance of biomarkers for early diagnosis, treatment and prognosis evaluation of liver cancer.ResultsWZ35 inhibited the proliferation activity of various cell lines of liver cancer, and showed good therapeutic effect in nude mice model of hepatocellular carcinoma without obvious toxic and side effects; WZ35 inhibited the absorption of glucose in hepatoma cells, and the drug effect glycolysis, phosphorylation and purine metabolism are relatively seriously damaged; WZ35 mainly inhibits YAP from entering the nucleus as a transcription factor activator by activating oxidative stress in liver cancer cells, reducing the transcription of GLUT1, and finally reducing its GLUT1. Tissue microarray and case analysis showed that GLUT1 and YAP were highly expressed and correlated in liver cancer patients, and were associated with poor patient prognosis. The GLUT1-YAP risk model had a high score in predicting prognosis.ConclusionThe study confirms that WZ35 is a small molecule glycolysis inhibitor, and through its properties, it mediates metabolic reprogramming dominated by impaired glycolysis, oxidative phosphorylation and purine metabolism to inhibit the proliferation activity of liver cancer cells. Our findings present novel insights into the pathology of liver cancer and potential targets for new therapeutic strategies. GLUT1-YAP has important reference significance for predicting the stages of disease progression in liver cancer patients and have the potential to serve as novel biomarkers for the diagnosis and treatment of liver cancer.

Machine learning algorithm and deep neural networks identified a novel subtype in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. Due to the lack of specific characteristics in the early stage of the disease, patients are usually diagnosed in the advanced stage of disease progression. This study used machine learning algorithms to identify key genes in the progression of hepatocellular carcinoma and constructed a prediction model to predict the survival risk of HCC patients. The transcriptome data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The differential expression analysis and COX proportional-hazards model participated in the identification of survival-related genes. K-Means, Random forests, and LASSO regression are involved in identifying novel subtypes of HCC and screening key genes. The prediction model was constructed by deep neural networks (DNN), and Gene Set Enrichment Analysis (GSEA) reveals the metabolic pathways where key genes are located. Two subtypes were identified with significantly different survival rates (p< 0.0001, AUC = 0.720) and 17 key genes associated with the subtypes. The accuracy rate of the deep neural network prediction model is greater than 93.3%. The GSEA analysis found that the survival-related genes were significantly enriched in hallmark gene sets in the MSigDB database. In this study, we used machine learning algorithms to screen out 17 genes related to the survival risk of HCC patients, and trained a DNN model based on them to predict the survival risk of HCC patients. The genes that make up the model are all key genes that affect the formation and development of cancer.

Development and validation of a prognostic 9-gene signature for colorectal cancer.

Colorectal cancer (CRC) is one of the most prevalent cancers globally with a high mortality rate. Predicting prognosis using disease progression and cancer pathologic stage is insufficient, and a prognostic factor that can accurately evaluate patient prognosis needs to be developed. In this study, we aimed to infer a prognostic gene signature to identify a functional signature associated with the prognosis of CRC patients. First, we used univariate Cox regression, least absolute shrinkage and selection operator (lasso) regression, and multivariate Cox regression analyses to screen genes significantly associated with CRC patient prognosis, from colorectal cancer RNA sequencing data in The Cancer Genome Atlas (TCGA) database. We then calculated the risk score (RS) for each patient based on the expression of the nine candidate genes and developed a prognostic signature. Based on the optimal cut-off on the receiver operating characteristic (ROC) curve, patients were separated into high- and low-risk groups, and the difference in overall survival between the two groups was examined. Patients in the low-risk group had a better overall survival rate than those in the high-risk group. The results were validated using the GSE72970, GSE39582, and GSE17536 Gene Expression Omnibus (GEO) datasets, and the same conclusions were reached. ROC curve test of the RS signature also indicated that it had excellent accuracy. The RS signature was then compared with traditional clinical factors as a prognostic indicator, and we discovered that the RS signature had superior predictive ability. The RS signature developed in this study has excellent predictive power for the prognosis of patients with CRC and broad applicability as a prognostic indicator for patients.

Single-Cell Analyses of Immune Microenvironment Informs Potential Benefits of Dual Macrophage-Targeted Therapy in Multiple Myeloma

Background: Multiple myeloma(MM) remains incurable as most patients endure multiple progressions. The complexity of tumor-associated environment(TME) in the progression of MM was not fully clarified. We investigated the atlas of TME during the process of disease progression and explored potential novel therapeutic target. Methods: We performed in-depth single-cell RNA sequencing(scRNAseq) analysis on the bone marrow(BM) cells from 14 MM patients at different disease stage and validate the findings from scRNAseq analysis by bulk RNAseq, flow cytometry analysis and in vitro & in vivo functional experiments. Results: We delineated a compromised TME during progression, characterized by abnormal enrichment of NK cells and exhausted-CD8+T cells, and reprogramming of macrophages(MΦs). A significant enrichment in NK cells and a decrease in CD34+ hematopoietic cells were observed, and the enrichment in NK cells was associated with the progression of disease stage. We found CD8+T cells expressing LAG3 and TIGIT were enriched in advanced disease stage. We further dissected the gene expression signatures of myeloid lineage cells and identified five monocyte/macrophage subsets, which were further divided into CD14+subsets (hm1, hm4, hm5) and CD16+subsets (hm3, hm6) （FigureA). In previous studies reported by other researchers, macrophages presenting M2 phenotype were highly enriched in the BM microenvironment and contributed to the progression of MM. We calculated M1/M2 polarization score for monocyte/macrophage clusters (Figure B). The gene expression signatures of the five macrophage clusters did not fit with either the canonical M1 or M2 classifications, demonstrating a reprogrammed phenotype rather than the M1/M2 paradigm. However, the two CD14+subsets (hm4 and hm5) only present in myeloma stage demonstrated high M2 score than other macrophage clusters (hm1, hm3 and hm6), implying the potential role of M2 polarization in myeloma progression. TAMs reprogramming was correlated with MM progression, mainly involving the CD14+subsets identified in late-stage-disease, featured by a prone-M2 phenotype and phagocytic dysfunction. Transcription factors associated with macrophage M2 polarization and immunosuppression were preferentially expressed in different TAMs clusters. We validate the reprogrammed phenotype of macrophages found in scRNAseq data by flow cytometry analysis and bulk RNAseq in patients samples and in vitro cell experiments. To interrogate global cell-cell interactions in myeloma during disease progression, we performed computational modeling using 'CellPhoneDB' to identify interactions between different monocyte/macrophage subclusters and plasma cells (PCs) in the BM microenvironment from different stage disease(Figure C). We identified two significantly enriched ligand-receptor pairs including the SIRPA-CD47 'don't eat me' pathway suppressing phagocytosis and the CD74-MIF(macrophage inhibitory factor) reshaping the MΦs phenotype. As CD47 and MIF molecules are linked with disease progression and adverse outcomes, we proposed the hypothesis that dual immunosuppression of TAMs by CD47 and MIF promotes disease progression in MM. Finally, we designed a dual-MΦs-targeted therapeutic strategy by combining anti-CD47 mAbs and MIF inhibitor to activate phagocytosis and repolarize MΦ to a functional phenotype, and proved the potent anti-tumor effect in vitro and in vivo. Conclusion: We identified compositional alterations in MM-TME during the disease progression and unraveled significant TAMs phenotype reprogramming and phagocytic dysfunction. We discovered critical dual cellular cross-talks (CD47 and MIF) between MΦs and PCs, and explored their function and clinical significance. Finally, we designed a dual MΦs-targeted therapeutic strategy and proved its anti-tumor effect and the potential clinical benefits. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Durable Clinical Impacts and Mechanisms of Action and Resistance in EZH1/2-Targeting Epigenetic Therapy

Background: Epigenomes allow the rectification of disordered gene expressions, thereby providing new targets for pharmacological interventions in cancer therapy. The clinical utility of targeting histone H3 lysine tri-methylation (H3K27me3) as an epigenetic hallmark has been demonstrated. However, in actual therapeutic settings, the mechanism by which H3K27me3-targeting therapies exert their effects and the response of tumor cells remain unclear. Results and Discussion: We conducted intensive molecular monitoring of three patients enrolled in the valemetostat first-in-human phase 1 clinical trial (NCT02732275) for adult T-cell leukemia/lymphoma (ATL). Valemetostat was administered orally once daily (200 mg/day) until a sign of disease progression could be observed. The number of abnormal lymphocytes (Ably) in these three patients drastically decreased after one week of treatment. All patients could stay on valemetostat single agent for more than 2 years with acceptable safety and durable response. PBMC samples (n = 55) were collected from these three patients immediately before (Pre) and during treatment, as well as during the progressive disease (PD) stage. Flow cytometry-based histone methylation assay demonstrated that tumor H3K27me3 level was generally high in the Pre-samples, but the valemetostat treatment reduced it to a normal level in all patients. In addition, ChIP sequencing (ChIP-seq) could directly assess how valemetostat affects the tumor epigenome. The pre-treatment tumor cells showed an overall increasing trend in H3K27me3. For all H3K27me3 peaks (51,683 peaks), 85.9% of the peak signals decreased at the average fold-change of 0.742 after the valemetostat treatment. Focusing on the gene loci, an overall decrease could be observed around the TSS and across the gene body. The characteristic H3K27me3 clusters initially observed in the tumor cells were demethylated. We also conducted integrative multilayered single-cell analyses (scATAC-seq and scRNA-seq) and showed that valemetostat abolishes the highly condensed chromatin structure formed by the plastic H3K27me3 and neutralizes multiple gene loci, such as tumor suppressor genes (TSGs), in all patients. These results demonstrated that valemetostat sufficiently restored the epigenome of the tumor cells close to the healthy state, leading to clinical improvements. Although all tested cases showed a durable response for more than 2 years, these responses were eventually interrupted due to the recurrence of ATL. We identified characteristic somatic mutations of EZH2 during clonal repopulation at PD. The identified amino acid substitutions were all located at the interface between EZH2 and valemetostat. Direct evaluation of the H3K27me3 level in the PD sample harboring the acquired EZH2 mutation showed that tumor cells in a hypermethylated state were repopulating. The scATAC-seq analysis also showed strong chromatin compaction of the same gene set occurred in the rapidly propagating resistant clone, indicating that the clonally selected mutations should be responsible for resistance. In patients free of the EZH2 resistant mutations, we detected TET2 mutation or elevated DNMT3A expression in the propagated resistant clones. Genome-wide DNA methylation analysis revealed increased DNA methylation near the TSS in the resistant clones. The genes characterized by the H3K27me3-related chromatin condensation were restored by valemetostat treatment but were again strongly re-condensed by mCpG gain at PD. Consequently, the gene regulation of several important TSGs restored by valemetostat was repressed again. Furthermore, in the single-cell platform, we successfully identified subpopulations with distinct metabolic and gene translation characteristics implicated in primary susceptibility until the acquisition of the heritable (epi)mutations. Conclusion: This study illustrates, for the first time, the molecular and cellular dynamics in patients in response to a molecular-targeting inhibitor designed for histone methyltransferases. Eliminating H3K27me3 leads to the reprogramming of the cancer epigenome, thereby exerting a sustained benefit on tumors. Targeting chromatin homeostasis might provide opportunities for further sustained epigenetic therapies.

Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report

Bovine leukemia virus (BLV) infects cattle, integrates into host DNA as a provirus, and induces malignant B-cell lymphoma. Previous studies have addressed the impact of proviral integration of BLV on BLV-induced leukemogenesis. However, no studies have monitored sequential changes in integration sites in which naturally infected BLV individuals progress from the premalignant stage to the terminal disease. Here, we collected blood samples from a single, naturally infected Holstein cow at three disease progression stages (Stage I: polyclonal stage, Stage II: polyclonal toward oligoclonal stage, Stage III: oligoclonal stage) and successfully visualized the kinetics of clonal expansion of cells carrying BLV integration sites using our BLV proviral DNA-capture sequencing method. Although 24 integration sites were detected in Stages I and II, 92% of these sites experienced massive depletion in Stage III. Of these sites, 46%, 37%, and 17% were located within introns of Refseq genes, intergenic regions, and repetitive sequences, respectively. At Stage III cattle with lymphoma, only two integration sites were generated de novo in the intergenic region of Chr1, and the intron of the CHEK2 gene on Chr17 was significantly increased. Our results are the first to demonstrate clonal expansion after the massive depletion of cells carrying BLV integration sites in a naturally infected cow.

Monitoring Alzheimer's Disease Progression in Mild Cognitive Impairment Stage Using Machine Learning-Based FDG-PET Classification Methods.

We previously introduced a machine learning-based Alzheimer's Disease Designation (MAD) framework for identifying AD-related metabolic patterns among neurodegenerative subjects. We sought to assess the efficiency of our MAD framework for tracing the longitudinal brain metabolic changes in the prodromal stage of AD. MAD produces subject scores using five different machine-learning algorithms, which include a general linear model (GLM), two different approaches of scaled subprofile modeling, and two different approaches of a support vector machine. We used our pre-trained MAD framework, which was trained based on metabolic brain features of 94 patients with AD and 111 age-matched cognitively healthy (CH) individuals. The MAD framework was applied on longitudinal independent test sets including 54 CHs, 51 stable mild cognitive impairment (sMCI), and 39 prodromal AD (pAD) patients at the time of the clinical diagnosis of AD, and two years prior. The GLM showed excellent performance with area under curve (AUC) of 0.96 in distinguishing sMCI from pAD patients at two years prior to the time of the clinical diagnosis of AD while other methods showed moderate performance (AUC: 0.7-0.8). Significant annual increment of MAD scores were identified using all five algorithms in pAD especially when it got closer to the time of diagnosis (p &lt; 0.001), but not in sMCI. The increased MAD scores were also significantly associated with cognitive decline measured by Mini-Mental State Examination in pAD (q &lt; 0.01). These results suggest that MAD may be a relevant tool for monitoring disease progression in the prodromal stage of AD.

Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease.

Crohn's disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn's. Ileal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn's patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type. We identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn's phenotypes, indicating changes in cellular activity. Our study identified cellular and transcriptional signatures associated with treatment-naïve Crohn's disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.

Analysis of Palliative Care Utilization and Medical Expenses among Patients with Chronic Diseases in Taiwan: A Population-Based Cohort Study.

Palliative care (PC) is an important alternative treatment for patients with chronic diseases, particularly for those in the later stages of disease progression. This is because these diseases are often irreversible, with progressive worsening of symptoms. By encouraging the use of tranquility resources for good death and spiritual relief, PC can reduce the physical and psychological burden on patients at the end of their lives. Currently, most discussions on PC have focused on patients with cancers, and few have further discussed the differences in medical expenses between PC and emergency treatment in patients with chronic diseases at the end of their lives. This study analyzed the top three chronic diseases in patients who used PC resources in the past decade and identified the impact of emergency treatment on mean survival time and medical expenses based on the medical records from the National Health Insurance Research Database. In total, 4061 patients with chronic diseases who were admitted to hospice wards were included in this study; of them, 85 patients still received emergency treatment, including urinary catheterization, nasogastric intubation, and respirator use, at the end of their lives. The mean survival time of patients aged 50–64 years who received emergency treatment was longer than that of the same age group who did not receive emergency treatment. Different comparisons of the mean survival time and medical expenses using real-world data provides important insights regarding PC management that may assist in establishing health policies in the future.

Staging heart failure patients with secondary mitral regurgitation undergoing transcatheter edge-to-edge repair

Abstract Background Heart failure with reduced ejection fraction (HFrEF) and secondary mitral regurgitation (SMR) are closely related. Progression of HFrEF-SMR is associated with characteristic pathophysiological changes. Recently, staging of HFrEF-SMR patients showed prognostic value in a SMR cohort on medical therapy. Whether these stages are prognostic for SMR patients undergoing transcatheter edge-to-edge mitral valve repair (M-TEER) in addition to drug therapy is unknown. Purpose The present study aimed at classifying HFrEF-SMR patients undergoing M-TEER into progressive disease stages based on cardiac and extracardiac involvement. We sought to evaluate the impact of the disease stages on survival outcome and symptomatic improvement after M-TEER Methods Based on echocardiographic transthoracic evaluation, patients were assigned into one of the following subsequent HFrEF-SMR stages representing disease progression (Figure 1): left ventricular (LV) dysfunction alone (Stage 1, LV end diastolic volume ≥159 ml and/or LV ejection fraction &amp;lt;50%); left atrial (LA) involvement (Stage 2, history of atrial fibrillation and/or indexed LA volume &amp;gt;34 ml/m2); right ventricular (RV) pressure/volume overload (Stage 3, tricuspid regurgitation ≥3+ and/or systolic pulmonary artery pressure &amp;gt;65 mmHg); biventricular failure (Stage 4, RV to pulmonary artery coupling &amp;lt;0.274 mm/mmHg). A Cox regression model was implemented to investigate the impact of HFrEF-SMR stages on two-year all-cause mortality and symptomatic outcome was assessed with New York Heart Association (NYHA) functional class at follow-up. Results Among a total of 849 included patients who underwent M-TEER for symptomatic MR from 2008 until 2019, 9.5% (n=81) presented with LV dysfunction alone, 46% (n=393) with LA involvement, 15% (n=129) with pressure/volume overload and 29% (n=246) with biventricular failure. At baseline and follow-up, successive HFrEF-SMR stages were associated with more severe heart failure symptoms as expressed by NYHA functional class. An increase in HFrEF-SMR stage was associated with increased two-year all-cause mortality rates after M-TEER (Hazard ratio 1.39, confidence interval 1.23–1.58, p&amp;lt;0.01, Figure 2). Conclusions Classifying HFrEF-SMR patients undergoing M-TEER into subsequent disease stages provides prognostic value regarding heart failure symptoms and survival. Funding Acknowledgement Type of funding sources: None.

P.129 One-year data from ENDEAVOR, a phase 1b trial of delandistrogene moxeparvovec in boys with DMD

Delandistrogene moxeparvovec (SRP-9001) is an investigational gene transfer therapy developed for targeted skeletal and cardiac muscle expression of a micro-dystrophin that is being studied in patients with Duchenne muscular dystrophy (DMD). Findings from ongoing Phase 1 and 2 trials demonstrate micro-dystrophin expression in patients treated with delandistrogene moxeparvovec clinical process material. ENDEAVOR (NCT04626674) is a two-part, open-label, Phase 1b study assessing the expression and safety of commercially representative delandistrogene moxeparvovec material in boys with DMD who represent different stages of disease progression. Four cohorts will be evaluated: Cohort 1: ≥4- to <8-year-old ambulatory boys; Cohort 2: ≥8- to <18-year-old ambulatory boys; Cohort 3: non-ambulatory boys; and cohort 4: ≥3- to <4-year-old ambulatory boys. Inclusion criteria include a genetic DMD diagnosis and stable steroid dosing (Cohorts 1 3 only, ≥12 weeks prior to screening). Participants received a single intravenous dose of commercially representative delandistrogene moxeparvovec material. The follow-up period consists of: Part 1, from post-infusion through to week 12, and Part 2, from week 12 through to week 260. The primary outcome measure is the change in micro-dystrophin protein expression from baseline to Week 12 (Part 1). Secondary outcome measures include change in micro-dystrophin expression at the sarcolemma from baseline to week 12 (Part 1) and safety (over 260 weeks). Exploratory functional endpoints include the North Star Ambulatory Assessment and timed function tests (Cohorts 1, 2 and 4) and performance of the upper limb and pulmonary function tests (Cohorts 2 and 3). We present 1-year safety and functional data and 12-week expression data following treatment with commercially representative delandistrogene moxeparvovec material. Delandistrogene moxeparvovec (SRP-9001) is an investigational gene transfer therapy developed for targeted skeletal and cardiac muscle expression of a micro-dystrophin that is being studied in patients with Duchenne muscular dystrophy (DMD). Findings from ongoing Phase 1 and 2 trials demonstrate micro-dystrophin expression in patients treated with delandistrogene moxeparvovec clinical process material. ENDEAVOR (NCT04626674) is a two-part, open-label, Phase 1b study assessing the expression and safety of commercially representative delandistrogene moxeparvovec material in boys with DMD who represent different stages of disease progression. Four cohorts will be evaluated: Cohort 1: ≥4- to <8-year-old ambulatory boys; Cohort 2: ≥8- to <18-year-old ambulatory boys; Cohort 3: non-ambulatory boys; and cohort 4: ≥3- to <4-year-old ambulatory boys. Inclusion criteria include a genetic DMD diagnosis and stable steroid dosing (Cohorts 1 3 only, ≥12 weeks prior to screening). Participants received a single intravenous dose of commercially representative delandistrogene moxeparvovec material. The follow-up period consists of: Part 1, from post-infusion through to week 12, and Part 2, from week 12 through to week 260. The primary outcome measure is the change in micro-dystrophin protein expression from baseline to Week 12 (Part 1). Secondary outcome measures include change in micro-dystrophin expression at the sarcolemma from baseline to week 12 (Part 1) and safety (over 260 weeks). Exploratory functional endpoints include the North Star Ambulatory Assessment and timed function tests (Cohorts 1, 2 and 4) and performance of the upper limb and pulmonary function tests (Cohorts 2 and 3). We present 1-year safety and functional data and 12-week expression data following treatment with commercially representative delandistrogene moxeparvovec material.