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PubMed2026

Non-coding RNAs in cancer: multi-omics insights, liquid biopsy advances, drug resistance mechanisms, and the road to clinical translation.

For most of the twentieth century, the transcriptional output of the human genome was thought to be biologically inert-a characterization that has been proven wrong in almost every important respect. Non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs) and PIWI-interacting RNAs (piRNAs) are now thought of as vital regulators of gene expression in all the stages of cancer pathogenesis, including the initial epigenetic changes, metastatic spread and the development of therapeutic resistance. This review highlights four areas where the clinical potential of ncRNAs is most promising: reconstruction of ncRNA regulatory networks by multi-omics integration; circulating ncRNAs as minimally invasive cancer biomarkers; causal roles of ncRNAs in drug resistance through epithelial-mesenchymal plasticity, metabolic reprogramming, and stromal communication; and translation of ncRNA targeting strategies to clinical trials. We will need to invest equally in mechanistic rigor and translational infrastructure to move forward.

antisense oligonucleotides↗

PubMed2026

MicroRNAs in Veterinary Viral Diseases: A Comprehensive Review from Molecular Mechanisms to Clinical Translation.

MicroRNAs (miRNAs) are small non-coding RNA molecules, approximately 22 nucleotides in length, that regulate post-transcriptional gene expression and have emerged as pivotal modulators of host-virus interactions. Veterinary viral diseases continue to pose substantial challenges to animal health, livestock productivity, food security, and public health, particularly due to their zoonotic potential. While miRNA research has advanced considerably, a comprehensive and critically integrated understanding of their biological functions and clinical applications across veterinary viral diseases remains incomplete. This comprehensive critical narrative synthesis addresses four overarching research questions: (1) What conserved and species-specific miRNA-mediated mechanisms govern major veterinary viral diseases? (2) What contextual factors determine antiviral vs. proviral duality? (3) To what extent do circulating miRNA signatures offer diagnostic and prognostic utility? (4) What translational barriers currently prevent clinical implementation, and how can the One Health framework help overcome them? Integrating three interconnected dimensions-molecular mechanisms, pathogen-specific responses, and translational applications-the review synthesizes evidence across PRRSV, avian oncogenic viruses (MDV, ALV), the immunosuppressive IBDV, FMD, BVDV, Ebola, Hendra, Rabies, and aquatic viral diseases. A key contribution of this review is the proposal of a four-axis contextual framework that explains the antiviral/proviral duality of miRNAs, and a 'One miRNA, One Health' convergence model with a concrete implementation roadmap. Key findings include: (a) a four-axis contextual framework (cell type, infection stage, viral strain, host-viral miRNA competition) that explains the antiviral/proviral duality; (b) virus-encoded miRNAs (v-miRNAs) as lower-risk therapeutic targets due to their absence from uninfected host genomes; (c) circulating miRNA biomarkers validated only at proof-of-concept stage (TRL 1-3), with no veterinary product yet at TRL ≥4; and (d) zoonotic conservation of miR-155, miR-146a, miR-21, and miR-122 across human and veterinary pathogens, supporting a 'One miRNA, One Health' convergence strategy. Critical short-term priorities are standardized pre-analytical protocols, open-access veterinary miRNA databases, and multicenter validation in natural infection cohorts.

Antiviral therapy↗

PubMed1976

Ethical considerations of study participants in dental caries clinical trials.

During the past 30 years there has been increasing concern for ethical considerations that pertain to the conduct of human biomedical research. Consequently, many national and international medical and dental organizations and agencies have developed regulations, policies or ethical guidelines for the protection of human subjects who take part in clinical investigations. In the United States, more than 500 research institutions have established permanent committees to review research in humans conducted by their institutions. Members of these committees must represent a broad range of backgrounds, interests, and concerns. Prospective study subjects must be able to make an informed decision on whether to participate in any study, without any element of force, deceit, duress, or other form of constraint or coercion. Obtaining informed consent for studies of children, the mentally infirm, and persons with restricted civil freedom presents special problems. Ethical considerations also raise questions on appropriate designs for clinical studies, e.g. use of untreated controls. Dental studies, particularly those testing caries-preventive agents, raise special questions of design, informed consent, ethical procedures and the use of diagnostic radiographs. The director of a clinical study is responsible for the conduct of all personnel connected with the investigation.

Child↗

PubMed2026

Non-coding RNAs as regulators of chromosomal instability in breast cancer.

Breast cancer is a highly heterogeneous disease characterized by extensive genomic and chromosomal instability (CIN), a hallmark that drives tumor evolution, intratumoral heterogeneity, therapeutic resistance, and poor clinical outcomes. Increasing evidence indicates that non-coding RNAs (ncRNAs) are important regulators of genome maintenance and chromosome stability. However, their specific contributions to CIN and the strength of the available evidence remain incompletely understood. This review examines the role of the major ncRNA classes, including circular RNAs, microRNAs, PIWI-interacting RNAs, small nucleolar RNAs, and long non-coding RNAs, in the regulation of CIN-related processes in breast cancer. We discuss the molecular mechanisms by which these ncRNAs regulate key pathways involved in CIN, while critically evaluating the strength of the experimental evidence supporting their functional roles. We also examine their associations with distinct breast cancer molecular subtypes and assess their potential as biomarkers and therapeutic targets, highlighting current limitations and knowledge gaps that hinder clinical translation. Collectively, the available evidence supports an emerging role for ncRNAs as regulators of CIN while underscoring the need for further mechanistic and subtype-specific studies to validate their clinical utility.

DNA repair↗

PubMed2026

Large-scale simulation of coverage and error rate tradeoffs for cancer detection in cell-free DNA whole-genome sequencing.

MOTIVATION: Cell-free DNA (cfDNA) whole-genome sequencing (WGS) is a promising approach for detecting cancer recurrence. It enables cancer detection by identifying all tumor-derived cfDNA (ctDNA) molecules carrying somatic single nucleotide variants (sSNVs). While ideally, a sequencing platform should be highly accurate for reliable ctDNA detection, in reality, all sequencing platforms introduce sequencing errors that generate false positives indistinguishable from true SNVs. Understanding how sequencing parameters influence ctDNA detection sensitivity at low tumor fractions (TFs) in cfDNA samples is essential for guiding sequencing strategies in clinical contexts. To model cfDNA sequencing for tumor detection, which contains asymmetric noise and multiple interacting parameters, analytical modeling is intractable, motivating large-scale parallelized simulation. RESULTS: We developed a simulation framework to generate in silico cfDNA data across 10 cancer types. In total, 480 million cfDNA samples were simulated from tumor WGS profiles. Overall, the lowest detectable TF differs substantially between cancer types under identical sequencing conditions due to variations in mutational load. For cancers with high mutational load, 3× coverage with low-error techniques reliably detects TFs below 0.1%. In contrast, cancers with low mutational load require at least six-fold higher coverage to achieve comparable detection thresholds. Increasing sequencing quality scores from Q30 to Q55 at 30× coverage further enhances sensitivity, enabling detection of TFs as low as 1 × 10-5. This study provides a comprehensive framework for optimizing sequencing parameters, offering valuable guidance for tailoring future technology development for specific cancer types and clinical applications. AVAILABILITY AND IMPLEMENTATION: The code is publicly available at https://github.com/UMCUGenetics/cfdetect/tree/main.

Whole Genome Sequencing↗

PubMed1979

Verbal response mode profiles of patients and physicians in medical screening interviews.

The medical importance of the patient-physician relationship is widely acknowledged, but research on its effects has been hampered by the lack of a method to quantify its clinically relevant features. In this study a new method of coding verbal interaction was applied to 52 interviews with adults in a general medical screening clinic. "Average interaction profiles" for patients and for physicians in the medical history, physical examination, and conclusion segments of the interviews provided detailed descriptions of the relationship that appear to be accurate and coincide with descriptions derived from clinical experience, textbooks, and other studies. The profiles yield quantitative indexes of such crucial aspects of the relationship as the manner in which patients give a history and physicians trasmit information to patients.

Adult↗

PubMed2025

STRUMP-I: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features.

The adaptive immune system monitors cellular integrity by recognizing short peptides from intracellular proteins presented on Major Histocompatibility Complex class I (MHC-I) molecules, collectively termed peptide-MHC complexes (pMHC), enabling detection of foreign or mutated proteins. With the rising importance of immunotherapies targeting neoantigens in cancers, the ability to accurately predict which peptides will bind to the diverse population of MHC alleles is critically important. Current computational methods for pMHC-I prediction fall broadly into sequence-based methods, which rely heavily on large training datasets, and structure-based methods that leverage structural modeling and energetics of pMHC binding. While sequence-based methods have been popularly used, their performance is dependent on the size and quality of training data. On the other hands, while structure-based approaches can generalize better across diverse MHC alleles, they traditionally depend on identifying a single global minimum energy conformation, an assumption that often fails due to the inherent binding promiscuity of MHC-I molecules. To address these limitations, we developed a STRUMP-I (STRUcture-based pMHC Prediction (for class I)), a novel pMHC binding prediction tool that directly leverages a broad set of force-field-derived energy terms as machine-learning features. STRUMP-I achieves performance comparable to state-of-the-art sequence-based models while significantly outperforming them on MHC alleles with limited representation in training data. Furthermore, STRUMP-I demonstrates strong synergy when integrated with sequence-based methods, notably enhancing prediction precision. The robustness and generalizability of STRUMP-I were confirmed by evaluating its predictive performance on independent, previously unseen datasets, including an experimentally validated cancer neoantigen dataset. This combined approach advances our capability to reliably identify clinically relevant neoantigen targets. The source code and trained models are available at https://github.com/yoonjoolab/STRUMP-I.

energy optimization↗

PubMed1977

Acute viral hepatitis in Italy. Results of a collaborative study.

The etiological and clinical aspects of viral hepatitis were evaluated by a retrospective survey of patients hospitalized in 1972, 1973 and 1974 in 12 specialized medical centers scattered throughout Italy. The data refer to 2788 patients suffering from acute viral hepatitis who were hospitalized during the initial 10 days of jaundice. The majority of patients (90%) had not been treated with steroids. For each case, the clinical and biochemical data were recorded, coded, computerized and statistically analyzed. In our patient population viral hepatitis was more frequent among younger patients. We observed a high frequency of HBsAg positive hepatitis (40.7%) which was seldom associated to a history of parenteral exposure and showed an irregular geographical distribution. HBsAg positive hepatitis was similarly distributed between males and females. It was more frequent in patients older than 30 (60%) than in children (18-23%) and younger patients (42%). In our series, the frequency of HBsAg hepatitis found in surgeons (81.8%) and nursing personnel (66.3%), but not in physicians (41.2%), was greater than that of the entire sample due to their exposure to blood.

Adolescent↗

PubMed1977

[The diagnostic value of the EEG in multiple sclerosis (author's transl)].

245 records of 178 multiple sclerotic patients were assessed from 110 EEG-parameters and 18 clinical points of view. According to the special code the data were stored on cards and later statistically evaluated. The following conclusions were made: 1. 64% of all records were abnormal. 2. The frequency of bilateral and generalized abnormalities was significantly higher with brain stem localization of clinical signs. 3. In the progressiv phase of the disease there was a significantly greater occurrance of bilateral slow EEG abnormalities and bilateral potentially epileptic signs (sharp waves, bilateral paroxysms). 4. Focal EEG abnormality is seldom found in multiple sclerosis.

Adolescent↗

PubMed2026

Pandemic-Related Disruptions and Hepatocellular Carcinoma Surveillance in Safety-Net Settings.

IMPORTANCE: Pandemic-related disruptions in cirrhosis care resulted in major gaps and delays in surveillance for hepatocellular carcinoma (HCC). Whether these initial declines improved and rebounded to prepandemic levels remains unclear. OBJECTIVE: To evaluate contemporary clinical practice data on HCC surveillance utilization from before the COVID-19 pandemic to 4 years after the onset of the pandemic among safety-net populations with cirrhosis. DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study was conducted at 5 safety-net health systems in the US. Adults with cirrhosis were evaluated longitudinally across 3 time periods: March 1, 2018, to February 29, 2020 (pre-COVID-19 period), March 1, 2020, to February 28, 2022 (COVID-19 era), and March 1, 2022, to February 29, 2024 (post-COVID-19 period). MAIN OUTCOMES AND MEASURES: The primary outcome was undergoing HCC surveillance identified using Current Procedural Terminology codes for ultrasonography, computed tomography, and magnetic resonance imaging, and corresponding International Statistical Classification of Diseases, Tenth Revision, Clinical Modification diagnosis codes for indication. Comparisons of HCC surveillance across time periods used paired t tests, and comparisons of HCC surveillance between subgroups within the same time period used χ2 tests. RESULTS: Among 6940 patients with cirrhosis, 4001 (57.7%) were men (median [IQR] age, 58 [52-64] years), 206 (3.0%) were Asian, 1720 (24.8%) were Hispanic, 1672 (24.1%) were non-Hispanic Black or African American, and 3081 (44.4%) were non-Hispanic White. The proportion who underwent HCC surveillance within 6 months after diagnosis was 30.8% (1940 patients) in the pre-COVID-19 era, which declined to 21.1% (1468 patients) in the COVID-19 era, and remained at 22.3% (1405 patients) in the post-COVID-19 era. Consistent trends were observed among men and women and among all age and race groups, except for Asian individuals, for whom there was an observed increase in the post-COVID-19 era. Similar trends of low HCC surveillance post-COVID-19 were observed across insurance types but was particularly concerning among uninsured or indigent care covered patients, among whom only 116 of 997 (11.9%) underwent surveillance in the most recent period. CONCLUSIONS AND RELEVANCE: In this observational study of US safety-net populations with cirrhosis, rates of HCC surveillance following pandemic-related declines remained persistently low even up to 4 years after the onset of the COVID-19 pandemic, with fewer than 1 in 4 patients having undergone guideline-concordant HCC surveillance.

Humans↗

PubMed1979

Interaction exchange structure and patient satisfaction with medical interviews.

The verbal interaction between patients and physicians in 52 initial interviews in a university hospital screening clinic was studied using a new discourse coding system. Factor analysis of category frequencies showed that each interview segment, medical history, physical examination, and conclusion, consisted mainly of two or three types of verbal exchange. Patient satisfaction with the interviews, assessed with a questionnaire that yields separate scores for satisfaction with cognitive and affective aspects, was found to be associated with exchanges involving the transmission of information in particular interview segments. Affective satisfaction was associated with transmission of information from patient to physician in "exposition" exchanges during the medical history, in which patients told their story in their own words. Cognitive satisfaction was associated with transmission of information from physician to patient in "feedback" exchanges during the conclusion segment, in which physicians gave patients information about illness and treatment.

Adolescent↗

PubMed1977

R plasmids coding for gentamicin, tobramycin, and carbenicillin resistance in Serratia, Klebsiella and Escherichia coli strains from a single clinical source.

Serratia marcescens, Klebsiella sp. and Escherichia coli strains bearing transferable resistance to aminoglycoside antibiotics, namely, gentamicin, tobramycin, kanamycin, streptomycin, lividomycin, and carbenicillin, as well as to a series of more classical drugs, began to emerge in materials from the Frankfurt University Hospital. Plasmids from Serratia, Klebsiella, and E. coli exhibit a broad host range in that they are transferable to E. coli, Proteus mirabilis and Salmonella typhimurium receipients. They are not transferable to Pseudomonas aeruginosa, although in that species plasmids of gentamicin and tobramycin resistance, was well as of resistance to further drugs, were detected in that area as early as in 1973. High-level carbenicillinase has been identified in Serratia and Klebsiella plasmids associated with drug resistance to aminoglycoside antibiotics.

Anti-Bacterial Agents↗

PubMed1979

Tumor antigen of human cervical squamous cell carcinoma: correlation of circulating levels with disease progress.

A double-antibody radioimmunoassay method was used for serial determinations of a tumor-antigen (TA-4) of cervical squamous cell carcinoma, and the correlation of serum antigen levels with the disease progess was investigated in 23 patients with cervical squamous cell carcinoma. Ten cases with widespread metastases received radiotherapy and/or chemotherapy. Nine of these cases who showed progression of the disease had a corresponding increase in serum antigen levels, while one case who had regression of the disease showed a corresponding decrease in serum antigen levels. Thirteen patients received radical surgery, and in all of these, high pretreatment antigen levels declined to undetectable levels 1 or 2 weeks after surgery. A panel of coded sera from the NCI-Mayo Clinic Serum Bank was also studied for evaluating the specificity of the assay. Thirteen of 25 patients (52%) with cervical squamous cell carcinoma showed positive serum antigen levels, while only one of 58 control cases (1.7%) showed false-positive result. These results suggest that serial TA-4 determinations may provide a useful method for evaluating regression or progression of the disease.

Adult↗

PubMed1992

Replication of human cytomegalovirus in the cells of the U937 monocytoid cell line.

Human cytomegalovirus (HCMV) infection in immunocompromized hosts sometimes occurs as a result of reactivation. Cells of the monocyte-macrophage linkage are suggested to be a site of latency and persistence for HCMV. The human monocytic cell line U937 was infected with the AD169 strain and a clinical isolate of HCMV. The expression of surface antigens on the cells was assessed by flow cytometry. The polymerase chain reaction (PCR) was used to detect viral DNA from infected cells. CMV immediate early antigen, early antigen, and late antigen (LA) were detected from both clinical isolate- and AD169-inoculated U937 cells by flow cytometry. CMV DNA which code major immediate early gene (US3) and LA gene (US14) were detected from the clinical isolate-inoculated U937 over a period of 31 days as tested by PCR. These U937 cells proliferated as well as uninfected U937 cell, but only a small number of AD169-inoculated U937 cells survived after 14 days of inoculation. Interleukin-2 activities were detected in the media on days 24-40 after inoculation with AD169. This chronic CMV infection model of U937 might be utilized to study the mechanisms of persistence and reactivation.

Antigens, Viral↗

PubMed1992

ECG data compression by corner detection.

An ECG sampled at a rate of 360, 500 samples s-1 or more produces a large amount of redundant data that are difficult to store and transmit. A process is therefore required to represent the signals with clinically acceptable fidelity and with the least code bits possible. In the paper, a real-time ECG data compressing algorithm, CORNER, is presented. CORNER is an efficient algorithm which locates significant samples and at the same time encodes the linear segments between them using linear interpolation. The samples selected include, but are not limited to, the samples that are significantly displaced from the encoded signal such that the allowed maximum error is limited to a constant epsilon which is specified by the users. The way in which CORNER computes the displacement of a sample from the encoded signal guarantees that the high activity regions are more accurately coded. The results are compared with those of the well known data compression algorithm, AZTEC, which is also a real-time algorithm. It is found that, under the same bit rate, a considerable improvement of the signal-to-noise ratio (SNR) and root mean square error (RMSerr) can be achieved by employing the proposed CORNER algorithm. An average value of SNR (RMSerr) of 27.0 dB (5.668) can be achieved even at an average bit rate of 0.79 bit sample-1 by employing CORNER, whereas the average value of SNR (RMSerr) achieved by AZTEC under the same bit rate is 16.60 dB (19.368).

Algorithms↗

PubMed1992

Eight novel inactivating germ line mutations at the APC gene identified by denaturing gradient gel electrophoresis.

Familial adenomatous polyposis (FAP) is a dominantly inherited condition predisposing to colorectal cancer. The recent isolation of the responsible gene (adenomatous polyposis coli or APC) has facilitated the search for germ line mutations in affected individuals. Previous authors have used the RNase protection assay and the single-strand conformation polymorphisms procedure to screen for mutations. In this study we used denaturing gradient gel electrophoresis (DGGE). DGGE analysis of 10 APC exons (4, 5, 7, 8, 9, 10, 12, 13, 14, and part of 15) in 33 unrelated Dutch FAP patients has led to the identification of eight novel germ line mutations resulting in stop codons or frameshifts. The results reported here indicate that (1) familial adenomatous polyposis is caused by an extremely heterogeneous spectrum of point mutations; (2) all the mutations found in this study are chain terminating; and (3) DGGE represents a rapid and sensitive technique for the detection of mutations in the unusually large APC gene. An extension of the DGGE analysis to the entire coding region in a sufficient number of clinically well-characterized, unrelated patients will facilitate the establishment of genotype-phenotype correlations. On the other hand, the occurrence of an extremely heterogeneous spectrum of mutations spread throughout the entire length of the large APC gene among the FAP patients indicates that this approach may not be useful as a rapid presymptomatic diagnostic procedure in a routine laboratory. Nevertheless, the above DGGE approach has incidentally led to the identification of a common polymorphism in exon 13. Such intragenic polymorphisms offer a practical approach to a more rapid procedure for presymptomatic diagnosis of FAP by linkage analysis in informative families.

Adenomatous Polyposis Coli↗

PubMed2026

diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application.

MOTIVATION: DNA methylation serves as a key biomarker in clinical diagnostics, especially in cancer detection. With methylation-specific PCR (MSP), a widely used approach, patient samples can be screened fast and efficiently for differential methylation. During MSP, methylated regions are selectively amplified with specific primers. With nanopore sequencing, knowledge about DNA methylation is generated during direct DNA sequencing without needing pretreatment of the DNA. Multiple methods, mainly developed for whole-genome bisulfite sequencing (WGBS) data, exist to predict differentially methylated regions (DMRs) in the genome. However, the predicted DMRs are often very large and not sufficiently discriminating to generate meaningful results in MSP, creating a gap between theoretical cancer marker research and practical application, as no tool currently provides methylation difference predictions tailored for PCR-based diagnostics. RESULTS: Here, we present diffMONT, a tool that predicts differentially methylated regions specifically suited for MSP primer design, enabling rapid translation into practical applications. diffMONT takes into account (i) the specific length of primer and amplicon regions, (ii) the fact that one condition should be unmethylated, and (iii) a minimal required amount of differentially methylated cytosines within the primer regions. We compared the results of diffMONT to metilene and DSS based on a publicly available nanopore sequencing dataset and show that the regions predicted by diffMONT are more specific toward hypermethylated regions. diffMONT accelerates the design of methylation-specific diagnostic assays, bridging the gap between theoretical research and clinical application. AVAILABILITY AND IMPLEMENTATION: The source code for diffMONT, an open-source Python-based tool, is available at https://github.com/rnajena/diffMONT/, with an archived release under https://zenodo.org/records/17641031.

DNA Methylation↗

PubMed2026

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

MOTIVATION: The plasma proteome offers a dynamic window of human health, capturing the real-time intersections between genetics and physiology. However, the application of deep learning to proteomics is currently hindered by a reliance on large-scale labeled datasets, rendering standard models ineffective for rare or novel diseases where patient samples are inherently scarce. RESULTS: Here, we present ProMeta, a meta-learning framework designed to enable robust disease modeling under extreme data restrictions. By integrating knowledge-guided pathway encoding with bi-level meta-optimization, ProMeta projects unstructured proteomic profiles into biologically interpretable functional tokens. This architecture allows the model to learn a global initialization containing transferable biological priors from biobank-scale data, facilitating rapid adaptation to novel tasks. Through comprehensive benchmark experiments, ProMeta consistently outperformed transfer learning and traditional machine learning baselines in both disease diagnosis and prediction tasks. In the most challenging 4-shot scenarios (utilizing only 2 cases and 2 controls), the model achieved robust generalization with an average AUROC of ∼0.69, representing a 24.6% relative improvement over the best-performing baseline methods. Mechanistic investigation revealed that ProMeta disentangles cases from controls in the latent space prior to task-specific adaptation, confirming the acquisition of universal biological rules rather than rote memorization. Furthermore, gradient-based interpretation identified disease-specific protein biomarkers and functional pathways consistent with known pathophysiology. Collectively, ProMeta overcomes the data-scarcity bottleneck in precision medicine, providing a scalable, interpretable framework for characterizing the full spectrum of human diseases, particularly for rare conditions lacking extensive clinical cohorts. AVAILABILITY AND IMPLEMENTATION: The source code of ProMeta is available at GitHub (https://github.com/lihan97/ProMeta).

Proteomics↗