High-concentration biologic formulations: challenges, strategies, and emerging technologies for subcutaneous delivery

Abstract: The growing demand for subcutaneous (SC) self-administration of biotherapeutics, driven by the rising prevalence of chronic diseases and healthcare cost-containment pressures, has accelerated the development of high-concentration formulations (HCFs). However, protein concentrations exceeding 100 mg/mL introduce significant challenges, including solubility limitations, high viscosity, aggregation propensity, injectability constraints, and manufacturing complexities. This review systematically examines the primary obstacles in HCF development and highlights recent advances in formulation and process technologies. Key strategies include: (i) excipient-based viscosity reducers; (ii) hyaluronidase-enabled large-volume SC delivery; (iii) lyophilization for decoupling manufacturing from final concentration; (iv) spray drying platforms including SnapShot™ and XeriJect®; (v) electrostatic spray drying (Elektroject™ Hypercon™); (vi) Microglassification™ dehydration technology; and (vii) protein crystallization (Crystalomics®). Collectively, these innovations are reshaping the landscape of high-concentration biologic drug products, enabling the transition from intravenous to subcutaneous administration for a broader range of therapeutics. This review serves as a strategic guide for formulation scientists and drug developers engaged in next-generation subcutaneous biologics.

Humans
Excipients
Injections, Subcutaneous
Biological Products
Chemistry, Pharmaceutical
Drug Delivery Systems
Animals
Solubility
Drug Compounding
Freeze Drying
Viscosity
Hyaluronoglucosaminidase
Crystallization
Technology, Pharmaceutical
Proteins


SEM/EDS analysis as a complementary tool for continuous improvement of cefixime granules for oral suspension

Abstract: The aim of this study was to evaluate scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDS) as complementary analytical tools for supporting continuous improvement in pharmaceutical granule manufacturing. Pilot-scale cefixime granules for oral suspension were prepared as defined process scenarios, including placebo, reference, intermediate, stress-exposed, and optimised batches. SEM was used to compare granule morphology, surface integrity, and agglomeration behaviour, whereas EDS provided qualitative and semi-quantitative information on localised elemental composition, with emphasis on sulfur as an API-related marker and oxygen-to--sulfur trends as surface-sensitive indicators of process- or stress-related variability. Intermediate and stress-exposed batches showed increased surface roughness, microstructural deterioration, and higher oxygen-to-sulfur ratios, whereas reference and optimised batches showed more uniform morphology and comparable elemental profiles. The findings indicate that SEM/EDS can provide useful material-level insight into process-related variability and may support root--cause investigation and process refinement. Overall, SEM/EDS is proposed as a complementary, localised, and semi-quantitative approach for supporting continuous improvement in pharmaceutical granule manufacturing.

Mitrevska I
Karpicarov D
Mihailovska A
Mirakovski D
Paneva O
Petrushevski G

Cefixime
Microscopy, Electron, Scanning
Spectrometry, X-Ray Emission
Anti-Bacterial Agents
Suspensions
Administration, Oral
Chemistry, Pharmaceutical
Drug Compounding
Surface Properties
Bulk Drugs


Hot-Melt Extrusion of Bupropion with Three Ethylcellulose Grades for Pellet Feedstock Preparation and Screw-Based 3D Printing of Sustained-Release Tablets

Abstract: 3D printing has emerged as a novel technology for producing personalized dosage forms tailored to patients' therapeutic needs. Hot-melt extrusion (HME) is commonly used to produce filaments for most extrusion-based 3D printers. This study aimed to investigate the effect of three different ethylcellulose (EC) grades (7N, 10N, and 20N) on the physicochemical properties, matrix restructuring, and sustained-release behavior of bupropion hydrochloride (BUP·HCl)-loaded tablets. The extrudates were fabricated using HME, pelletized, and used as feedstock for screw-based 3D printing, thereby overcoming the limitations of filament-based systems. The formulations were evaluated for drug release, hardness, swelling, and porosity before and after dissolution using micro-computed tomography (microCT). The influence of tablet geometry on drug release was also investigated. Morphology, crystallinity, and thermal properties were characterized using scanning electron microscopy (SEM), X-ray powder diffraction (XRPD), differential scanning calorimetry (DSC), and thermogravimetric analysis (TGA). All formulations exhibited sustained BUP·HCl release, with drug release decreasing as EC viscosity grade increased. Tablets prepared with higher-viscosity EC showed greater hardness, reduced swelling, and lower post-dissolution porosity. MicroCT analysis revealed raster-related internal pores in all tablets before dissolution. However, initial porosity did not correlate with release behavior; tablets containing EC 20N exhibited the highest initial porosity but the lowest post-dissolution porosity and slowest drug release, whereas EC 7N tablets showed the opposite trend. Larger, thinner tablets released drug faster due to higher surface-area-to-volume ratio. The findings demonstrate that EC molecular weight plays a critical role in governing hydration-driven matrix restructuring and controlling sustained-release behavior of the 3D-printed tablets.

Protopapa C
Junqueira LA
Kolipaka SS
Economidou S
Pappas D
Douroumis D
Vlachou M

Printing, Three-Dimensional
Delayed-Action Preparations
Cellulose
Tablets
Bupropion
Drug Liberation
Porosity
Drug Compounding
Solubility
Chemistry, Pharmaceutical
Hot Melt Extrusion Technology
Calorimetry, Differential Scanning
Viscosity
Excipients
X-Ray Microtomography
Hardness
X-Ray Diffraction


Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study

Abstract: Predicted deleterious mutations (SNPs) have different distributions of effects compared to random SNPs based on population composition. Variant prioritization of markers based on deleterious scores can improve the prediction of yield. Favoring mating schemes between parents with fewer highly deleterious mutations can increase the rate of genetic gain. The study of mutations is fundamental to understanding evolution, domestication, and genetics. Characterizing mutations has potential to accelerate breeding programs through selection and purging deleterious mutations (DelMut). We investigated how predicting DelMut in breeding populations informs genomic prediction (GP) increasing the rate of genetic gain. DelMut were annotated in three independent common bean populations using a previously developed random forest (RF) model for common bean incorporating phylogenetic and protein information. Deleterious scores from the RF model were around 0.25, with the top 1% (highly DelMut) of variants scoring between 0.78 and 0.82 among populations. All populations showed variation in the number of highly DelMut per line (max. 13-197) and in genetic load. We assessed the impact of incorporating a priori information on DelMut for variant prioritization and weighting in GP models for yield and flowering time. Stochastic simulations were conducted to evaluate how designing mating schemes based on variable numbers of DelMut per parent can affect genetic gain. Variants with higher predicted scores had significantly different effect distributions compared to random or lower-scored markers. Simulated breeding cycles showed that selecting parents with fewer highly DelMut consistently increases the rate of genetic gain, and depending on the population, can be superior to phenotypic selection. These results highlight the potential of DelMut information for variant prioritization and the optimization of common bean breeding programs. The approaches we developed can be applied to other species to improve the efficacy of crop improvement.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

Phaseolus
Mutation
Models, Genetic
Genome, Plant
Plant Breeding
Computer Simulation
Polymorphism, Single Nucleotide
Genomics
Phenotype
Genotype
Random Forest
Genetic Markers


Genomic and polyphasic characterization of six novel Hymenobacter species isolated from soil in Korea

Abstract: Six bacterial strains (BT523T, BT559T, 15J16-1T3BT, BT730T, DG25AT, and DG25BT) were isolated from soil samples in Korea and assigned to the family Hymenobacteraceae (order Cytophagales, class Cytophagia). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed distinct lineages within the genus Hymenobacter. Strains BT523T, BT559T, and 15J16-1T3BT exhibited highest sequence similarities to Hymenobacter armeniacus BT189T (97.6%), Hymenobacter polaris RP-2-7 T (97.8%), and Hymenobacter paludis KBP-30 T (98.3%), respectively, while strains BT730T, DG25AT, and DG25BT were most closely related to Hymenobacter tibetensis XTM003T, with similarities of 96.3-96.6%. All strains were Gram-negative, aerobic, rod-shaped, and formed red to pink pigmented colonies. Whole-genome analysis revealed genome sizes ranging from 3.78 to 6.33 Mb with G + C contents of 55.5-65.0%. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the strains and their closest relatives were below the accepted thresholds for species delineation, supporting their classification as novel species. Functional annotation indicated the presence of genes associated with core metabolism, stress response, and pigment biosynthesis, reflecting adaptation to soil environments. Secondary metabolite analysis further revealed the presence of biosynthetic gene clusters, including terpene and siderophore pathways. Based on polyphasic taxonomic evidence, the six strains are proposed to represent six novel species of the genus Hymenobacter, for which the names Hymenobacter miniatus sp. nov., Hymenobacter madidus sp. nov., Hymenobacter convexus sp. nov., Hymenobacter rubellus sp. nov., Hymenobacter erythromyxa sp. nov., and Hymenobacter radioresistens sp. nov. are proposed. The type strains are BT523T (= KCTC 72341 T = NBRC 114851 T), BT559T (= KACC 21821 T = NBRC 114852 T), 15J16-1T3BT (= KCTC 42995 T = NBRC 112818 T), BT730T (= KACC 22457 T = NBRC 116482 T), DG25AT (= KCTC 32451 T = TBRC 19856 T), and DG25BT (= KCTC 32452 T = JCM 19444 T).

Soil Microbiology
Phylogeny
Republic of Korea
RNA, Ribosomal, 16S
Cytophagaceae
DNA, Bacterial
Genome, Bacterial
Sequence Analysis, DNA
Bacterial Typing Techniques
Base Composition
Genomics
Fatty Acids


Toxicoproteomic analysis reveals arsenic-induced alterations in eye lens proteins of Labeo rohita

Abstract: Arsenic occurs extensively in the environment and is classified as a potent carcinogenic substance in humans. Prolonged intake of water contaminated with arsenic results in the development of arsenicosis. In the present study, a toxicoproteomic approach was employed to elucidate arsenic-induced alterations in lens proteins using a fish model. Juveniles of Labeo rohita were exposed to sodium meta-arsenite (NaAsO2) at concentrations of 5, 10, 15, and 20 ppm for a period of 10 days in triplicate experimental groups. Soluble lens proteins were analyzed using one- and two-dimensional gel electrophoresis, immunoblotting of αA-crystallin and MALDI-TOF mass spectrometry. Cataract development was observed at arsenic concentrations ≥ 15 ppm. Proteomic analyses revealed concentration-dependent alterations in lens protein abundance, including significant reductions in βB1, βB2, and βA2b-crystallin, small heat shock protein and skeletal α-actin (p < 0.05). In addition, αA, βA2, and βA2a-crystallin exhibited reduced abundance trends, although these changes were not statistically significant. Two-dimensional immunoblotting revealed 15 distinct αA-crystallin isoforms in control lenses, several of which showed a progressive decrease with increasing arsenic exposure, culminating in complete degradation at 20 ppm. These findings demonstrate that arsenic exposure is associated with substantial alterations in lens crystallins and other proteins involved in structural organization and protein homeostasis, coinciding with cataract development at higher exposure concentrations. The identified proteins may serve as potential toxicoproteomic biomarkers of lens damage in aquatic organisms and provide a foundation for future studies investigating the molecular mechanisms of arsenic-induced lens toxicity.

Bhattacharjee S
Pati MK
Bisai K
Mohanty BP

Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


Ancient Transposable Elements Sustain Global Ecological Adaptation Despite Chronically Low Nucleotide Diversity

Abstract: Transposable elements (TEs) are dynamic components of eukaryotic genomes and a major source of structural and regulatory variation, yet their contribution to ecological adaptation over evolutionary time remains unresolved. This uncertainty is particularly acute in species that occupy broad environmental niches despite chronically low nucleotide diversity, where conventional models predict limited adaptive potential. Here we show that ancient TE polymorphisms underpin global ecological adaptation in Spirodela polyrhiza, one of the smallest flowering plants with low genome-wide nucleotide diversity. Most TE polymorphisms predate continental population divergence. Cold-season temperature emerges as the dominant selective axis, with adaptive signals overwhelmingly associated with TE polymorphisms rather than SNPs. These adaptive TEs bear signatures of selection on standing variation and are embedded in genomic regions shaped by relaxed selective constraint rather than recent hard sweeps. Our results reveal how ancient TE variation sustains ecological adaptation despite chronically depleted nucleotide diversity, resolving a longstanding evolutionary paradox.

DNA Transposable Elements
Adaptation, Physiological
Araceae
Selection, Genetic
Evolution, Molecular
Genetics, Population
Polymorphism, Genetic
Sequence Analysis, DNA
Genetic Variation
DNA, Plant
Polymorphism, Single Nucleotide
Genome, Plant
Adaptation, Biological


Genomics of Subsequent Neoplasms in Childhood Cancer Survivors

Abstract: Brady and colleagues investigated the mutational consequences of cancer treatment on the genomes of 160 childhood cancer survivors who developed a subsequent neoplasm (SN). Their research aids in directing the next steps toward the prevention of SNs. See related article by Brady et al., p. 1590.

Humans
Neoplasms
Genomics
Cancer Survivors
Child
Mutation


Application of a 64-plex Panel in the Study of Genetic Polymorphism and Population Structure of Kyrgyz Group

Abstract: Objective To assess the forensic application value of 59 InDel loci and two miniSTR loci in Chinese Kyrgyz group,and to explore the genetic structure and genetic background of this group. Methods A total of 99 Kyrgyz individuals were genotyped through the 64-plex panel,which was developed independently by our lab.Allele frequencies and forensic parameters were calculated for the InDel loci and miniSTR loci included in the 64-plex panel.The application potential of these loci for full sibling identification was assessed by simulating 5 000 pairs of full siblings and unrelated individuals,respectively,via Familias v3 software.Additionally,various population analysis methods were employed to systematically explore the genetic relationships among the Kyrgyz group and 35 reference populations from five continents. Results The average polymorphism information content of the 59 InDel loci and two miniSTR loci in the Kyrgyz group were 0.365 1 and 0.753 6,respectively.The cumulative discrimination power and cumulative probability of exclusion of the 61 loci mentioned above were 1-1.928 4×10-27 and 0.999 996 539 2,respectively.When the likelihood threshold was set at 100,the accuracy of this panel in distinguishing full siblings from unrelated individuals reached 93.93%.The results of population genetic analyses indicated that the Kyrgyz group had the mixed genetic components of East Asian and European populations,and was genetically closer to the East Asian populations,particularly the Mongolian group. Conclusions The 59 InDel loci and two miniSTR loci show high forensic application value in individual identification and parentage testing and demonstrate certain application potential in full sibling relationship identification.Meanwhile,the results further reveal the mixed East Asian-European genetic background of the Kyrgyz group.This study enriches the genetic resource information on Chinese ethnic minorities and provides basic data to support forensic practice.

Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae

Humans
Polymorphism, Genetic
Genetics, Population
Gene Frequency
Asian People
Microsatellite Repeats
Genotype
INDEL Mutation
Kyrgyzstan


[Clinical management of familial platelet disorder with associated myeloid malignancies: at the crossroads of hematology and clinical genetics]

Abstract: With the widespread adoption of genomic testing, germline predisposition syndromes such as RUNX1-familial platelet disorder with associated myeloid malignancy (FPD-MM) are increasingly encountered in routine hematological practice. FPD-MM is driven by RUNX1 haploinsufficiency, which initially manifests as quantitative and qualitative platelet abnormalities. Over time, this constitutional defect promotes the formation of an inflammation-dominant bone marrow microenvironment, facilitating clonal hematopoiesis, clonal expansion, and the stepwise accumulation of secondary somatic alterations, ultimately leading to myeloid or lymphoid malignancies. Accurate diagnosis requires careful interpretation of tumor-based sequencing results, followed by confirmatory testing using appropriate germline specimens in conjunction with standardized variant classification frameworks. Clinical management encompasses bleeding risk mitigation and disease-specific therapy for overt hematologic neoplasms, including allogeneic hematopoietic stem cell transplantation. Genetic counseling is an essential component of donor coordination in FPD-MM, given the documented risk of donor-derived leukemia when related donors harbor the same pathogenic germline variant as the proband. Beyond the management of affected individuals, surveillance for asymptomatic variant carriers is also essential for early intervention before disease progression. This review summarizes the pathobiology, diagnostic strategy, and practical clinical management of FPD-MM, emphasizing family management as a central medical and ethical challenge at the intersection of hematology and clinical genetics.

[Rinsho ketsueki] The Japanese journal of clinical hematology

Humans
Blood Platelet Disorders
Myeloproliferative Disorders
Hematologic Neoplasms
Genetic Predisposition to Disease
Genetic Counseling
Germ-Line Mutation
Core Binding Factor Alpha 2 Subunit
Genetic Testing
Hematopoietic Stem Cell Transplantation
Leukemia, Myeloid, Acute
Blood Coagulation Disorders, Inherited


[Hematopoietic cell transplantation in the era of genome analysis]

Abstract: Genomic information for hematologic malignancies is now routinely available in clinical practice, supporting the adaptation of hematopoietic cell transplantation, selection of conditioning intensity, and implementation of post-transplant maintenance therapy through refinement of disease risk assessment and minimal residual disease (MRD) measurement. This review presents the current evidence on the effective utilization of genomic information for acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPN). It also presents an up-to-date framework for optimal donor selection based on donor genome information, addressing both donor clonal hematopoiesis of indetermined significance and the risk that related donor candidates may carry the same hereditary predisposition. Finally, it discusses research showing that patient and donor genetic polymorphisms (SNPs) can predict transplant complications such as GVHD, and that reduced gut microbiota diversity, as detected by metagenomic analysis, impacts GVHD severity and survival. These examples illustrate the multifaceted role of genomic information in research efforts to improve hematopoietic cell transplantation outcomes.

Humans
Hematopoietic Stem Cell Transplantation
Myelodysplastic Syndromes
Genomics
Neoplasm, Residual
Polymorphism, Single Nucleotide
Hematologic Neoplasms
Leukemia, Myeloid, Acute
Graft vs Host Disease


[Genomic abnormalities in myeloproliferative neoplasms]

Abstract: Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs) are driven by recurrent driver mutations and evolve through the stepwise accumulation of additional genetic alterations and clonal evolution. Some large cohort studies have demonstrated that individual additional mutations significantly influence prognosis, leukemic transformation, and progression to myelofibrosis. Furthermore, certain mutations frequently co-occur with other adverse mutations and may act as molecular hubs that amplify clinical impact. Based on these findings, mutation-integrated scoring systems have been developed to improve risk stratification and refine therapeutic decision-making. However, despite the recent adoption of comprehensive genomic testing in clinical practice, there is still limited evidence to guide treatment selection or determine the optimal timing of therapeutic intervention based on mutational profiles or molecular monitoring results. A deeper understanding of clonal evolution, grounded in genomic abnormality data, will be essential for establishing more rational and biology-driven therapeutic strategies.

Humans
Myeloproliferative Disorders
Mutation
Genomics
Prognosis


[Development of Drug Discovery Research Based on the Discovery of AlkB Homolog 3 and Establishment of an Academic Drug Discovery Platform]

Abstract: The field of epitranscriptomics, an area of genetics concerning the regulation of gene expression via post-transcriptional RNA modification, is currently attracting substantial research attention. In epitranscriptomics, proteins, collectively termed writers, erasers, and readers, enter into complex interactions that contribute to modifying RNA, thereby maintaining biological homeostasis. However, abnormalities in the expression or function of these proteins can lead to the onset and progression of cancers and neuropsychiatric disorders. Using prostate cancer clinical specimens, I cloned a novel gene, prostate cancer antigen-1 (PCA-1), containing a domain similar to the 2-oxoglutarate, iron(II) [Fe(II)]-dependent oxygenase domain of the Escherichia coli AlkB protein and characterized by enzymatic activity associated with the demethylation of methylated RNA. This was accordingly designated AlkB homolog 3 (ALKBH3). I demonstrate that ALKBH3 is highly expressed in tumor cells in prostate, pancreatic, lung, and other cancers, and its activity is correlated with a poor prognosis. In addition, I developed novel compounds that inhibit the RNA demethylase activity of ALKBH3, thereby providing a basis for developing a first-in-class cancer therapeutic. I also succeeded in cloning the ALKBH8 gene. High ALKBH8 expression was also observed in bladder cancer cells. Furthermore, abnormalities in development and behavior were noted in the generated Alkbh8 knockout mice. On the basis of the experience gained from ALKBH3 drug discovery research, I have established a foundation system for supporting academic drug discovery research. In this review, I describe the pathway followed in integrating the findings of basic pharmaceutical and drug discovery research and further developments.

Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan

AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase


[Investigation on antidepressant mechanism of Piper laetispicum extract based on quantitative proteomics and zebrafish model of depression induced by chronic unpredictable mild stress]

Abstract: This study aimed to evaluate the antidepressant activity of Piper laetispicum extract and preliminarily explore its underlying mechanism using a zebrafish model of depression combined with quantitative proteomics. A chronic unpredictable mild stress(CUMS) paradigm was employed to establish the depression model. AB strain zebrafish were randomly assigned into four groups: control, model, P. laetispicum, and fluoxetine, with 15 fish in each group. Except the control group, all groups were subjected to CUMS for 2 weeks. Intervention of P. laetispicum extract or fluoxetine lasted for 3 consecutive weeks. Upon completion of the experiment, the pathological morphology of zebrafish brain tissue was observed, and the expression levels of tumor necrosis factor-alpha(TNF-α), interleukin-1 beta(IL-1β), brain-derived neurotrophic factor(BDNF), and 5-hydroxytryptamine receptor 2A(5-HT2A) were measured in each group. Brain tissue proteins were extracted and subjected to quantitative proteomic analysis to identify differentially expressed proteins(DEPs), which was followed by bioinformatics analysis. Key DEPs were validated using Western blot and RT-qPCR. The results demonstrated that P. laetispicum extract significantly ameliorated CUMS-induced brain histopathological damage, reduced the levels of the inflammatory cytokines TNF-α and IL-1β, and reversed the aberrant expression of BDNF and 5-HT2A. Proteomic profiling identified a total of 11 633 proteins, among which the expression levels of 81 proteins were markedly reversed following P. laetispicum extract treatment. Subsequent validation by Western blot and RT-qPCR confirmed that P. laetispicum significantly modulated the expression of annexin A1(Anxa1) and transcription factor JunB(JunB). Collectively, these findings suggest that P. laetispicum exerts antidepressant effects potentially through the regulation of Anxa1 and JunB expression.

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica

Animals
Zebrafish
Proteomics
Antidepressive Agents
Depression
Piper
Disease Models, Animal
Male
Tumor Necrosis Factor-alpha
Interleukin-1beta
Brain-Derived Neurotrophic Factor
Humans
Stress, Psychological
Drugs, Chinese Herbal
Brain
Plant Extracts


[Research and application of omics technologies in genetic breeding of medicinal plants]

Abstract: Medicinal plants represent a critical resource for both traditional medicine and contemporary natural product research. Studies on their genetic breeding are of paramount significance in ensuring the quality of medicinal materials, enhancing the content of bioactive constituents, and cultivating elite varieties. With the rapid advancement of sequencing technologies, omics approaches have evolved from reliance on single molecular markers to multidimensional research paradigms encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and single-cell omics. This article systematically reviews the concepts of various omics sequencing technologies and their applications in the identification of germplasm resources, analysis of genetic diversity, elucidation of geo-authenticity mechanisms, biosynthesis of active compounds, and molecular breeding in medicinal plants. Furthermore, it prospects the potential of multi-omics integration in future precision breeding of medicinal plants, aiming to provide a theoretical reference for systematic, precision, and efficient genetic breeding research for medicinal plants.

Liu Y
Qi YJ
Quan WY
Jia XW
Zeng CY
Wang HZ
Gao SF
Guo DQ
Guo WC
Zhang XJ
Chen HG
DU T

Plants, Medicinal
Plant Breeding
Genomics
Multiomics
Proteomics
Metabolomics


Profiling O-Acetylation in Sialoglycans Using MALDI-TOF and LC-MS/MS with Methylamidation and Permethylation Derivatization

Abstract: O-acetylation of sialoglycans plays a critical role in modulating the structural and functional properties of glycoproteins, with implications in immune response, cell signaling, and disease pathology. Among sialic acids, N-acetylneuraminic acid (Neu5Ac) and its derivatives have garnered attention as biomarkers for various cancers and inflammatory conditions due to their terminal positioning on glycan chains and their susceptibility to biochemical modification. Despite their biological relevance, comprehensive analysis of O-acetylation patterns remains challenging due to their chemical lability and loss during conventional glycomic workflows, such as permethylation. This protocol outlines a robust workflow combining methylamidation and permethylation with porous graphitic carbon (PGC)-based purification and high-resolution MALDI-MS and LC-MS/MS to analyze O-acetylation in serum/plasma-derived N-sialoglycans. We demonstrate sensitive and reproducible profiling of sialylated glycan structures. This method enables deeper insight into glycan modification dynamics and can be broadly applied to biomarker discovery and comparative glycomics.

Methods in molecular biology (Clifton, N.J.)


PEPPI-SP3: A Gel-Based High-Resolution Sample Preparation Workflow for In-Depth Top-Down Analysis of Intact Proteoforms by Mass Spectrometry

Abstract: Top-down proteomics enables large-scale identification of proteoforms by analyzing intact proteins extracted from biological samples using mass spectrometry systems coupled with liquid chromatography or capillary electrophoresis. In this chapter, we present the PEPPI-SP3 workflow, a high-resolution sample prefractionation method that significantly enhances the analytical depth of top-down proteomics by combining highly efficient passive extraction of in-gel proteins separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis with SP3 bead-based purification of intact proteins.

Takemori A
Kline JT
Fornelli L
Takemori N

Proteomics
Mass Spectrometry
Electrophoresis, Polyacrylamide Gel
Workflow
Proteins
Chromatography, Liquid
Proteome


Combining SDS-PAGE with Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics Analysis of Intact Histone Proteoforms

Abstract: Mass spectrometry (MS)-based top-down proteomics (TDP) analysis of histone proteoforms provides critical information about combinatorial posttranslational modifications (PTMs), which is vital for pursuing a better understanding of epigenetic regulation of gene expression. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separates histone proteins (H1, H2, H3, and H4) based on their molecular weight, while capillary zone electrophoresis (CZE) provides additional separation of proteoforms of each histone protein based on their electrophoretic mobility, which is affected by PTMs, e.g., acetylation and phosphorylation. Here, we describe the combination of SDS-PAGE-based protein fractionation with CZE-tandem MS (MS/MS) for high-resolution characterization of histone proteoforms. Over 200 histone proteoforms from a commercial calf thymus histone sample were identified with good reproducibility.

Histones
Proteomics
Tandem Mass Spectrometry
Electrophoresis, Capillary
Electrophoresis, Polyacrylamide Gel
Protein Processing, Post-Translational
Animals
Cattle


Enrichment and Metaproteomic Analysis of Lysine Acetylation in Fecal Microbiome Samples

Abstract: Among the various posttranslational modifications (PTMs) found in microbiome samples, lysine acetylation is known to be abundant and plays an important role in regulating microbial short-chain fatty acid (SCFA) metabolism. The latter is a crucial microbiome function that significantly impacts human intestinal health. This chapter describes a detailed protocol for lysine acetylomic profiling of microbial proteins in human fecal microbiome samples. The protocol consists of stool sample preprocessing, microbiome protein extraction and digestion, immunoaffinity enrichment of lysine acetylated peptides, and high-resolution mass spectrometry analysis for the identification and quantification of lysine-acetylated proteins.

Acetylation
Humans
Lysine
Proteomics
Feces
Protein Processing, Post-Translational
Proteome
Microbiota
Gastrointestinal Microbiome


Mapping Cellular Protein Lysine Methylation Using Targeted-Mass Spectrometry

Abstract: Lysine methylation is a dynamic posttranslation modification (PTM) involved in the regulation of numerous biological processes. Depending on the context, site- and state-specific lysine methylation has been shown to regulate key features of proteins, such as stability, activity, and interactions. Assessing site- and state-specific lysine methylation within the proteome is difficult without access to antibodies that are able to detect the modification site. As the commercially available options for reliable antibodies that are specific to a methylation site and state are limited, mass spectrometry (MS)-based methods are more appealing as they enable detection of site- and state-specific methylation events with broad applicability. Here, we describe the use of immunoprecipitation and targeted-MS to detect and perform relative quantification of site-specific lysine methylation events occurring on endogenous proteins of interest. As an example, detection and relative quantification of hypoxia-responsive PGC1α-K224me2 and RNF20-K610me3/K614me3 lysine methylation, occurring in hypoxia-treated human colorectal cancer cells, are described.

Chopra A
Hoekstra M
Willmore WG
Biggar KK

Lysine
Humans
Methylation
Protein Processing, Post-Translational
Mass Spectrometry
Immunoprecipitation
Proteomics


Phosphoproteomics Protocol for the Identification of Novel Biomarkers from Extracellular Vesicles of Cancerous Cells

Abstract: In this chapter, we describe a general sample preparation workflow for small extracellular vesicles (sEVs) from breast cancer cell lines using techniques such as protein solubilization, enzymatic digestion, and Fe3+-immobilized metal affinity chromatography (IMAC) and titanium dioxide (TiO2) enrichment prior to mass spectrometry-based proteomic analysis. This workflow can be used to perform global phosphoproteomics of sEVs enabling the study of tumor biology and the discovery of biomarkers for cancer diagnosis and treatment.

Minic Z
Poolsup S
Li Y
D'Mello R
Berezovski MV

Humans
Proteomics
Extracellular Vesicles
Biomarkers, Tumor
Chromatography, Affinity
Titanium
Phosphopeptides
Phosphoproteins
Cell Line, Tumor
Breast Neoplasms
Mass Spectrometry
Female


O- and N-Phosphoproteomic Analysis Using Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry

Abstract: Protein phosphorylation (O-linked and N-linked) is associated with a wide range of biological processes and cell signaling pathways. Aberrant phosphorylation is often observed as a hallmark of diseases, including cancer, neurodegenerative disorders, and metabolic syndromes. Mass spectrometry (MS) is an indispensable tool for studying protein phosphorylation. This is primarily due to its high sensitivity and throughput, which allows for comprehensive identification and quantification of phosphorylation events in complex biological samples. In this chapter, we describe a detailed protocol for phosphoproteomic analysis using one-dimensional online alkaline-pH reversed-phase nanoelectrospray-tandem MS (alkaline-pH-MS/MS). It complements traditional online low-pH reversed-phase nanoelectrospray-tandem MS (low-pH-MS/MS) by modulating the charge state distribution of phosphopeptides, which may facilitate the characterization of phosphoproteins with significant biological functions.

Spectrometry, Mass, Electrospray Ionization


Endogenous Phosphopeptidomics Analysis by Using Mesoporous IMAC Materials

Abstract: The analysis of endogenous phosphopeptides is crucial for identifying biomarkers of cellular signaling alterations and monitoring disease-related pathophysiological changes in vivo. While phosphoproteomics has seen remarkable progress in recent years, the field of endogenous phosphopeptidomics has lagged behind. A major challenge in endogenous phosphopeptidomics analysis lies in the presence of highly abundant nonmodified peptides and proteins within complex biological matrices, such as biofluids, which can obscure the detection of low-abundance phosphopeptides. In this chapter, we describe a protocol of a recently developed approach by utilizing Zirconium (IV)-grafted mesoporous beads for selective phosphopeptide enrichment, followed by high-resolution nanoRPLC-MS/MS analysis, enabling enhanced sensitivity and specificity in the detection of endogenous phosphopeptides from serum samples.

Phosphopeptides
Proteomics
Tandem Mass Spectrometry
Humans
Zirconium
Porosity
Chromatography, High Pressure Liquid


Decoding the SUMO Proteome: A Mass Spectrometry Workflow for Site-Specific Identification

Abstract: Protein SUMOylation is a dynamic post-translational modification that regulates numerous cellular processes, including DNA repair, transcription, and proteostasis. SUMO modifiers are conjugated to lysine residues on substrate proteins via a conserved enzymatic cascade and can form diverse chain architectures that encode specific cellular outcomes. The identification of SUMOylated proteins and their modification sites has historically been challenging due to the low abundance of SUMOylation and the complexity of SUMO remnants after proteolysis. Recent advances in proteomics have led to the development of enrichment strategies and mass spectrometry (MS)-based methods that now enable the site-specific mapping of SUMO modifications. This chapter provides an overview of the biological roles and structural diversity of SUMOylation, and presents an MS-based workflow designed to identify SUMOylation sites with high specificity and depth. These tools offer new opportunities to dissect the SUMO-modified proteome in health and disease.

Small Ubiquitin-Related Modifier Proteins


Proteomic comparison of hippocampal neurofibrillary tangles in PART, intermediate Alzheimer's disease and advanced Alzheimer's disease

Abstract: Alzheimer's disease (AD) is characterised by the intraneuronal aggregation of phosphorylated Tau (pTau) into neurofibrillary tangles and by the extracellular deposition of β-amyloid (Aβ). Tau pathology restricted to the hippocampal formation is frequently observed in the elderly brain in the absence of any Aβ deposition and considered as "primary age-related tauopathy" (PART). Here, we applied an unbiased proteomic approach to determine how concomitant Aβ pathology modifies the neurofibrillary tangle proteome. Neurofibrillary tangles were isolated by dissecting Tau pSer202/pThr205 "AT8" immunopositive neuronal profiles, combining chromogenic immunohistochemistry with laser capture microdissection, from hippocampal sections of 17 post-mortem brains spanning three groups: PART (n = 5; A0, B1-2, C0 scores), intermediate AD (n = 6; A1-2, B2-3, C1-2 scores) and advanced AD (n = 6; A3, B3, C3 scores). A label-free quantitative liquid chromatography-mass spectrometry based proteomic analysis, using data independent acquisition (DIA) on a Bruker timsTOF, was performed. A conserved core of 63 proteins was identified as enriched in tangles across all groups, mostly associated with "RNA binding" and "regulation of mRNA metabolic process", based on the Gene Ontology database. Group-specific signatures were also observed: 33 proteins were significantly enriched only in tangles collected from PART cases and were predominantly linked to "structural molecule activity", whereas Aβ-positive cases showed specific enrichment of "RNA binding" and "cytoplasmic translation" pathways-with intermediate AD cases displaying a transitional profile. Our findings are consistent with PART having distinct tangle proteomic features; however, the majority of its proteomic signature is in common with tangles within the AD continuum. By addressing how Aβ accumulation alters the tangle proteome, this study provides mechanistic insights into the expansion of Tau pathology, paving the way towards the identification of biomarkers and therapeutic strategies that would allow for stabilisation of Tau pathology in the elderly.

Thierry M
Leitner D
Balcomb K
Kavanagh T
Tang L
Kanshin E
William C
Oakley D
Hyman B
Ueberheide B
Drummond E
Wisniewski T

Humans
Neurofibrillary Tangles
Alzheimer Disease
Hippocampus
Proteomics
Aged, 80 and over
Female
tau Proteins
Male
Aged
Amyloid beta-Peptides
Laser Capture Microdissection


Emergence of gene associations in high-risk K. pneumoniae clones: bla(NDM-1) + bla(OXA-48-like) in ST15 and bla(VIM) + bla(NDM-1) in ST405

Abstract: Immunocompromised patients, especially hematopoietic stem cell transplants (HSCT) / bone marrow transplant recipients, are at risk for colonization and infection with carbapenem-resistant Klebsiella pneumoniae (CR-KP) which is associated with increased bloodstream infections and mortality in this population. In this susceptible population, we investigated the molecular epidemiology of CR-KP. The strains isolated over a five-year period (2017-2021) were then characterized by PCR and sequencing targeting carbapenemase genes. ERIC-PCR was utilized to examine clonal relations, while multilocus sequence typing was carried out on representative isolates. Analysis of 142 CR-KP uncovered remarkable genetic heterogeneity with six predominant clusters making up for 83,8% of strains and one major cluster. Novel findings in K. pneumoniae included: undescribed MLST profile ST5187, emergence of blaVIM-1 in ST397, emergence of blaOXA-48-like in ST219, co-carriage of either blaNDM-1 + blaOXA-48-like in ST15 or blaVIM-like + blaNDM-1 in ST405. CR-KP, brought to light new carbapenemase gene associations and undescribed MLST profiles. To prevent transmission of high-risk clones in immunocompromised populations, enhanced molecular surveillance and robust infection control are of high importance.

Ben Hamza A
Raddaoui A
Frigui S
Chebbi Y
Achour W

beta-Lactamases
Klebsiella pneumoniae
Humans
Multilocus Sequence Typing
Klebsiella Infections
Bacterial Proteins
Anti-Bacterial Agents
Carbapenems
Molecular Epidemiology
Microbial Sensitivity Tests


Generation Scotland - Linking all the records we can

Abstract: We started a family-based genetic epidemiology study in 2006-11 which recruited 24,000 adult volunteers from 7000 families across Scotland with consent for follow-up through medical record linkage and re-contact. In 2022-25 we have recruited a further 16,000 volunteers, with consent extended to administrative records, and age range now 12+. Original volunteers completed demographic, health and lifestyle questionnaires, provided biological samples, and underwent detailed clinical assessment. The samples, phenotype and genotype data form a resource for research on the genetics of conditions of public health importance. This has become a longitudinal dataset by linkage to routine NHS records: hospital, maternity, lab test, prescriptions, dentistry, mortality, imaging, cancer screening, GP data, Covid-19 testing and vaccinations, as well as follow-up questionnaires. The new wave of recruitment is all online with DNA from saliva collected by post. Teenagers aged 12-15 can join with parental consent. Researchers can find prevalent and incident disease cases and controls to test research hypotheses on a stratified population. They can also do targeted recruitment of participants to new studies, including recall by genotype. We have established and validated E-HR linkage with the NHS Scotland CHI Register, overcoming technical and governance issues in the process. We contribute to major international consortia, with collaborators from institutions worldwide, both academic and commercial. The Research Tissue Bank resources are available to academic and commercial researchers through a managed access process.

International journal of population data science

Humans
Scotland
Female
Adolescent
Adult
Child
Medical Record Linkage
Male
Young Adult
Middle Aged
Surveys and Questionnaires
Molecular Epidemiology


Implementing a Scalable, Secure Genomics Ingest and Processing Pipeline in a Trusted Research Environment for Dementia Research

Abstract: The integration of genomics data into dementia research offers transformative potential for understanding disease mechanisms and enabling precision medicine. However, its utility is constrained by significant challenges in data sharing, privacy, standardization, and computational scale. To address these barriers, we designed and implemented a secure, novel and scalable genomics ingest and processing pipeline within the Dementias Platform UK (DPUK) Trusted Research Environment. Our comprehensive, end-to-end framework encompasses a seven-stage process, including cohort discovery via an interactive metadata matrix, rigorous quality and privacy controls using bioinformatic tools (e.g. PLINK, VCFtools, etc.), a genomic data organization standard for scalability and balance between interoperability and flexibility, as well as secure provisioning within a Five Safes governance model. A key innovation is the use of a MinIO-based object storage architecture with custom metadata tagging, enabling efficient, privacy-preserving data access at large scale. We also operationalized a standardized polygenic risk score (PRS) pipeline to generate validated, derived datasets. This integrated system now facilitates secure research access to harmonized genomic data across 15 diverse cohorts, including population-based, clinical, and family studies, significantly expanding the resources available for dementia research. This work presents a replicable and governance-first model for the responsible management of complex, high-volume linked data. Looking ahead, we plan to migrate key computational modules, particularly the PRS generation and quality control workflows, to Nextflow. This migration will enhance computational reproducibility, enable portable and parallelized execution across high-performance environments, and further standardize analytical processes, directly advancing the methodological innovation and scalability goals of population data science.

Saraband Moghaddam A
Hotchkiss L
Squires E
Thompson S

Dementia
Genomics
Humans
Computer Security
Metadata
Information Dissemination
Genetic Risk Score
Computational Biology


Application of metagenomic next-generation sequencing as an adjunct to conventional microbiological testing for the diagnosis of infection in kidney transplant recipients

Abstract: Kidney transplant recipients are highly susceptible to opportunistic and nosocomial infections that demand rapid and accurate diagnosis due to the broad and complex spectrum of pathogens. Conventional microbiological testing (CMT) is often limited, particularly when patients are already receiving antimicrobial therapy at the time of sampling. This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) as a complementary diagnostic approach to CMT, with a focus on concordance and discrepancies between the two methods across peripheral blood, sputum, bronchoalveolar lavage fluid (BALF), and urine samples. We conducted a retrospective study of kidney transplant recipients with suspected infections who underwent simultaneous mNGS and CMT testing between March 2022 and May 2024. The impact of prior antibiotic exposure on diagnostic yield was assessed. Detection of antimicrobial resistance (AMR) genes by mNGS and subsequent modifications in anti-infective management were also analyzed. A total of 243 samples (57 blood, 96 sputum, 71 BALF, 19 urine) were included. Across all sample types, mNGS demonstrated significantly higher positive rates than CMT (blood: 78.95% vs 21.05%; BALF: 90.14% vs 19.72%; sputum: 92.71% vs 20.83%; urine: 89.47% vs 36.84%; all P<0.001). Prior antibiotic exposure markedly reduced CMT positivity but had minimal impact on mNGS detection. Concordance analysis showed 40.35% of samples were positive by both methods, while 60.1% were negative by CMT but positive by mNGS. In addition to pathogens identified by CMT, mNGS detected a broader range of microorganisms, including viruses (e.g., cytomegalovirus, Epstein-Barr virus, SARS-CoV-2), fungi (Pneumocystis jirovecii), and parasites (Strongyloides stercoralis, Toxoplasma gondii). Overall, mNGS-guided results refined antibiotic treatment strategies in 110 cases (60.11%). mNGS serves as a valuable adjunct to CMT in kidney transplant recipients, providing rapid and comprehensive pathogen identification. However, from a health economics perspective, mNGS should be applied selectively according to clinical needs, rather than as a universal first-line diagnostic method.

Frontiers in cellular and infection microbiology

Vuth H
Wang W
Qin W
Yang M
Li Y
Zhou Q
Xu X
Zhang J
Zhao H

Humans
Kidney Transplantation
High-Throughput Nucleotide Sequencing
Metagenomics
Retrospective Studies
Female
Male
Transplant Recipients
Bronchoalveolar Lavage Fluid
Middle Aged
Adult
Sputum
Bacteria
Microbiological Techniques
Aged


Metabolic control of RNA methylation in rheumatoid arthritis: from synovial stress to pathogenic cellular adaptation

Abstract: Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovitis, invasive pannus formation, cartilage degradation, and bone erosion. Although metabolic reprogramming and epigenetic dysregulation are increasingly recognized as central features of rheumatoid arthritis, the mechanisms by which local metabolic stress is converted into durable pathogenic cellular states remain incompletely understood. Recent advances in epitranscriptomics suggest that dynamic RNA modifications, particularly RNA methylation, act as critical post-transcriptional regulators of immune and stromal cell adaptation. Local hypoxia, enhanced glycolytic flux, lactate accumulation, mitochondrial dysfunction, oxidative stress, and lipid metabolic imbalance collectively influence the expression, activity, substrate availability, and transcript selectivity of RNA methylation regulators. These metabolically conditioned RNA modification programs, including canonical N6-methyladenosine (m6A) and emerging non-m6A marks such as internal N7-methylguanosine (m7G), may help stabilize pathogenic phenotypes across multiple cell types. In fibroblast-like synoviocytes (FLS), RNA methylation sustains glycolytic fitness, invasive behavior, and resistance to apoptosis and ferroptosis. In macrophages, it reinforces inflammatory polarization and extracellular vesicle-mediated communication. In T cells and neutrophils, it contributes to Th17 skewing, defective autophagy, oxidative stress responses, and excessive neutrophil extracellular trap (NET) formation. We further discuss how RNA methylation integrates non-coding RNA networks, extracellular vesicle signaling, and regulated cell death pathways to maintain chronic synovial inflammation and tissue destruction. Finally, we highlight the translational implications of this metabolic-epitranscriptomic interface, including biomarker discovery, patient stratification, and microenvironment-informed therapeutic strategies. Targeting both metabolic stress and RNA methylation-dependent adaptation may provide new opportunities for precision-oriented intervention in rheumatoid arthritis.

Humans
Arthritis, Rheumatoid
RNA Methylation
Animals
Epitranscriptome
Metabolic Reprogramming
Epitranscriptomics
Synoviocytes
Epigenesis, Genetic
Stress, Physiological
Synovial Membrane


Genomic insights into flooding tolerance of Distylium chinense in the water-level fluctuation zone of the Three Gorges Reservoir

Abstract: The intensification of climate change has led to frequent extreme flooding events, which threaten plant growth and food security. Studying the molecular mechanisms underlying plant flooding resistance is crucial for germplasm improvement. Distylium chinense, a perennial shrub found in the water-level fluctuation zone of the Three Gorges Reservoir, has both strong flooding tolerance and high ornamental value, making it an ideal material for studying plant flooding resistance mechanisms. By integrating multiple sequencing technologies, we assembled a high-quality 917 Mb near telomere-to-telomere genome of D. chinense with a contig N50 size of 73 Mb, representing the first high-quality genome of the Hamamelidaceae family. Whole-genome duplication analysis revealed that D. chinense experienced gamma events that are common to those of core eudicots. In addition, this study revealed three different flooding stress response stages in D. chinense, namely, the acute stress period, the outbreak period, and the long-term adaptation period. Among these, the outbreak period could be an important turning point, during which D. chinense switches from survival mode to adaptation mode. This study also revealed that the expression of the group VII ethylene-responsive factor (ERF-VII) gene g3958 was significantly upregulated under flooding stress and that this gene can be directly activated by the AtWRKY33-homologous gene g19705. On the basis of a comprehensive analysis, a potential dual pathway regulatory model between MKK9 and ERF-VII was further proposed. This study provides important genetic resources for improving flood-resistant germplasms and further contributes to the protection and restoration of the ecosystem in the water-level fluctuation zone of the Three Gorges Reservoir.

The Plant journal : for cell and molecular biology

Xia C
Ding B
Zhang X
Zhang X
Li W
Zeng J
Zhao F
Jiang S
Deng H
Huang M

Floods
Plant Proteins
Genome, Plant
Gene Expression Regulation, Plant
Adaptation, Physiological
Water
Genomics
Stress, Physiological


Graph designs for deep learning-based multi-omics integration

Abstract: Modern sequencing technologies can now capture multiple omic layers from the same biological system, but integrating these views into a coherent model is far from trivial. Graph-based deep learning has become an attractive strategy because it can represent complex molecular interactions and sample relationships in a flexible way. In this review, we survey how graphs are constructed and used in multi-omics deep learning models, organizing methods by node schema, edge semantics, interaction type, integration strategy, graph context, and model architecture across bulk, single-cell, and spatial settings. We summarize the strengths and weaknesses of different design choices in terms of interpretability, data requirements, robustness to noise and missing modalities, and suitability for tasks ranging from prediction to mechanism-oriented discovery. Based on these insights, we outline a general, practical pipeline for constructing, curating, and evaluating graphs that can serve as a starting point for new multi-omics studies.

Multiomics
Deep Learning
Humans
Computational Biology
Genomics


RiSpy: a feature selection-based fingerprinting framework for accurate identification of genome-edited rice lines

Abstract: The European Union (EU) enforces strict regulations on the traceability and labeling of genetically modified organisms (GMOs), including genome-edited (GE) lines produced through new genomic techniques (NGTs). Identifying GE organisms created by single nucleotide variations (SNVs) is however challenging, as a single SNV alone cannot unambiguously define a GE line. Recently, we introduced the concept of generating a genetic fingerprint to distinguish a specific GE rice line. This proof-of-concept approach integrated whole-genome sequencing (WGS)-based characterization with the Illumina technology, the public 3 K Rice Genomes (3KRG) database, and statistical feature-selection tools, to select and combine key genetic elements, including GE on-target site(s) and cultivar-specific 2-SNV barcodes, into a unique genetic fingerprint. In the present study, we expand this concept into a generalized data-driven framework allowing identification of multiple rice lines. Supported by newly developed bioinformatics and statistical feature-selection-based pipelines, this optimized strategy enables the generation of genetic fingerprints irrespective of a rice cultivar's inclusion in publicly available databases like 3KRG. In addition, this refined strategy can leverage WGS data generated from both Illumina and Oxford Nanopore Technologies (ONT) platforms for fingerprint generation and GE line identification. Using two distinct in-house GE rice lines from different cultivars, along with various publicly available WGS datasets, we demonstrated the robustness, scalability, and specificity of this approach for reliable GE rice line identification. Our findings provide a methodological foundation for data-driven traceability of GE rice lines, reinforcing regulatory compliance, supporting intellectual property (IP) protection, and contributing to the responsible implementation of EU GMO/NGT legislation.

Zolfaghari A
Fraiture MA
Vanneste K
Stuyts A
Frouin J
Meunier AC
Deforce D
Roosens NHC
D'aes J

Oryza
Genome, Plant
Plants, Genetically Modified
Gene Editing
Software
Computational Biology
Polymorphism, Single Nucleotide
Whole Genome Sequencing
Genomics
DNA Fingerprinting


The quantitative proteomics analysis of multi-stage gastric mucosal lesions associated with Helicobacter pylori infection

Abstract: Helicobacter pylori (H. pylori) infection is the principal etiological factor for gastric cancer (GC), which ranks as the fourth leading cause of cancer-related mortality globally. Although the Correa cascade describes the stepwise progression from chronic gastritis to intestinal-type GC, the molecular events underlying this "inflammation-to-cancer" transition remain incompletely characterized. This study aimed to delineate stage-specific proteomic alterations across H. pylori-associated gastric mucosal lesions and to identify candidate progression-associated biomarkers in GC. Label-free quantitative proteomic analysis (LC-MS/MS) was performed on gastric tissue specimens from 22 patients stratified into four histopathological stages: H. pylori-negative chronic non-atrophic gastritis (HpN-CG), H. pylori-positive chronic non-atrophic gastritis (HpC-CG), H. pylori-positive chronic atrophic gastritis (HpC-CAG), and intestinal-type GC. Functional enrichment (GO, KEGG), temporal clustering (Mfuzz), and protein-protein interaction (PPI) network analyses were conducted. Key hub genes were externally assessed using GEPIA RNA-seq data from TCGA and GTEx. A total of 6,019 proteins were quantified. Differential expression analysis identified 771 DEPs between HpC-CG and HpN-CG, 101 DEPs between HpC-CAG and HpC-CG, and 535 DEPs between GC and HpC-CAG. Immune response pathways were up-regulated upon H. pylori infection, whereas oxidative phosphorylation was progressively suppressed throughout disease progression. Mfuzz clustering revealed that Cluster 4 ribosome-biogenesis proteins, including NIP7 and PDCD11 identified in the proteomic/PPI analysis, exhibited continuous up-regulation from precancerous stages to GC. External RNA-expression validation supported significant up-regulation of seven Cluster 4 hub genes, whereas Cluster 6 proteins did not show concordant transcript-level down-regulation. This study provides a comprehensive proteomic landscape of H. pylori-driven gastric carcinogenesis. Cluster 4 ribosome-biogenesis proteins represent candidate progression-associated protein markers requiring further protein-level validation, while the progressive decline in oxidative phosphorylation underscores mitochondrial dysfunction as a hallmark of disease progression.

Huang X
Ma J
Xiao Y
Pan J
Xu Q
Cao X
Liu Y
Yi X
Tian F

Humans
Helicobacter Infections
Proteomics
Helicobacter pylori
Gastric Mucosa
Stomach Neoplasms
Female
Gastritis, Atrophic
Male
Middle Aged
Tandem Mass Spectrometry
Protein Interaction Maps
Proteome
Disease Progression
Gastritis


Genomic and regulatory basis of visual opsin genes in the cleaner wrasse behavior: features, expression, and enhancer mechanisms

Abstract: Cleaner wrasse (Labroides dimidiatus) undergoes sex reversal to male, and the two sexes exhibit distinctive cleaning behavior mediated by vision. As a keystone cleaner species in coral reef ecosystems, this fish plays an indispensable ecological role. Yet, the visual regulatory mechanisms underlying its sex-specific cleaning behaviors remain unknown. Through genome annotation and phylogenetic analysis, visual opsin genes were identified in the cleaner wrasse genome. Gene expression levels were quantified by RT-qPCR to examine sexual dimorphism. Additionally, 4 C-seq coupled with dual-luciferase reporter assays was employed to identify and validate putative enhancers regulating opsin gene expression. Eight visual opsin genes in five families were identified: rhodopsin (RH1), green-sensitive (RH2), ultraviolet-sensitive (SWS1), blue-sensitive (SWS2), and red-sensitive (LWS). Notably, RH2 has undergone diversification into four genes, indicating a high degree of functional specialization in hue resolution. All opsins maintain high homology in conserved motifs and functional domains, while also possessing distinct regions that may facilitate adaptation to complex photic environments. RT-qPCR revealed significant sexual dimorphism in opsin expression. Females exhibited higher expression of SWS1, SWS2B and RH2 family genes, consistent with their primary role as cleaners, which requires precise visual discrimination of client fish coloration and ectoparasites. In contrast, males showed significantly higher expression of RH1 and LWS, likely reflecting adaptation for territorial patrol and social competition following sex change. Furthermore, using 4 C-seq coupled with dual-luciferase reporter assays, we identified and validated active enhancers upstream of RH1 and RH2-1 genes. RH1 was found to be regulated by multiple enhancers acting in concert, suggesting a capacity for robust environmental responsiveness and developmental stage-specific modulation. In contrast, RH2-1 appears to be under the control of a single enhancer binding to transcription factors. These findings help elucidate the molecular basis of visual system adaptation in cleaner wrasse and provide preliminary insights into the potential links between visual opsin gene regulation, cleaning behavior, and ecological adaptation.

Animals
Male
Female
Phylogeny
Opsins
Gene Expression Regulation
Perciformes
Fish Proteins
Sex Characteristics
Enhancer Elements, Genetic
Behavior, Animal
Rod Opsins
Genomics


Pigmented fungi derived from hot and cold deserts ecosystems: taxonomy, genomic and biotechnological approach

Abstract: Safer and more efficient products and processes are current global demands that drive the field of bioprospective research. Microbial sources are the main natural alternative solutions that have contributed to this biotechnological line, with environmental fungi representing important promising forces. Particularly, those inhabiting the most unexplored extreme geographical areas of the planet, marked by severe aridity, with hot and/or cold thermal profiles, e.g., the Atacama Desert, Saudi Arabia, Taklamakan Desert, semi-arid regions (Caatinga and Mexico), and polar and alpine ecosystems. In these habitats, many abiotic stressors are present, and fungi thrive through a combination of adaptations, including the production of pigmented secondary metabolites with diverse active biological functions that have high potential for innovative industrial applications, which is being explored in greater depth at the present time. In this sense, this article has aimed to review pigmented fungi from extreme arid environments from a taxonomic, genomic and biotechnological perspective. An attempt has been made to compile information on pigmented fungi in pure culture, their chromatic aspects, chemical classes, genomic data and application across diverse domains. There were more ascomycete and basidiomycete representatives producing a wide spectrum of endo- and extracellular colors categorized as melanins, carotenoids, and polyketides. Furthermore, they prove useful across multiple biotechnological sectors, ranging from agriculture, food, cosmetics, and medicine to astrobiology. Those with investigated genomes showed genes linked to the biosynthesis of these pigments and to environmental adaptation. Thus, with this initiative, we accessed the bioprospective importance of extremophilic colored fungi from arid habitats.

World journal of microbiology & biotechnology

da Silva MK
da Silva RC
de Souza Melo BM
Cavalcante TJC
da Silva Santos L
E Silva JGP
Maia VRT
da Silva Bernardo M
da Silva Sousa K
da Silva AV
de Oliveira AJ
de Queiroz AC
Rosa LH
Duarte AWF

Desert Climate
Fungi
Biotechnology
Genomics
Ecosystem
Pigments, Biological
Cold Temperature
Genome, Fungal
Ascomycota
Melanins
Phylogeny
Basidiomycota


Phylogenetic analysis of serotype 19A-sequence type (ST)2331 Streptococcus pneumoniae associated with the Pneumococcal Molecular Epidemiology Network (PMEN)34 clone predominant in Japan after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7)

Abstract: Following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7), serotype 19A Streptococcus pneumoniae emerged as a major cause of paediatric pneumococcal disease in Japan. Unlike global trends, in which multidrug-resistant serotype 19A-sequence type (ST)320 predominated, serotype 19A-ST2331 became one of the dominant lineages in Japan. The evolutionary origins of serotype 19A-ST2331 and the reasons for its domestic success remain unclear. To investigate the evolutionary origin and dissemination of the serotype 19A-ST2331 lineage, we analysed whole-genome sequences of 42 clonal complex (CC)2331 isolates collected in Japan between 2004 and 2017 and compared them with 825 genetically related global isolates. Phylogenetic analysis showed that Japanese serotype 19A-ST2331 isolates formed a distinct Japan-associated cluster within Global Pneumococcal Sequence Cluster 32 that was closely related to the globally disseminated Pneumococcal Molecular Epidemiology Network (PMEN)34 clone, typically represented by serotype 12F-ST218. Among the 42 Japanese CC2331 isolates, 40 were serotype 19A, whereas only two non-19A isolates were identified. Serotype 19A was absent from the 825 non-Japanese isolates, indicating that serotype 19A-ST2331 represents a globally rare, Japan-specific lineage. Most Japanese isolates remained susceptible to β-lactams, whereas 83.3% were erythromycin-resistant and carried either mefA/E or ermB. A highly clonal mefA/E-positive subclade was dated to a most recent common ancestor at ∼1998.5. These findings indicate that serotype 19A-ST2331 emerged before 2000 from an ST218-related ancestor through serotype switching and subsequently underwent local expansion in Japan. Although the ancestral intermediate was not represented in the present collection, the successful establishment of this clone may have been facilitated by the combined selective advantages conferred by the serotype 19A capsule and macrolide resistance in the post-PCV7 setting in Japan.

Koide S
Nakano S
Fujisawa T
Ito Y
Chang B
Suga S
Sugawara Y
Akeda Y
Sugai M

Heptavalent Pneumococcal Conjugate Vaccine


Umbilical Cord: A Non-Invasive DNA Source for Sea Turtle Genomics

Abstract: High-throughput sequencing has revolutionised conservation genomics by enabling genome-wide information even in non-model species. However, obtaining non-invasive samples for genomics remains challenging in species like sea turtles, which spend most of their lives in the open ocean. In addition, traditional sampling methods are often impractical or unsafe for hatchlings, highlighting the need for alternative approaches. We investigated the potential of umbilical cords (UCs), both from the proximal and distal regions, as a non-invasive sampling method. We assessed the suitability of UC sampling by evaluating prevalence under different incubation conditions, and whether the UC reflected a genetic origin from the mother or offspring. We analysed 76 samples with 2bRAD from five Spanish loggerhead turtle (Caretta caretta) emerging nests, including UCs from 13 hatchlings (both proximal and distal region), 48 hatchling blood samples (four with genotyped UCs) and blood from two breeding females. Using the Percentage of Shared Genotypes (PSG) analysis, we determined that the UC genotype from both sides matched the hatchling blood genotype (97.7%), while PSG were lower between related individuals (73.5%) and even lower between unrelated individuals (56.5%). UC prevalence varied by incubation type, appearing in 100% of artificially incubated nests in Spain, in 25% of Spain's naturally incubated nests, an emergent nesting population, and in only 4.5% of nests naturally incubated in Cape Verde, an established nesting population. Our findings establish UCs as a reliable non-invasive DNA source for hatchlings, particularly in incubator-hatched eggs. This approach advances genomic analysis while minimising disturbance, offering insights into population genetics and conservation strategies.

Marín-Capuz G
Abella E
Pascual M
Pegueroles C
Carreras C

Animals
Turtles
DNA
Female
Genomics
Umbilical Cord
Spain
Genotype


Shared genetics of IgA nephropathy and cardiometabolic diseases revealed by integrative genomic analysis

Abstract: Immunoglobulin A nephropathy (IgAN), the most common primary glomerular disease and a leading cause of end-stage kidney disease (ESKD), is associated with cardiovascular and metabolic abnormalities. To explore these genetic overlaps, we integrated large-scale GWAS data from IgAN, 21 pan-vascular diseases (PVDs), 13 metabolic traits, 11 immune cell phenotypes, and established IgAN risk factors. Cross-trait analyses (LDSC, GNOVA, SUPERGNOVA) revealed significant genetic correlations between IgAN and multiple PVDs, including coronary artery disease, heart failure, stroke, aortic aneurysm, and varicose veins. Multi-omics prioritization (TWAS, SMR, MAGMA, and fastBAT) identified shared variants and candidate genes associated with immune regulation, lipid transport, and cardiovascular function. Gene expression profiling demonstrated enrichment of these genes in endothelial cells, macrophages, spleen, lung, and blood. Drug repurposing analysis based on gene-drug matching scores (>0.5) identified promising therapeutic candidates, including immunosuppressants (prednisolone, cyclosporine, azathioprine), lipid-lowering agents (pitavastatin, fenofibrate), and the antiplatelet drug aspirin. These findings offer novel opportunities for precision medicine and drug repurposing in IgAN patients with cardiometabolic disorders.

Dai L
Chen G
Yang Y
Yan Y
Zhao Q
He N
Xiang Y
Li Z
Chen Y

Humans
Glomerulonephritis, IGA
Genome-Wide Association Study
Cardiovascular Diseases
Genomics
Genetic Predisposition to Disease
Immunosuppressive Agents
Gene Expression Profiling
Multiomics
Metabolic Diseases


Comparative Proteomics Reveals Conserved and Lineage-Specific Molecular Toolkits in Lophotrochozoan Biomineralization

Abstract: Animal biomineralization has evolved repeatedly, yielding diverse skeletal structures. A key question is whether this diversity stems from molecular convergence or a shared ancestral toolkit. Studying lophotrochozoans-a group with carbonate, phosphate, iron, and mixed mineralization systems-provides an ideal framework for addressing this issue but remains underrepresented in comparative omics studies. Here, we present a genome assembly and shell matrix proteome of the phosphate-biomineralizing brachiopod Lingula anatina CN, derived from a geographically distinct population. By integrating these data with comparative proteomic analysis across seven lophotrochozoan lineages representing diverse mineralization chemistries, we provide novel insights into the molecular basis of biomineralization. Sequence-based comparisons reveal extensive lineage specificity of shell matrix proteins, with little conservation across distant taxa. In contrast, domain-level analyses uncover a broadly conserved repertoire of functional modules-including EF-hand, von Willebrand factor type A, collagen-related, chitin-binding, and ferritin-like domains-recurrently recruited into shell matrix proteins across lineages. Importantly, similarity in shell matrix protein composition correlates more strongly with mineralization chemistry than with phylogenetic distance. Specifically, phosphate-mineralizing systems share a higher proportion of conserved shell matrix proteins and domains across deep evolutionary distances than do carbonate-based systems, indicating that mineral chemistry exerts a dominant selective pressure on the evolution of biomineralization-associated proteins. Lineage-specific innovations appear to arise primarily through domain shuffling, expansion of low-complexity regions, and gene family diversification. These findings support a model wherein lophotrochozoan biomineralization is underpinned by a shared ancestral molecular toolkit, differentially filtered and elaborated according to mineral chemistry, providing new insights into the early evolution of animal skeletal systems.

Chen Y
Li J
Peng Z
Lv F
Wang Y
Teng W
Li C
Zhang L

Animals
Biomineralization
Proteomics
Phylogeny
Invertebrates
Proteome
Evolution, Molecular
Calcification, Physiologic
Animal Shells


Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments

Abstract: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology. The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4. The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways. Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.

Guitart-Matas J
Bravo M
Tort-Miró C
Giler-Baquerizo N
Fraile L
Caldas-Ramayo Y
Ballester M
Migura-Garcia L

Animals
Archaea
Swine
Metagenomics
Gastrointestinal Microbiome
Feces
Metagenome
Weaning
Biodiversity
Anti-Infective Agents
Gene Expression Profiling
Phylogeny
Diarrhea
Anti-Bacterial Agents


Proteomic dynamics in endochondral ossification: insights from antler tip analysis

Abstract: The antler primary growth center, located at the distal tip of the growing antler, comprises five consecutive tissue zones beneath the velvet skin. Because the outermost reserve mesenchyme contains blastema progenitor cells with multipotent differentiation capacity, antler regeneration recapitulates embryonic skeletal development through endochondral ossification (ECO). The molecular mechanisms governing cell fate decisions and tissue morphogenesis across these zones remain poorly understood. We profiled the proteome of the sika deer (Cervus nippon) antler growth center across all five tissue zones using the Orbitrap Astral platform in data-independent acquisition (DIA) mode. Protein identification and quantification were performed with DIA-NN. Proteome dynamics were analyzed by integrating three complementary clustering approaches including weighted gene co-expression network analysis (WGCNA), Fuzzy C-means clustering, and monotonic feature selection. Differentially expressed proteins were annotated by gene ontology (GO) enrichment analysis. Transcriptomic data from the same tissue zones were reanalyzed to assess mRNA-protein concordance. A total of 8,173 proteins were identified across the five tissue zones, representing the most comprehensive proteomic coverage of the antler growth center. Clustering analyses resolved distinct protein expression modules corresponding to sequential ECO stages from mesenchymal proliferation in the reserve mesenchyme to cartilage mineralization in the innermost zone. Deep proteome coverage enabled detection of low-abundance chondrogenic transcription factors SOX9, SOX6, and RUNX3, whose spatial expression matched their known roles in chondrogenesis. At the protein level, the reserve mesenchyme co-expressed 11 embryonic and 23 mesenchymal stem cell markers, indicating that antler stem cells represented a unique mesenchymal stem cell (MSC) population possessing partial embryonic stem cell (ESC)-like features. This study provides a spatially resolved proteomic atlas of the complete antler growth center and identifies key regulatory proteins at each stage of endochondral ossification. The findings offer new insights into progenitor cell characteristics, transcription factor activity, and protein dynamics during bone development, with potential relevance to bone repair and regenerative medicine.

Xi X
Cao X
Zhou Y
Tian Z
Hou N
Li Z
Zhou Z
Li X
Su H

Animals Antlers Osteogenesis Deer Proteomics Proteome Chondrogenesis


Phylogeographic history of the ring distribution in Malcus flavidipes (Heteroptera: Malcidae) shaped by directional dispersal and island adaptation in the South China Sea region

Abstract: The ring distribution pattern offers a unique perspective for analysing the mechanisms of species or population differentiation. The semi-closed South China Sea (SCS) region, with its islands, peninsulas, and continental margins, is ideal for studying the formation of ring distribution patterns and the evolutionary dynamics of island populations. This study focused on Malcus flavidipes, a species distributed in the SCS region. Based on double-digest restriction-associated DNA data and geographic distribution data, population genetic approaches and species distribution modeling were employed to investigate its distribution pattern formation and the evolutionary characteristics of island populations. The results revealed five geographic clades around the SCS, located on the Yunnan-Indochina Peninsula, southern China, Hainan Island, Kalimantan and the Philippines. Genetic diversity evidence supported that the ring distribution pattern originated in the Yunnan-Indochina Peninsula and diffused through the land bridges exposed during the Pleistocene glaciation along two routes: the northern route extended from southern China to Hainan Island, whereas the southern route stretched from Kalimantan to the Philippines. Island populations show significantly lower genetic diversity and higher within-population inbreeding coefficients than mainland ones. The genetic structural differences among different island populations are closely related to their geographic distance from mainland, responses to historical climatic fluctuations, and selective pressures from island environments. This study provides important empirical evidence for the ring differentiation of species in the SCS region, and offers a new perspective for understanding the evolutionary mechanisms of island populations under the combined effects of geographical isolation, genetic drift, and environmental selection.

Li YF
Guo MQ
Chen JH
Ai DQ
Li ZH
Zhang JY
Ye Z
Xue HJ
Wang SJ
Bu WJ

Animals
China
Phylogeography
Heteroptera
Genetic Variation
Islands
Animal Distribution
Adaptation, Physiological


From Collapse to Active Self-Repair: Integrative Multi-Omics and Machine Learning Analysis Map the Hepatic Metabolic Adaption in Response to Simulated Spaceflight Stress

Abstract: Long-term spaceflight poses substantial challenges to human physiology, with the liver being highly susceptible due to its central metabolic role. To determine whether hepatic alterations represent transient stress or sustained remodeling, we performed an integrated multi-omics analysis in a rat model simulating chronic space radiation and microgravity. Herein, we applied an integrated multi-omics and AI-driven analytical framework combining histopathology, cytokine and miRNA profiling, proteomics, metabolomics and Western blot validation. After 21 days of simulated space conditions, rats exhibited significant hepatic atrophy, histopathological injury, and metabolic dysfunction resembling a NAFLD-like phenotype, accompanied by multi-omics signatures of impaired oxidative phosphorylation, disrupted TCA cycle activity, altered lipid-metabolic regulation, and inflammatory remodeling. During a 14-day recovery phase, hepatic atrophy and histological lesions were incompletely improved, with omics changes suggesting partial restoration of mitochondrial related energy metabolism, PPAR associated lipid regulation, and fatty acid β-oxidation. Machine learning-based proteomics identified a panel of energy-related and lipid-metabolic proteins that robustly distinguished injury from recovery states. External validation with NASA GeneLab transcriptomic datasets supported the suppression of extracellular matrix programs and structural repair during injury. Together, these findings organize the hepatic response to simulated spaceflight into (1) AMPK/PPAR-γ/PGC-1α-centered energy-related lipid/mitochondrial regulation, (2) ACSM5/CRAT-associated fatty-acid utilization and carnitine-shuttle remodeling, and (3) TGF-β/IGF1-related structural repair and anabolic signaling. This study provides a comprehensive organ-level overview for understanding hepatic adaptation to extreme spaceflight environments and identifies potential targets for mitigating astronaut health risks during long-duration missions.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

Animals
Space Flight
Rats
Liver
Multiomics
Machine Learning
Male
Weightlessness Simulation
Adaptation, Physiological
Proteomics
Metabolomics
Stress, Physiological
Energy Metabolism
Lipid Metabolism
Rats, Sprague-Dawley


Development and Usability Testing of an Information Needs-Based Chatbot for Individuals With Pathogenic Variants in BRCA Genes in Korea: A Methodological Study

Abstract: Korean individuals with BRCA pathogenic/likely pathogenic (P/LP) variants have limited access to genetic counseling due to shortages of genetic professionals and lack of reimbursement. Despite the growing interest in digital health interventions, few digital counseling support tools have been designed to address the diverse information needs of this population. This study aimed to develop a user information needs-based chatbot for providing individualized information for individuals with BRCA pathogenic variants and to evaluate its usability. The chatbot, All about BRCA, was developed using a commercial chatbot platform through three stages from October 2021 to September 2022: identifying information needs via a systematic review and web-crawling analysis of patient-generative questions from online communities; developing a prototype chatbot validated by seven healthcare professionals and implementing it as rule-based system; conducting usability testing with individuals with P/LP variants in BRCA genes, using the modified mHealth App Usability Questionnaire and daily usage diaries. The modified mHealth App Usability Questionnaire scores were analyzed using descriptive statistics, and narrative diary data were analyzed using content analysis. Following iterative rounds of reviews and usability testing, the final chatbot comprised 10 information categories with 62 predefined question-scenario-responses. Nineteen participants evaluated the chatbot, yielding a mean modified mHealth App Usability Questionnaire score of 5.7 ± 0.8 out of 7. Scoring on all subscales, that is, ease of use, interface/satisfaction, and usefulness, exceeded 5.5. Responses on narrative diary data were predominantly positive, with users valuing systematic, detailed, and practical information. Key limitations of the chatbot included restricted question recognition and limited information depth. Despite limitations in question recognition, the chatbot demonstrated acceptable usability as a complementary tool to support individuals with BRCA pathogenic variants. It may help address constraints of limited consultation time and genetic expert shortages. Future development should strengthen conversational capabilities.

Humans
Female
Republic of Korea
Genetic Counseling
Genes, BRCA1
Genes, BRCA2
Adult
Surveys and Questionnaires
BRCA1 Protein


Time in tight range and time in range in relation to diabetic retinopathy and OCTA-derived retinal microvascular parameters in hospitalized adults with type 1 diabetes

Abstract: Time in Tight Range (TITR) is physiologically closer to normoglycemia than time in range (TIR) and has been linked to microvascular risk. We aimed to evaluate associations of TITR with diabetic retinopathy (DR) and optical coherence tomography angiography (OCTA)-derived retinal parameters in adults with type 1 diabetes (T1D) and to compare its performance with TIR. We retrospectively included adults with T1D who underwent continuous glucose monitoring (CGM) and OCTA. TITR-DR associations were tested using multivariable logistic regression with restricted cubic splines. Linear mixed-effects models assessed TITR/TIR associations with OCTA-derived parameters, followed by exploratory threshold-based comparisons. DR discrimination of TITR versus TIR was assessed using ROC analysis. We analyzed 259,568 glucose readings from 153 participants. Each 10-percentage-point increase in TITR was associated with 29.5% lower odds of DR (adjusted OR 0.705; p = 0.004), without evidence of nonlinearity. In continuous analyses, both TITR and TIR were positively associated with deep vascular complex (DVC) vessel density and perfusion area; in exploratory threshold-based analyses, the TITR 50% cutoff showed significant DVC differences, whereas the TIR 70% cutoff showed no consistent differences. DR discrimination was similar for TITR and TIR (p = 0.635), whereas TITR was more closely related to hypoglycemia exposure (p < 0.01). Higher TITR was associated with lower odds of DR and more favorable DVC vessel density and perfusion area in hospitalized adults with T1D. TITR showed DR discrimination comparable to TIR but may provide complementary information on hypoglycemia exposure and DVC differences in threshold-based analyses.

Zheng R
Zhang C
Sun X
Li J
Wang L
Huang S
Hou R
Dong S
Wu S
Li H
Zhang L
Kuang B
Zheng L
Zhang B
Yang C
Kuang H

Humans
Diabetes Mellitus, Type 1
Diabetic Retinopathy
Female
Male
Adult
Continuous Glucose Monitoring
Retrospective Studies
Tomography, Optical Coherence
Middle Aged
Retinal Vessels
Blood Glucose
Microvessels
Hospitalization
Time Factors


Prevalence and factors associated with ultrasound-detected hepatopathy in Indian adolescents with type 1 Diabetes Mellitus

Abstract: Hepatic involvement in Type 1 Diabetes Mellitus (T1DM) is increasingly recognized, with hepatopathy emerging as an important but underexplored comorbidity. Data on its prevalence and associated factors, particularly in Indian children and adolescents, remain limited. To estimate the prevalence of ultrasound-diagnosed hepatopathy and identify its associated risk factors among Indian children and adolescents with T1DM. This cross-sectional study included 510 children and adolescents with T1DM from a tertiary care center in western India. Clinical, anthropometric, biochemical, dietary, physical activity, and resting metabolic rate (RMR) data were collected. Hepatopathy was assessed using ultrasonography. Logistic regression analysis was performed to identify independent associated factors. The prevalence of hepatopathy was 10.4%. Children with hepatopathy had significantly higher waist circumference, blood pressure, insulin requirements, and lower moderate-to-vigorous physical activity (p < 0.05). They also exhibited poorer glycemic control, dyslipidemia, elevated liver enzymes, and reduced insulin sensitivity. RMR adjusted for insulin was significantly lower in those with hepatopathy. Multivariable analysis identified that higher waist circumference, higher insulin dose, elevated triglycerides, poor glycemic control, lower physical activity, and lower RMR were associated with hepatopathy (p < 0.05). Hepatopathy is a clinically relevant comorbidity among Indian children and adolescents with T1DM, associated with metabolic dysfunction, lifestyle factors, and altered energy metabolism. Early identification through ultrasound-based screening and targeted interventions focusing on glycemic control, adiposity, and physical activity may be critical in preventing long-term hepatic and cardiometabolic complications.

Mondkar S
Deshpande M
Wagle S
Khadilkar A
Khadilkar V

Humans
Adolescent
Diabetes Mellitus, Type 1
India
Male
Female
Ultrasonography
Cross-Sectional Studies
Prevalence
Child
Risk Factors
Liver Diseases
Comorbidity
Insulin Resistance


Association of the triglyceride glucose-Chinese visceral adiposity index with incident sarcopenia among middle-aged and older adults with diabetes: a prospective cohort study

Abstract: Longitudinal association of triglyceride glucose-Chinese visceral adiposity index (TyG-CVAI) with the risk of new-onset sarcopenia in middle-aged and older adults with diabetes remains unclear. This study aimed to investigate whether baseline and cumulative TyG-CVAI is associated with incident sarcopenia risk in middle-aged and older adults with diabetes. We included participants aged ≥ 50 years with diabetes from the China Health and Retirement Longitudinal Study (CHARLS) 2011-2012. TyG-CVAI was calculated as TyG index multiplied by CVAI. Multivariable Cox regression and logistic regression were used to examine the associations of baseline and cumulative TyG-CVAI with new-onset sarcopenia. Receiver operating characteristic (ROC) curves were employed to compare the predictive capability of TyG-CVAI with its individual components. A total of 763 participants with diabetes were included in the baseline analysis. During the 4-year follow-up, 62 (8.1%) participants developed new-onset sarcopenia. Compared with the lowest quartile (Q1) of baseline TyG-CVAI, the highest quartile (Q4) was significantly associated with an increased risk of sarcopenia (HR = 2.368, 95% CI: 1.014-5.532) in the fully adjusted model, with a significant trend across quartiles (P for trend = 0.017). Compared with the low-stable group (Cluster 1, n = 198), the high-stable group (Cluster 2, n = 276) had a significantly higher risk of new-onset sarcopenia (OR = 1.100, 95% CI: 1.020-1.321). The predictive performance of baseline TyG-CVAI (AUC = 0.685, 95% CI: 0.611-0.747) and cumulative TyG-CVAI (AUC = 0.917, 95% CI: 0.845-0.962) was higher than that of baseline and cumulative TyG and CVAI. Elevated baseline and cumulative TyG-CVAI are associated with new-onset sarcopenia in middle-aged and older Chinese adults with diabetes.

Humans
Sarcopenia
Female
Middle Aged
Male
Aged
China
Prospective Studies
Triglycerides
Blood Glucose
Adiposity
Intra-Abdominal Fat
Incidence
Diabetes Mellitus
Risk Factors
Longitudinal Studies
East Asian People


Circadian distribution of carbohydrate intake during adolescence and association with risk markers of type 2 diabetes in adulthood-the role of chronotype

Abstract: Adolescence is a critical phase characterized by temporary insulin resistance and a tendency for a later chronotype, potentially influencing the risk of developing type 2 diabetes (T2D) later in life. This study explores how morning and evening carbohydrate (CHO) intake during adolescence are prospectively related to T2D risk factors-such as insulin resistance (HOMA2-IR), liver fat indices, and subclinical inflammation- in adulthood while considering the role of chronotype. This analysis utilizes data from 224 DONALD study participants (58% female) who provided 3-day weighed dietary records during adolescence (median age = 12 years) and a blood sample in adulthood (median age = 22 years). Owing to detected interactions between the timing of CHO intake i.e. CHOevening(E%)-CHOmorning(E%), (eveningness in CHO intake) and chronotype, analyses were stratified accordingly. An inverse relationship was found between morning CHO intake (before 11 a.m.) and adult HOMA2-IR levels (beta and 95% CI for high (T3) vs. low (T1): -0.12 (-0.21; -0.04), ptrend = 0.01). For individuals with an earlier chronotype, a higher "eveningness in CHO intake" was linked to higher HOMA2-IR (ptrend = 0.03). Conversely, those with a later chronotype exhibited the lowest HOMA2-IR in the median "eveningness in CHO intake" category (T2). No significant associations were observed between evening CHO intake and other risk markers. Consuming CHOs in the morning during adolescence is associated with lower HOMA2-IR in adulthood, irrespective of chronotype. However, the favorable morning CHO intake amount appears to vary by chronotype, indicating a personalized approach may be beneficial.

Jankovic N
Schmitting S
Perrar I
Hohoff E
Lesani A
Goletzke J
Stutz B
Herder C
Wudy SA
Nöthlings U
Alexy U

Humans
Chronotype
Diabetes Mellitus, Type 2
Female
Dietary Carbohydrates
Adolescent
Risk Factors
Male
Young Adult
Biomarkers
Circadian Rhythm
Child
Insulin Resistance
Adult
Prospective Studies


[Regional features of the main indicators of carbohydrate metabolism in young residents of various climatic and geographical zones of residence]

Abstract: Vitamin D deficiency is one of the most common endocrine disorders and plays a significant role in the pathogenesis of carbohydrate metabolism disturbances. Low serum 25(OH)D levels are associated with the development of insulin resistance, metabolic syndrome, prediabetes, and type 2 diabetes mellitus (T2DM). However, data on the prevalence of vitamin D deficiency and its age-related characteristics in the population of Uzbekistan remain limited. To investigate the prevalence of vitamin D deficiency in individuals with prediabetes and newly diagnosed T2DM based on screening data from the city of Andijan and the Markhamat district of the Andijan region, Uzbekistan. A total of 3,400 individuals over 40 years of age were screened (1,800 in Markhamat district, 1,600 in Andijan city) using the FINDRISC questionnaire. Serum 25(OH)D levels, carbohydrate and lipid metabolism parameters, and HOMA-IR index were assessed in 205 subjects with prediabetes, 102 patients with newly diagnosed T2DM, and 60 controls. Prediabetes and T2DM were diagnosed according to WHO criteria. Mean vitamin D levels were significantly lower in patients with prediabetes and T2DM compared to the control group (p<0.05). The most severe deficiency was observed in patients with T2DM, especially among women and individuals aged 45-59 and 60-74 years. In Andijan city, vitamin D deficiency was detected in 100% of T2DM patients, while in Markhamat district the prevalence reached 40.3%. Vitamin D deficiency is highly prevalent among patients with prediabetes and T2DM, with severity increasing with age and more pronounced in women. These findings highlight the need for routine monitoring of serum 25(OH)D and preventive strategies in high-risk groups.

Yusupova SK
Nishanova MS
Yusupov KA
Abdurazakova DS
Mukhamedova VM
Abdulazizhojiyeva RB
Chartakova KK
Juliyeva YG
Khamidova MI
Ismoilova SK
Khalilova SR
Supichakov KK

Humans
Female
Vitamin D Deficiency
Diabetes Mellitus, Type 2
Carbohydrate Metabolism
Prediabetic State
Middle Aged
Adult
Male
Uzbekistan
Insulin Resistance
Vitamin D
Prevalence
Climate