Biology subjects

Juppi, H.-K.

Publications and source records attributed to Juppi, H.-K..

5 recordsLinked to original sources

bioRxiv2026

Integrating Semantic Retrieval, LLM-based Refinement, and Structured Expert Curation for Scalable AOP Gene Mapping

Toxicogenomics can support regulatory toxicology, but its use is limited by the difficulty of translating molecular responses into mechanistic, decision-relevant interpretations. Adverse Outcome Pathways (AOPs) provide a framework for this translation, yet omics applications require scalable mapping of Key Events (KEs) to molecular features. Here, we present an AI-assisted, multi-step workflow for KE-to-gene mapping that uses embedding-based semantic retrieval to identify candidate ontology/pathway terms, large language model-assisted refinement to filter these candidates, and double-independent expert group curation with rule-based consolidation to finalize mappings and derive confidence scores. Compared with earlier NLP-based approaches, the workflow improves KE-to-ontology/pathway mapping performance and generates candidate annotations that better align with expert judgment while substantially reducing the need for manual augmentation. Explicit gene and protein mentions in KE titles were additionally grounded to improve specificity, and each curated mapping was assigned curator reason codes to support transparent, traceable, and confidence-aware reuse. Applied across AOP-Wiki, the workflow produced a comprehensive KE-to-gene set resource covering 1,254 KEs across 523 AOPs and linking 15,833 human genes. Utility is demonstrated through CTD-based AOP fingerprinting of curated reference chemical groups, highlighting expanded coverage and confidence-informed interpretation of chemical-associated gene signatures in an AOP context. The workflow and resulting resource provide a practical bridge between toxicogenomics and AOP-based mechanistic interpretation and support routine updating and future extension to additional omics layers within OECD Omics2AOP.

bioinformatics↗

bioRxiv2023

Menopausal transition alters female skeletal muscle transcriptome

Menopause is associated with unfavorable changes in body composition. Skeletal muscle cells are targets of hormonal regulation and are affected by the interplay between coding and non-coding RNAs. Muscle transcriptome, including messenger-RNA (mRNA), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) has not previously been studied in women during the menopausal transition. Thus, we took a multi-RNA omics approach to get insight into transcriptome-wide events of menopause. Our study included baseline and follow-up muscle samples from seven early (EarlyMT) and 17 late perimenopausal (LateMT) women transitioning to early postmenopause during the study. Total RNA was sequenced and differential expression (DE) of the transcriptome was investigated. The potential gene functions were investigated with pathway analyses and protein level expression with Western Blot. We found 30 DE mRNA genes in EarlyMT and 19 in LateMT participating in pathways controlling cell death, growth, and interactions with external environment. Lack of protein level changes may indicate a specific role of the regulatory RNAs during menopause. Ten DE lncRNA transcripts were identified but did not result in DE lncRNAs genes. No DE miRNAs were found. Despite the lack of DE findings in regulatory RNAs, we identified putative regulatory networks, likely to be affected by estradiol availability. The changes in gene expression were correlated with observed changes in body composition variables, indicating muscularity and adiposity regulators to be affected by menopausal transition. In essence, the observed DE genes and their regulatory networks may offer novel mechanistic insights on factors affecting body composition during and after menopause.

molecular biology↗

bioRxiv2022

Age but not menopausal status is linked to lower resting energy expenditure

ContextIt remains uncertain whether aging before late adulthood and menopause are associated with fat-free mass and fat mass-adjusted resting energy expenditure (REEadj). ObjectivesWe investigated whether REEadj differs between middle-aged and younger women and between middle-aged women with different menopausal statuses. We repeated the age group comparison between middle-aged mothers and their daughters to partially control for genotype. We also explored whether serum estradiol and follicle-stimulating hormone concentrations explain REEadj in midlife. MethodsWe divided 120 women, including 16 mother-daughter pairs, into age groups; group I (n = 26) consisted of participants aged 17-21, group II (n = 35) of those aged 22-38 and group III (n = 59) of those aged 41-58 years. The women in group III were further categorized as pre- or perimenopausal (n = 19), postmenopausal (n = 30) or postmenopausal hormone therapy users (n = 10). REE was assessed using indirect calorimetry, body composition using dual-energy X-ray absorptiometry and hormones using immunoassays. ResultsThe REEadj of group I was 126 kcal/d (95% CI: 93-160) higher than that of group III, and the REEadj of group II was 88 kcal/d (95% CI: 49-127) higher. Furthermore, daughters had a 100 kcal/d (95% CI: 63-138 kcal/d) higher REEadj than their middle-aged mothers (all P < 0.001). In group III, REEadj was not lower in postmenopausal women and did not vary by sex hormone concentrations. ConclusionsWe demonstrated that REEadj declines with age in women before late adulthood, also when controlling partially for genetic background, and that menopause may not contribute to this decline.

physiology↗

bioRxiv2022

Extracellular vesicles and high-density lipoproteins: Exercise and estrogen-responsive small RNA carriers

Decreased systemic estrogen levels (i.e., menopause) affect metabolic health. However, the detailed mechanisms underlying this process remain unclear. Both estrogens and exercise have been shown to improve metabolic health, which may be partly mediated by circulating microRNA (c-miR) signaling. In recent years, extracellular vesicles (EV) have increased interest in the field of tissue crosstalk. However, in many studies on EV-carried miRs, the co-isolation of high-density lipoprotein (HDL) particles with EVs has not been considered, potentially affecting the results. Here, we demonstrate that EV and HDL particles have distinct small RNA (sRNA) content, including both host and nonhost sRNAs. Exercise caused an acute increase in relative miR abundancy in EVs, whereas in HDL particles, it caused an increase in transfer RNA-derived sRNA. Furthermore, we demonstrate that estrogen deficiency caused by menopause blunts acute exercise-induced systemic miR-response in both EV and HDL particles. HIGHLIGHTSO_LIExtracellular vesicles and HDL particles have a distinct sRNA content C_LIO_LIExtracellular vesicles and HDL particles carry both host and nonhost sRNA cargo C_LIO_LIEstrogen deficiency blunts the c-miR-response induced by acute exercise C_LIO_LIExercise responsive miRs in HT users may regulate the choice of energy substrate C_LI

molecular biology↗

bioRxiv2018

Estrogen Regulates the Satellite Cell Compartment in Females

Skeletal muscle mass, strength, and regenerative capacity decline with age, with many measures showing greater deterioration in females about the time estrogen levels decrease at menopause. Here we show that maintenance of muscle stem cells, satellite cells, as well as self-renewal and differentiation into muscle fibers, are severely compromised by estrogen deficiency. Mechanistically, by hormone replacement, use of a selective estrogen-receptor modulator (bazedoxifene), and conditional estrogen receptor knockout, we implicate 17{beta}-estradiol and satellite cell expression of estrogen receptor (ER) and show that estrogen signaling through this receptor is necessary to prevent apoptosis of satellite cells. Early data from a biopsy study of women who transitioned from peri-to post-menopause are consistent with the loss of satellite cells coincident with the decline in estradiol in humans. Together, these results demonstrate an important role for estrogen in satellite cell maintenance and muscle regeneration in females.

cell biology↗