bims-musmir 2025-09-21 papers

bims-musmir

Biomed News

on microRNAs in muscle

Issue of 2025–09–21
sixteen papers selected by
Katarzyna Agnieszka Goljanek-Whysall, University of Galway

Pancreatic Cancer Induces Population-Specific Switching of Myosin Isoforms and Discrete Activation of Cachexia Genes in Skeletal Muscle Myocytes.
Transcriptome and microRNAome profiling of human skeletal muscle in pancreatic cancer cachexia.
STX4 is indispensable for mitochondrial homeostasis in skeletal muscle.
miR-146a is a Pleiotropic Regulator of Motor Neuron Degeneration.
Molecular mechanisms by which mitochondrial dysfunction drives neuromuscular junction degeneration in amyotrophic lateral sclerosis.
Targeting RUNX3/PARP1 signaling ameliorates colorectal cancer cachexia.
Simultaneous RNA Fluorescent In Situ Hybridization and Immunofluorescent Staining of Mouse Muscle Stem Cells on Fresh Frozen Skeletal Muscle Sections.
Zinc and circulating microRNAs in women with insulin resistance.
Fatty acid trafficking to mitochondria and peroxisomes in Tetrahymena thermophila, a new frontier for lipid droplet biology.
Early changes in exosomal microRNAs after a one-week low-calorie diet predict sustained glycaemic and weight outcomes in patients with type 2 diabetes.
Why does the m6A writer complex require so many proteins?
miR-101-3p overexpression suppresses NSCLC progression through Immune-Related gene CALCRL regulation and lncRNA NEAT1 axis.
The Prolyl Isomerase PIN1 Impacts Fibroblast Differentiation States and Crosstalk in Pancreatic Cancer.
Isoflurane aggravates cognitive deficits in aged rats via lncRNA GABPB1-AS1/miR-361-3p-mediated NLRP3 inflammasome activation.
Dysregulation of Neuronal Activity-Dependent Immediate Early Genes in a Mouse Model of Angelman Syndrome.
tDR-quant: a reliable electroporation-based approach for quantifying tRNA-derived fragments binding to ribosomes.

bioRxiv. 2025 Sep 05. pii: 2025.09.01.673500. [Epub ahead of print]

Pancreatic Cancer Induces Population-Specific Switching of Myosin Isoforms and Discrete Activation of Cachexia Genes in Skeletal Muscle Myocytes.

Brittany R Counts, Sephora Jean, Omnia Gaafer, Sara K Ota, Iishaan Inabathini, Tingbo Guo, Denis C Guttridge, Michael C Ostrowski, Leonidas G Koniaris, Sha Cao, Hyun C Roh, Teresa A Zimmers.

Skeletal muscle loss in pancreatic cancer is a significant cause of morbidity and mortality for patients. In order to understand myocytes changes we examined myonuclei- and myofiber-specific dynamics during pancreatic cancer cachexia progression. Single-nucleus RNA-seq was used to interrogate myonuclear gene expression, and RNAscope and immunofluorescence characterized myofiber-specific changes. Bulk RNA-seq of skeletal muscle provided a whole-muscle transcriptomic profile. Cachexia induces a progressive loss of muscle differentiation factor Maf and its target Myh4 , accompanied by increased expression of Myh1 and Myh2 . This myofiber dedifferentiation occurs without evidence for fiber type shifting, regeneration, or proliferation. Single-nuclei analysis reveals global shifts in myofiber gene expression identity including the identification of a cachexia only myonuclear subpopulation. Cachexia gene expression was not restricted solely to this PDAC-specific myonuclear subpopulation and did not overlap with Myh1 and Myh2 expressing myonuclei early in cachexia. Altogether, PDAC cachexia elicits distinct transcriptional responses across different myonuclear populations. These results reveal population-specific heterogeneity in cachexia gene activation, rather than a uniform upregulation of cachexia mediators across muscle tissue. Our data suggest that myonuclei fate occurs prior to overt muscle wasting when cachexia gene expression only modestly overlaps with differentiation factors, with a strong association after irreversible muscle wasting. These findings explain the challenge of effectively targeting skeletal muscle wasting in cancer cachexia requires addressing the changing cell population induced through non overlapping mechanisms.

DOI: https://doi.org/10.1101/2025.09.01.673500
medRxiv. 2025 Sep 04. pii: 2025.09.02.25334959. [Epub ahead of print]

Transcriptome and microRNAome profiling of human skeletal muscle in pancreatic cancer cachexia.

Ashok Narasimhan, Xiaoling Zhong, Brittany R Counts, Andrew Young, Sha Cao, Jun Wan, Sheng Liu, Leonidas G Koniaris, Teresa A Zimmers.

Background and Aims: Over 80% of patients with pancreatic cancer experience cachexia, characterized by severe muscle and fat loss. While all the mechanistic understanding comes from preclinical models, the translatable nature of these findings to humans remains a critical gap due to the limited knowledge of human cachexia biology.
Methods: We generated matched gene and microRNA profiles from rectus abdominis muscle of 55 pancreatic ductal adenocarcinoma and 18 control subjects. Differentially expressed genes and microRNAs were identified at 1.5-fold change and p<0.05.
Results: Gene expression results revealed a striking sex-specific difference at the expression and pathway levels. In both sexes, co-expression gene network analysis identified more significant modules and hub genes at 1-month of weight loss than the traditionally used six months, suggesting that gene alterations may be more dynamic in the early stages of the disease progression. When comparing hub genes from humans to experimental models of cachexia, genes such as RELA, DDX21, WDR75, PTPN1, and CRIP3 exhibited similar patterns of expression, suggesting their potential role in cachexia. microRNAs also exhibited sex-specific expression. Although several common miRNAs were identified between sexes, their gene targets differed, indicating that microRNAs may regulate gene targets in a sex-specific manner.
Conclusions: The dataset can serve as a resource for validating preclinical findings and exploring previously unexplored molecules in cachexia. Future studies will functionally characterize the role of the hub genes and microRNAs in cachexia. This is the first study to identify sex-specific genes and microRNAs from a single cancer type.

DOI: https://doi.org/10.1101/2025.09.02.25334959
bioRxiv. 2025 Sep 03. pii: 2025.09.02.673840. [Epub ahead of print]

STX4 is indispensable for mitochondrial homeostasis in skeletal muscle.

Joseph M Hoolachan, Rekha Balakrishnan, Erika M McCown, Karla E Merz, Chunxue Zhou, Elizabeth Bloom-Saldana, Patrick T Fueger, Angelica Hamilton, Tali Kiperman, Ke Ma, Eunjin Oh, Lei Jiang, Patrick Pirrotte, Orian Shirihai, Debbie C Thurmond.

Background: Mitochondrial homeostasis is vital for optimal skeletal muscle integrity. Mitochondrial quality control (MQC) mechanisms that are essential for maintaining proper functions of mitochondria include mitochondrial biogenesis, dynamics and mitophagy. Previously, Syntaxin 4 (STX4) traditionally considered a cell surface protein known for glucose uptake in skeletal muscle, was also identified at the outer mitochondrial membrane. STX4 enrichment was sufficient to reverse Type 2 diabetes-associated mitochondrial damage in skeletal muscle by inactivation of mitochondrial fission. However, whether STX4 could modulate skeletal muscle mitochondrial homeostasis through MQC mechanisms involving mitochondrial biogenesis or mitophagy remains to be determined.
Methods: To determine the requirements of STX4 in mitochondrial structure, function and MQC processes of biogenesis and mitophagy, we implemented our in-house generated inducible skeletal muscle-specific STX4-knockout (skmSTX4-iKO) mice ( Stx4 fl/fl ; Tg(HSA-rtTA/TRE-Cre )/B6) and STX4-depleted immortalized L6.GLUT4myc myotubes via siRNA knockdown (siSTX4).
Results: We found that non-obese skmSTX4-iKO male mice (>50% reduced STX4 abundance, Soleus and Gastrocnemius ***p<0.001, Tibialis anterior (TA) ****p<0.0001) developed insulin resistance (**p<0.01), together with reduced energy expenditure (AUC *p<0.05), respiratory exchange ratio (AUC **p<0.01), and grip strength (*p<0.05). STX4 ablation in muscle also impaired mitochondrial oxygen consumption rate (****p<0.0001). Mitochondrial morphological damage was heterogenous in STX4 depleted muscle, presenting with small fragmented mitochondria (****p<0.0001) and deceased electron transport chain (ETC) abundance (CI ***p<0.001, CII *p<0.05, CIV **p<0.01) in oxidative soleus muscle, while glycolytic TA fibers display enlarged swollen mitochondria (****p<0.0001) with no change in ETC abundance. Notably, >60% reduction of STX4 in siSTX4 L6.GLUT4myc myotubes (****p<0.0001) also decreased ETC abundance (CI ****p<0.0001, CII ****p<0.0001, CIV *p<0.05) without changes in mitochondrial glucose metabolism, as shown by [U- 13 C] glucose isotope tracing. For MQC, both skmSTX4-iKO male mice (*p<0.05) and siSTX4 L6.GLUT4myc myotubes (*p<0.05) showed decreased mitochondrial DNA levels alongside reduced mRNA expression of mitochondrial biogenesis genes Ppargc1a (PGC1-α, *p<0.05) and Tfam (*p<0.05) in skmSTX4-iKO soleus muscle and PGC1-α (mRNA *p<0.05, protein ***p<0.001), NRF1 (mRNA and protein *p<0.05) and Tfam (mRNA *p<0.05) in siSTX4 L6.GLUT4myc myotubes. Furthermore, live cell imaging using mt-Keima mitophagy biosensor in siSTX4 L6.GLUT4myc cells revealed significantly impaired mitochondrial turnover by mitophagy (*p<0.05) and mitochondria-lysosome colocalization (*p<0.05). STX4 depletion also reduced canonical mitophagy markers, PINK1 and PARKIN in both skmSTX4-iKO muscle (PARKIN *p<0.05, PINK1 **p<0.01) and siSTX4 L6.GLUT4myc myotubes (PARKIN ****p<0.0001, PINK1 *p<0.05).
Conclusions: Our study demonstrated STX4 as a key mitochondrial regulator required for mitochondrial homeostasis in skeletal muscle.

DOI: https://doi.org/10.1101/2025.09.02.673840
bioRxiv. 2025 Sep 09. pii: 2025.09.04.674013. [Epub ahead of print]

miR-146a is a Pleiotropic Regulator of Motor Neuron Degeneration.

Dylan A Galloway, Hunter L Patterson, Mariah L Hoye, Tao Shen, Mark Shabsovich, Kathleen M Schoch, Cindy V Ly, Timothy M Miller.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting motor neurons. Here, we have profiled motor neuron microRNAs (miRNAs) during motor neuron degeneration in vivo to gain a better understanding of ALS pathophysiology. We demonstrate that one miRNA, miR-146a, is downregulated in diseased motor neurons despite upregulation in bulk tissue. Genetic deletion of miR-146a significantly extended survival in SOD1 G93A mice with heterozygous animals demonstrating the largest benefit. A corresponding reduction in spinal cord gliosis but not motor neuron loss was observed. Finally, we observed that a proportion of miR-146a knockout animals develop spontaneous paralysis, motor neuron loss and chronic neuroinflammation with advanced age. Together these findings demonstrate that a single miRNA influences multiple aspects of motor neuron disease and highlights the complex role for neuroinflammation in ALS pathogenesis.

DOI: https://doi.org/10.1101/2025.09.04.674013
Neurobiol Dis. 2025 Sep 15. pii: S0969-9961(25)00320-1. [Epub ahead of print] 107103

Molecular mechanisms by which mitochondrial dysfunction drives neuromuscular junction degeneration in amyotrophic lateral sclerosis.

Xie Yipeng, Wang Guiqian, Zhu Qiaochu, He Tengjie, Zhao Yan, Huang Hai, Zhou Jing.

   BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder marked by progressive degeneration of motor neurons and early deterioration of neuromuscular junctions (NMJs). Increasing evidence indicates that mitochondrial dysfunction plays a pivotal role in driving NMJ degeneration in ALS.
OBJECTIVE: This review aims to comprehensively summarize the molecular mechanisms by which mitochondrial defects contribute to NMJ instability, with a particular focus on bioenergetics, calcium homeostasis, oxidative stress, and impaired mitochondrial biogenesis.
CONCLUSION: Mitochondrial dysfunction is a core driver of NMJ degeneration in ALS. Targeting mitochondrial biogenesis and metabolism-particularly through the PGC-1α pathway-represents a promising strategy to preserve NMJ integrity and slow disease progression.

Keywords:  Amyotrophic lateral sclerosis; Calcium homeostasis; Mitochondria; Mitochondrial biogenesis; Neuromuscular junction; PGC-1α; ROS

DOI:  https://doi.org/10.1016/j.nbd.2025.107103
Biomed Pharmacother. 2025 Sep 18. pii: S0753-3322(25)00755-3. [Epub ahead of print]192 118561

Targeting RUNX3/PARP1 signaling ameliorates colorectal cancer cachexia.

Abinash Swain, Pinaki Prasad Mahapatra, Abhishek Nirwan, Neelam Gupta, Arun Kumar, Rashi Saxena, Jaspreet Kaur, Shakil Ahmed, Durga Prasad Mishra.

  Cancer cachexia characterized by significant muscle atrophy and muscle loss is a defining hallmark of colorectal cancer associated morbidity and mortality. Despite advances in treatment, current therapeutic strategies are often limited by their side effects like systemic toxicity, cardiovascular complications and low response rates, necessitating alternatives for colorectal cancer cachexia management. The Poly (ADP-ribose) polymerases 1 (PARP1) is known to regulate oxidative stress, and protein catabolism in the muscle. However, the role of PARP1 in the regulation of muscle atrophy remains poorly understood and is yet to be fully elucidated. The PARP inhibitor Olaparib has demonstrated anticancer effects in multiple cancer models; however, its effects on colorectal cancer cachexia remains unknown. Therefore, in the current study we investigated the role of PARP1 in regulation of colorectal cancer cachexia using Olaparib and its underlying molecular mechanisms. Pharmacological inhibition of PARP1 with Olaparib reversed the muscle atrophy parameters both in the in vitro and in vivo models of colorectal cancer cachexia. Further, we identified that the transcription factor RUNX3 regulated the muscle atrophy associated E3 ubiquitin ligase MuRF1 expression through PARP1 mediated PARylation in colorectal cancer cachexia. Additionally, the MuRF1 promotor engagement by RUNX3 led to the activation of MuRF1 transcription in colorectal cancer cachexia. In conclusion, the current study is the first to demonstrate the critical role of RUNX3 PARylation in regulation of muscle atrophy in colorectal cancer cachexia. These findings suggest that the RUNX3/PARP1 signalling holds promise for devising novel strategies for colorectal cancer cachexia management.

Keywords:  Cancer cachexia; MuRF1; Olaparib; PARP1; RUNX3; muscle atrophy

DOI:  https://doi.org/10.1016/j.biopha.2025.118561
Bio Protoc. 2025 Sep 05. 15(17): e5435

Simultaneous RNA Fluorescent In Situ Hybridization and Immunofluorescent Staining of Mouse Muscle Stem Cells on Fresh Frozen Skeletal Muscle Sections.

Vedant R Lakkundi, Maria L Perez, Kartik Soni, Albert E Almada.

  Adult muscle stem cells (MuSCs) are the key cellular source for regenerating skeletal muscle in vertebrates. MuSCs are typically identified in skeletal muscle by the expression of the paired box protein 7 (PAX7) protein. Here, we developed a combined RNA fluorescent in situ hybridization (FISH) using RNAscope technology and an immunofluorescence (IF) protocol for the simultaneous detection of Pax7 mRNA and PAX7 protein in individual MuSCs in vivo. Interestingly, we show that while most PAX7+ (protein) MuSCs express Pax7 mRNA, there is a subset of Pax7 + (mRNA) cells that do not express PAX7 protein. Altogether, we developed a combined FISH/IF protocol that allows for the co-detection of mRNA and protein in MuSCs in vivo, a strategy that can be applied to any target gene. The functional significance of the Pax7-expressing subset of cells lacking PAX7 protein prior to injury remains unknown. Key features • Extensive step-by-step details for an optimized protocol combining traditional immunofluorescence with RNA fluorescent in situ hybridization (FISH) using ACDBio's RNAscope technology. • Allows for the co-detection of protein and mRNA in muscle stem cells (MuSCs) in mouse skeletal muscle tissue in vivo in ~2 days. • Validation of our protocol uncovers a subset of cells expressing Pax7 mRNA but not PAX7 protein.

Keywords:  Fluorescent in situ hybridization (FISH); Immunofluorescence (IF); Muscle stem cells; PAX7; RNAscope; Skeletal muscle

DOI:  https://doi.org/10.21769/BioProtoc.5435
J Trace Elem Med Biol. 2025 Sep 12. pii: S0946-672X(25)00161-0. [Epub ahead of print]92 127748

Zinc and circulating microRNAs in women with insulin resistance.

Danielle Caroline da Silva Dias, Graziela Biude Silva Duarte, Leonam da Silva Pereira Batista, Marcelo Macedo Rogero, Fernando Barbosa, Silvia Maria Franciscato Cozzolino, Raquel Costa Silva Dantas-Komatsu, Karina Zaira Silva Marinho Costa, Bruna Zavarize Reis.

   INTRODUCTION: Insulin resistance (IR) is a key factor in the development of type 2 diabetes and is potentially associated with zinc deficiency due to the role of this mineral in the metabolism of this hormone. MicroRNAs (miRs) can regulate insulin signaling pathway, glucose metabolism, and inflammation, and their expression can be modulated by different nutrients and bioactive compounds. Nutrimiromics investigates how nutrients modulate gene expression through miRs. However, the associations between miRNAs related to IR mechanisms and zinc status in the body remains unclear. Therefore, this study aimed to evaluate the associations of plasma zinc concentration with the expression of miR-191-5p, miR-188-5p, miR-145-5p, and miR-143-3p in overweight and IR women.
MATERIALS AND METHODS: This comparative cross-sectional study included 50 overweight or obese women, aged between 18 and 60 years. IR classification followed Stern's criteria. Circulating miR expression, plasma zinc concentration, biochemical profile, inflammatory biomarkers, and anthropometric parameters were evaluated.
RESULTS: Six percent of the participants had plasma zinc concentrations below the reference value (<70 µg/dL). When categorizing plasma zinc values by their median concentration (≤90 µg/dL and >90 µg/dL), a significant difference was observed in the fibrinogen concentration (p = 0.016) and the expression of three miR evaluated (miR-191-5p, miR-145-5p, and miR-143-3p). A significant inverse correlation was found between plasma zinc concentration and miR-145-5p (p = 0.006), miR-143-3p (p = 0.011), miR-191-5p (p = 0.002), and the serum fibrinogen concentration (p = 0.038). Significant inverse correlations were observed between insulin and miR-191-5p (p = 0.007), miR-188-5p (p = 0.029), miR-145-5p (p = 0.015), and miR-143-3p (p = 0.001). miR-191-5p (p = 0.037) and miR-143-3p (p = 0.021) were inversely correlated with HOMA-IR. The miR-145-5p was negatively correlated with IL-1β (p = 0.006), IL-6 (p = 0.004), and IFN-γ (p = 0.020), and miR-143-3p was negatively correlated with IL-6 (p = 0.018). According to the adjusted logistic regression model, high expression of miR-191-5p (OR=0.06; p = 0.012) was inversely associated with the plasma zinc concentration. In the functional enrichment analysis conducted with the list of target genes, six Gene Ontology (GO) terms were significantly enriched.
CONCLUSION: All four miRs showed an inverse correlation with insulin, indicating that zinc status may influence miR expression, potentially affecting biological processes involved in IR. This study identified significant expression of miR-143-3p, miR-145-5p, and miR-191-5p at plasma zinc concentrations above 90 μg/dL.

Keywords:  Insulin resistance; MicroRNA; Zinc

DOI:  https://doi.org/10.1016/j.jtemb.2025.127748
Mol Biol Cell. 2025 Sep 17. mbcE24080381

Fatty acid trafficking to mitochondria and peroxisomes in Tetrahymena thermophila, a new frontier for lipid droplet biology.

Laura Listenberger, Elizabeth A Strandberg, Byunghyun Ahn, Vivienne Vinton, Gillian Bode, Abigail Williams, Hayden Reid, Lia Wallace, Daaé Ransom, Kim Kandl.

Lipid droplets are increasingly recognized as necessary organelles. However, the cellular pathways that regulate lipid droplets have only been defined in select fungi, algae, plants, and animals. Our experiments expand the study of lipid droplets to an evolutionarily distinct model organism, the ciliate Tetrahymena thermophila. We identify conserved pathways that promote lipid droplet homeostasis while also uncovering features that suggest adaptation. We show that Tetrahymena accumulate lipid droplets in response to nutrient deprivation, including starvation and stationary phase. Pulse chase experiments with a fluorescent fatty acid analogue demonstrate lipid trafficking to lipid droplets in starved cultures. Unlike other cell types, starved Tetrahymena appear to use both peroxisomes and mitochondria (not vacuoles) for further fatty acid catabolism. We observe co-occurence of the fluorescent fatty acid analogue with markers of peroxisomes and a subpopulation of mitochondria, suggesting specialized catabolic roles for both organelles. We demonstrate a decrease in survival following starvation in the presence of inhibitors of mitochondrial fatty acid import or peroxisomal fatty acid metabolism. Together, our experiments add Tetrahymena to the expanding list of eukaryotes that increase lipid droplets in response to nutrient depletion while also uncovering important and distinct roles for mitochondrial and peroxisomal catabolism in survival pathways.

DOI: https://doi.org/10.1091/mbc.E24-08-0381
Food Funct. 2025 Sep 16.

Early changes in exosomal microRNAs after a one-week low-calorie diet predict sustained glycaemic and weight outcomes in patients with type 2 diabetes.

Sujing Wang, Shuxiao Shi, Deshan Wu, Kexin Li, Guangrui Yang, Ruijie Qi, Lan Xu, Nannan Feng, Victor W Zhong, Xihao Du.

Background: Exosomal microRNAs (miRNAs) are key regulators of type 2 diabetes (T2D), yet their rapid response to caloric restriction remains undefined. Objective: To characterise plasma exosomal miRNA changes after one week of a low-calorie diet (LCD) in adults with T2D and determine whether these early shifts predict weight and glycaemic outcomes at 12 and 24 weeks. Methods: Sixteen adults with T2D consumed 820-840 kcal day-1 for seven days. Plasma exosomes collected at baseline and day 7 underwent small-RNA sequencing. Differential expression was set at |log2 fold change| > 1 with P < 0.05 (DESeq2). Target-gene enrichment, correlations with clinical biomarkers, and linear models relating week-1 miRNA changes to body-weight and glycaemic indices at follow-up were performed. Results: Participants lost 3.2 ± 0.9 kg in the first week (P < 0.001). Thirty-two miRNAs were differentially expressed: miR-122-5p, miR-3158-3p and miR-483-5p were down-regulated, whereas miR-126-5p and miR-454-3p were up-regulated. Target genes were enriched in PI3K-Akt, FoxO and endocrine-resistance pathways. Early rises in miR-1268a and miR-6770-3p correlated with interleukin-6 and tumour necrosis factor-α. An increase in miR-494-3p predicted larger HbA1c reductions at 12 weeks (β = -0.47; 95% CI: -0.67 to -0.21) and 24 weeks (β = -0.50; 95% CI: -0.76 to -0.18). Conversely, greater miR-362-5p elevations at week 1 were associated with smaller weight loss. Conclusions: A single week of LCD induces swift, pathway-linked shifts in plasma exosomal miRNAs in T2D. miR-494-3p and miR-362-5p emerge as promising early biomarkers for long-term glycaemic improvement and weight reduction, respectively.

DOI: https://doi.org/10.1039/d5fo02781k
PLoS Biol. 2025 Sep 15. 23(9): e3003386

Why does the m6A writer complex require so many proteins?

Kiran Pandey, Hui Xian Poh, Samie R Jaffrey.

The conversion of adenosine to N6-methyladenosine (m6A) is the most common internal modification made to eukaryotic mRNA and is involved in post-transcriptional control of gene expression. When dysregulated, m6A has been linked to a variety of diseases, including cancer. Unlike other RNA methyltransferases, m6A conversion is catalyzed by a multi-protein writer complex with only one catalytic subunit. So why is the m6A writer complex composed of so many proteins? This Unsolved Mystery explores the possible functions of the proteins of the m6A writer complex and discusses why it might require multiple subunits. Understanding the roles of these proteins could provide insight into how m6A is regulated and reveal new strategies for targeting diseases linked to m6A dysregulation.

DOI: https://doi.org/10.1371/journal.pbio.3003386
Mol Biol Rep. 2025 Sep 20. 52(1): 932

miR-101-3p overexpression suppresses NSCLC progression through Immune-Related gene CALCRL regulation and lncRNA NEAT1 axis.

Gulnaz Tabassum, Shweta Arora, Prithvi Singh, Mohd Mohsin, Salman Khan, Aman Khan, Ravins Dohare, Kapil Dev, Mansoor Ali Syed.

   INTRODUCTION: Non-Small Cell Lung Cancer (NSCLC), a predominant subtype of lung cancer, remains a major cause of cancer-related mortality worldwide and continues to present significant clinical challenges. While microRNAs (miRNAs) are established regulators of cellular pathways, their specific involvement in modulating immunometabolic processes in NSCLC remains underexplored. This study aimed to uncover novel regulatory mechanisms in lung adenocarcinoma (LUAD) through an integrative approach combining computational and experimental strategies, with particular emphasis on miRNA, mRNA, and long non-coding RNA (lncRNA) interactions.
METHODS: By analyzing RNA-Seq datasets, we identified differentially expressed miRNAs, genes, and immune-associated transcripts specific to LUAD. Subsequent enrichment and network analyses highlighted key molecular players involved in immune dysregulation and cancer progression. A competing endogenous RNA (ceRNA) network involving miR-101-3p, the gene CALCRL, and lncRNA NEAT1 were constructed to elucidate regulatory hierarchies. Experimental validation included qRT-PCR, Western blot, and luciferase reporter assays to confirm miRNA-mRNA-lncRNA interactions. Functional assays were conducted to assess cancer cell proliferation, oxidative stress, mitochondrial integrity, and apoptosis.
RESULTS: Analysis revealed significant downregulation of miR-101-3p and concurrent upregulation of CALCRL and NEAT1 in LUAD cell lines. Experimental assays confirmed that miR-101-3p directly targets and negatively regulates CALCRL, while NEAT1 enhances CALCRL expression by competitively binding miR-101-3p. Restoration by doing overexpression of miR-101-3p led to reduced cancer cell growth, increased oxidative stress, disrupted mitochondrial function, decreased ATP levels, and increased apoptotic cell death.
CONCLUSION: The study identifies the miR-101-3p/NEAT1/CALCRL regulatory axis as a key mediator of immunometabolic remodeling in LUAD. These findings underscore the potential of targeting this axis for miRNA-guided therapeutic interventions, presenting a novel strategy to counteract tumor progression in NSCLC.

Keywords:  Immune regulation; Lung cancer; NSCLC; Non-coding-RNA; Tumor suppression; miRNA

DOI:  https://doi.org/10.1007/s11033-025-11043-8
Cancer Res. 2025 Sep 18.

The Prolyl Isomerase PIN1 Impacts Fibroblast Differentiation States and Crosstalk in Pancreatic Cancer.

Chloe L Bowman, Colin J Daniel, Eric J Carlson, Vidhi M Shah, Amy S Farrell, Kayleigh M Kresse, Xiaoyan Wang, Kyra A Lindley, Madeline R Kuhn, Kevin MacPherson-Hawthorne, Brittany L Allen-Petersen, Jennifer Eng, Motoyuki Tsuda, Isabel A English, Carl Pelz, Arslan Amer, Aaron R Doe, Megan A Turnidge, Zina P Jenny, Trent Waugh, Zinab O Doha, Nicholas D Kendsersky, Kristof Torkenczy, Katherine R Pelz, Andrew J Fields, Gabriel M Cohn, Gabrielle S Dewson, Mary C Thoma, Taylor S Amery, Mara H Sherman, Koei Chin, Anupriya Agarwal, Jason M Link, Brett C Sheppard, Andrew C Adey, Rosalie C Sears, Ellen M Langer.

The prolyl isomerase PIN1 is overexpressed in cancer and contributes to cancer cell-intrinsic phenotypes including proliferation and migration. However, PIN1 may also function in stromal cells within the tumor microenvironment (TME). Here, we showed that PIN1 is a critical regulator of pancreatic stellate cell (PSC) state at baseline and in response to the myofibroblast activating factor TGF-β. Loss or inhibition of PIN1 altered the epigenetic and transcriptional response of PSCs to TGF-β, preventing PSC differentiation to a myofibroblast state and altering expression of secreted matrix proteins and signaling molecules. Consistent with inhibition of the TGF-β response, low fibroblast PIN1 expression in mouse and human pancreatic ductal adenocarcinoma (PDAC) correlated with low expression of α-SMA, a marker of myofibroblast activation. Decreased PIN1 expression at baseline also altered paracrine HGF signaling from fibroblasts to tumor cells. PSCs with low PIN1 expression displayed reduced expression and secretion of HGF, resulting in an attenuation of c-MET receptor phosphorylation and signaling in nearby cancer cells. In allograft models, host PIN1 was critical for normal growth of a subset of pancreatic cancer cell lines that are responsive to HGF signaling. Through the identification of changes to fibroblast activation state and crosstalk following PIN1 loss or inhibition, these data suggest that systemic targeting of PIN1 will suppress the pro-tumorigenic PDAC microenvironment and may differentially affect heterogeneous patient populations.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-3437
Toxicol Appl Pharmacol. 2025 Sep 17. pii: S0041-008X(25)00347-3. [Epub ahead of print] 117571

Isoflurane aggravates cognitive deficits in aged rats via lncRNA GABPB1-AS1/miR-361-3p-mediated NLRP3 inflammasome activation.

Guorui Miao, Yiwei Zhang, Hui Wang.

   OBJECTIVE: Postoperative cognitive dysfunction (POCD) following isoflurane (ISO) anesthesia in elderly patients is associated with neuroinflammation, but the molecular mechanisms remain unclear. This study aimed to elucidate the role and mechanism of long non-coding RNA (lncRNA) GA binding protein beta 1 subunit antisense RNA 1 (GABPB1-AS1) in ISO-induced POCD.
METHODS: Aged rats were exposed to ISO to establish a POCD model. Cognitive deficits were assessed via morris water maze tests. Hippocampal expression of GABPB1-AS1, microglial activation markers (Iba1), pro-/anti-inflammatory cytokines, and NLRP3 inflammasome components was quantified using quantitative Reverse Transcription-PCR (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), and Western blotting. In vitro, BV-2 microglia treated with ISO were analyzed for polarization markers and cytokine secretion. Dual-luciferase assays validated interactions between GABPB1-AS1, microRNA-361-3p (miR-361-3p), and NLR family pyrin domain containing 3 (NLRP3).
RESULTS: ISO upregulated hippocampal GABPB1-AS1 in aged rats, correlating with prolonged escape latency, reduced target quadrant time, and elevated pro-inflammatory cytokines. GABPB1-AS1 knockdown reversed these effects. In microglia, ISO increased GABPB1-AS1 expression, M1 polarization markers, and NLRP3 inflammasome activation, while suppressing M2 markers and miR-361-3p. GABPB1-AS1 acted as a competing endogenous RNA (ceRNA) to sponge miR-361-3p, relieving translational inhibition of NLRP3 and activating the NLRP3 inflammasome. GABPB1-AS1 knockdown restored miR-361-3p expression, suppressed NLRP3 inflammasome activation, and attenuated ISO-induced microglial M1 polarization and neuroinflammatory responses.
CONCLUSION: ISO induces POCD via the GABPB1-AS1/miR-361-3p/NLRP3 axis, driving microglial M1 polarization and neuroinflammation. Targeting this axis may offer therapeutic strategies to mitigate anesthesia-related cognitive decline in elderly patients.

Keywords:  Isoflurane; NLRP3 inflammasome; POCD; lncRNA GABPB1-AS1; miR-361-3p

DOI:  https://doi.org/10.1016/j.taap.2025.117571
J Neurochem. 2025 Sep;169(9): e70238

Dysregulation of Neuronal Activity-Dependent Immediate Early Genes in a Mouse Model of Angelman Syndrome.

Bhaskarjyoti Giri, Sagarika Das, Sudipta Jana, Nihar Ranjan Jana.

  Angelman syndrome (AS) is a debilitating neurodevelopmental disorder triggered by impaired function of the maternal UBE3A gene, which codes a protein that functions as a ubiquitin ligase and transcriptional coactivator. Ube3a maternal deficient mice replicate many key behavioral deficits associated with AS; however, the underlying molecular mechanisms remain poorly understood. Using an RT2 Profiler PCR array that summarizes the expression of 84 genes regulating synaptic plasticity, we identified a number of dysregulated genes in the visual cortex of AS mice brains at postnatal day 25 (P25) compared to wild-type animals. In-depth analysis revealed that various immediate early genes (IEGs), like Arc, Egr1-4, and Homer, are dramatically downregulated in the visual cortex of AS mice with regard to wild-type controls at P25. Moreover, the dark rearing of wild-type mice considerably decreased the levels of these IEGs to nearly the same level as those found in AS mice, along with the downregulation of Ube3a. Furthermore, a significant reduction in the expression of these IEGs can also be observed in the hippocampus of AS mice. Finally, we demonstrate that the augmented activity of Hdac2 in the AS mice brain might be connected with the downregulation of various IEGs and other synaptic plasticity-regulating genes. These findings indicate that the deregulated expression of neural activity-dependent IEGs could be linked with abnormal synaptic plasticity and associated behavioral deficits observed in AS mice.

Keywords:  Angelman syndrome; Hdac2; Ube3a; coactivator; immediate early gene

DOI:  https://doi.org/10.1111/jnc.70238
FEMS Yeast Res. 2025 Sep 16. pii: foaf051. [Epub ahead of print]

tDR-quant: a reliable electroporation-based approach for quantifying tRNA-derived fragments binding to ribosomes.

Kamilla Bąkowska-Żywicka, Agata Tyczewska.

  Ribosome-associated non-coding RNAs (rancRNAs), particularly tRNA-derived fragments (tDRs), have emerged as key regulators of translation, especially under stress conditions. In Saccharomyces cerevisiae, tDRs interact with small ribosomal subunits to modulate protein biosynthesis, yet methods to quantitatively assess these interactions have been lacking. Here, we present tDR-quant, a robust technique for in vivo quantification of tDR/ribosome associations using electroporation of radiolabeled tDRs into yeast spheroplasts, followed by polysome profiling and radioactivity detection. We show that tDR interactions with ribosomes are stress- and dose-dependent, primarily associating with the 40S subunit but also with 60S, monosomes, and polysomes under specific conditions. Translation assays revealed that increased tDR levels inhibit protein synthesis without altering polysome profiles. Northern blot and qRT-PCR validated tDR-quant results, confirming its reliability. Stress-specific association patterns suggest that tDRs dynamically regulate translation by interacting with different ribosomal components in response to environmental cues. Importantly, these interactions do not correlate directly with tDR abundance, indicating selective ribosome binding. This study provides the first comprehensive method to quantify tDR-ribosome interactions in vivo and demonstrates that tDRs act as regulatory elements fine-tuning translation during cellular stress in yeast.

Keywords:  Saccharomyces cerevisiae; abiotic stress; protein biosynthesis regulation; ribosome; ribosome-associated noncoding RNAs; tRNA-derived fragments

DOI:  https://doi.org/10.1093/femsyr/foaf051