Abstract A desmoplastic reaction in the solid tumor microenvironment (TME), typically characterized by extracellular matrix (ECM) dysregulation and an immune suppressive milieu, is a key factor contributing to tumor aggression, therapeutic resistance, metastasis and inevitably poor patient prognosis. Cancer-associated fibroblasts (CAFs), in particular myofibroblast-like CAFs (myCAFs), are central players in the development of TME desmoplasia in the most common and aggressive solid cancers such as breast, lung, head & neck and pancreatic. The contribution of myCAFs to standard-of-care treatment resistance and immunotherapy failure has raised their attraction as therapeutic targets. However, myCAF-targeting therapies have not yet proven to be effective for clinical use and is still a largely unexplored area of solid cancer therapeutics. Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of epigenomic and transcriptomic cellular processes and characterized by highly cell-state and disease-specific expression. Targeting myCAF-specific regulatory lncRNAs constitutes a novel therapeutic approach to reduce myCAF-driven detrimental changes in the TME, coupled to an increased susceptibility to combination treatments. Here we identified a novel lncRNA SEAL1 which is restrictively expressed in the pan-cancer myCAF cell state associated with poor patient prognosis and treatment response. Independent analyses of breast, head & neck and pancreatic cancer patient datasets demonstrated SEAL1 as a key component of disease-driving myCAF co-regulatory networks. By antisense oligonucleotide (ASO)-mediated targeting of SEAL1, and of the murine functional analog Seal1, we demonstrated that the myCAF identity was potently reduced in in vitro cellular models. In contrast, ASO- or CRISPRi-mediated targeting of LRRC15/Lrrc15, a SEAL1 downstream marker associated with the myCAF cell identity, had no effect on the disease-driving myCAF cell state. LRRC15 has previously been associated with poor prognosis and an unfavorable response to immunotherapy, being actively pursued as a potential CAF therapeutic target. Moreover, by utilizing a xenograft co-injection in vivo model, SEAL1 targeting in patient-derived myCAFs reduced tumor volume whereas LRRC15 targeting had no effect. Taken together, this study emphasizes that the Regulatory Genome is still largely under explored and that novel discoveries such as SEAL1 may uncover previously unknown biological mechanisms. By leveraging regulatory lncRNAs as potent modifiers of specific disease-states, we conclude that the SEAL1 lncRNA is a major determinant of myCAF pro-tumorigenic transcriptional programs of therapeutic value. Citation Format: Emely Möller, Baroj Abdulkarim, Venkatesh Kancherla, Soumitra Ghosh, Sanne Schrevens, René Dreos, Kristen Gentry, Claire Roberts, Marco Mina, Rudi Micheletti, G. Paolo Dotto, Daniel Blessing, Samir Ounzain. The novel lncRNA SEAL1 - key regulator of the pan-cancer myCAF cell state dictating prognosis ans immunotherapy response - is a promising new therapeutic target for solid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3513.

Introduction: IPF is a progressive pulmonary disease where precision medicine approaches and novel therapeutic targets could greatly improve patient quality of life and outcomes. In silico network analysis of our lncRNA pulmonary atlas integrating IPF patients’ RNA-seq data allowed the mapping of co-expressing lncRNAs and coding genes within gene networks enriched in IPF patient populations. We were able to identify the functionality of therapeutic-relevant lncRNAs specifically overexpressed in myofibroblasts. The knockdown of [PUlmonary Fibrosis-Induced lncRNA] PUFIN1 and PUFIN7 using ASOs corroborated their predicted biological function. Methods: Cell state reprogramming potential of PUFIN lncRNAs was predicted by inferring affected pathways from gene co-expression network analysis of patient bulk IPF RNA-Seq data. In silico proprietary ASO design was performed. ASO efficacy was determined through the modulation of fibrosis, IPF pathogenesis gene signatures and target engagement panels (TEPs) via bulk RNA-Seq and multi-omics single nuclei readouts. Machine learning was used to generate gene signatures to evaluate on-target efficacy and demonstrate therapeutic effects. PUFINs’ regulatory functions were assessed in our Pulmonary Atlas (Cut and Run, snATAC-Seq, and CHiP-Seq). PUFIN1 in vivo on-target efficacy and anti-fibrotic therapeutic effects were studied utilizing a novel humanized transchromasomic murine model and evaluated with RNA-Seq, histology scoring, and an IPF mortality risk signature. Results: PUFIN1 and PUFIN7 were discovered to be in separate co-expression networks, but both are associated with pro-fibrotic genes and IPF-associated pathways (ECM structure, cell-substrate adhesion, Wnt signaling, and wound healing). ASOs targeting PUFINs knock down their respective lncRNAs and TEPs and demonstrate anti-fibrotic on-target effects and cell-state reprogramming (single-cell resolution). We mapped these PUFINs and their dose-responsive genes into an IPF-associated transcription regulatory network (TRN). PUFIN7 is located upstream of a canonical fibrotic gene, and we confirmed via chromatin structure that PUFIN7 is located and expressed in the same TAD as this gene. Novel enhancers were mapped in both PUFINs locus by PRO-seq analysis. A genetic variant associated with IPF patients’ outcomes was identified in PUFIN1 locus in addition to a RUNX1 transcription factor motif at its promoter. PUFIN1 ASO-targeting downregulated internally generated disease-relevant gene signatures and an IPF mortality risk signature, showing strong anti-fibrotic effects and on-target efficacy in vivo. Conclusion: A multi-omics-based precision medicine approach leveraging disease-specific molecular gene signatures was utilized to identify and predict that suppression of novel PUFIN1 and PUFIN7 lncRNAs results in potent anti-fibrotic activity with high potential to improve IPF patient experience and outcomes.

tRNAs play a central role in protein synthesis. Besides this canonical function, they were recently found to generate non-coding RNA fragments (tRFs) regulating different cellular activities. The aim of this study was to assess the involvement of tRFs in the crosstalk between immune cells and beta cells and to investigate their contribution to the development of type 1 diabetes. Global profiling of the tRFs present in pancreatic islets of 4- and 8-week-old NOD mice and in extracellular vesicles released by activated CD4+ T lymphocytes was performed by small RNA-seq. Changes in the level of specific fragments were confirmed by quantitative PCR. The transfer of tRFs from immune cells to beta cells occurring during insulitis was assessed using an RNA-tagging approach. The functional role of tRFs increasing in beta cells during the initial phases of type 1 diabetes was determined by overexpressing them in dissociated islet cells and by determining the impact on gene expression and beta cell apoptosis. We found that the tRF pool was altered in the islets of NOD mice during the initial phases of type 1 diabetes. Part of these changes were triggered by prolonged exposure of beta cells to proinflammatory cytokines (IL-1β, TNF-α and IFN-γ) while others resulted from the delivery of tRFs produced by CD4+ T lymphocytes infiltrating the islets. Indeed, we identified several tRFs that were enriched in extracellular vesicles from CD4+/CD25− T cells and were transferred to beta cells upon adoptive transfer of these immune cells in NOD.SCID mice. The tRFs delivered to beta cells during the autoimmune reaction triggered gene expression changes that affected the immune regulatory capacity of insulin-secreting cells and rendered the cells more prone to apoptosis. Our data point to tRFs as novel players in the crosstalk between the immune system and insulin-secreting cells and suggest a potential involvement of this novel class of non-coding RNAs in type 1 diabetes pathogenesis. Sequences are available from the Gene Expression Omnibus (GEO) with accession numbers GSE242568 and GSE256343.

OBJECTIVE:DNAJC3, also known as P58IPK, is an Hsp40 family member that interacts with and inhibits PKR-like ER-localized eIF2α kinase (PERK). Dnajc3 deficiency in mice causes pancreatic β-cell loss and diabetes. Loss-of-function mutations in DNAJC3 cause early-onset diabetes and multisystemic neurodegeneration. The aim of our study was to investigate the genetic cause of early-onset syndromic diabetes in two unrelated patients, and elucidate the mechanisms of β-cell failure in this syndrome.METHODS:Whole exome sequencing was performed and identified variants were confirmed by Sanger sequencing. DNAJC3 was silenced by RNAi in INS-1E cells, primary rat β-cells, human islets, and induced pluripotent stem cell-derived β-cells. β-cell function and apoptosis were assessed, and potential mediators of apoptosis examined.RESULTS:The two patients presented with juvenile-onset diabetes, short stature, hypothyroidism, neurodegeneration, facial dysmorphism, hypoacusis, microcephaly and skeletal bone deformities. They were heterozygous compound and homozygous for novel loss-of-function mutations in DNAJC3. DNAJC3 silencing did not impair insulin content or secretion. Instead, the knockdown induced rat and human β-cell apoptosis and further sensitized cells to endoplasmic reticulum stress, triggering mitochondrial apoptosis via the pro-apoptototic Bcl-2 proteins BIM and PUMA.CONCLUSIONS:This report confirms previously described features and expands the clinical spectrum of syndromic DNAJC3 diabetes, one of the five monogenic forms of diabetes pertaining to the PERK pathway of the endoplasmic reticulum stress response. DNAJC3 deficiency may lead to β-cell loss through BIM- and PUMA-dependent activation of the mitochondrial pathway of apoptosis.

Long non-coding RNAs (lncRNAs) contribute to diverse cellular functions and the dysregulation of their expression or function can contribute to diseases, including diabetes. The contributions of lncRNAs to β-cell development, function and survival has been extensively studied in vitro . However, very little is currently known on the in vivo roles of lncRNAs in the regulation of glucose and insulin homeostasis. Here we investigated the impact of loss-of-function in mice of the lncRNA A830019P07Rik, hereafter P07Rik, which was previously reported to be associated with reduced plasma insulin levels. Compared with wild-type littermates, male and female P07Rik mutant mice did not show any defect in glycaemia and plasma insulin levels in both fed and fasted state. Furthermore, P07Rik mutant mice displayed similar glucose and insulin levels in response to an intra-peritoneal glucose tolerance test. Ex vivo , islets from mutant P07Rik released similar amount of insulin in response to increased glucose concentration as wildtype littermates. In contrast with previous reports, our characterization of P07Rik mouse mutants revealed that loss of function of this lncRNA does not affect glucose and insulin homeostasis in mice.

Almost a third of genes we predict to be miRNA targets lack sequence complementarity to the miRNA seed region (noncanonical targets). These noncanonical targets have higher complementary with the miRNA 3’ end. The impact of miRNAs on the levels of their canonical or noncanonical targets is identical supporting the relevance of this poorly explored mechanism of targeting.

Cell cycle progression is controlled by the interplay of established cell cycle regulators. Changes in these regulators' activity underpin differences in cell cycle kinetics between cell types. We investigated whether long intergenic noncoding RNAs (lincRNAs) contribute to embryonic stem cell cycle adaptations. Using single-cell RNA sequencing data for mouse embryonic stem cells (mESCs) staged as G1, S, or G2/M we found differentially expressed lincRNAs are enriched among cell cycle-regulated genes. These lincRNAs (CC-lincRNAs) are co-expressed with genes involved in cell cycle regulation. We tested the impact of two CC-lincRNA candidates and show using CRISPR activation that increasing their expression is associated with deregulated cell cycle progression. Interestingly, CC-lincRNAs are often differentially expressed between G1 and S, their promoters are enriched in pluripotency transcription factor (TF) binding sites, and their transcripts are frequently co-regulated with genes involved in the maintenance of pluripotency, suggesting a contribution of CC-lincRNAs to mESC cell cycle adaptations.

Posttranscriptional repression by microRNA (miRNA) occurs through transcript destabilization or translation inhibition. Whereas RNA degradation explains most miRNA-dependent repression, transcript decay occurs co-translationally, raising questions regarding the requirement of target translation to miRNA-dependent transcript destabilization. To assess the contribution of translation to miRNA-mediated RNA destabilization, we decoupled these two molecular processes by dissecting the impact of miRNA loss of function on cytosolic long noncoding RNAs (lncRNAs). We show, that despite interacting with miRNA loaded RNA-induced silencing complex (miRISC), the steady state abundance and degradation rates of these endogenously expressed non-translated transcripts are minimally impacted by miRNA loss. To validate the requirement of translation for miRNA-dependent decay, we fused a miRISC bound lncRNA, whose levels are unaffected by miRNAs, to the 3’end of a protein-coding gene reporter and show that this results in its miRNA-dependent transcript destabilization. Furthermore, analysis of the few lncRNAs whose levels are regulated by miRNAs revealed these tend to associate with translating ribosomes and are likely misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. Our analyses reveal the strict requirement of translation for miRNA-dependent transcript destabilization and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs.

Supplementary data of paper entitled: "DNAJC3 deficiency induces mitochondrial β-cell apoptosis and causes young-onset diabetes and neurodegeneration". The file entitled "supplementary material" contains tables 1-4 and figure legends for supplementary figures 1-4. Supplementary figures 1-4 are provided as separate files.

Friedreich ataxia is an autosomal recessive neurodegenerative disease associated with a high diabetes prevalence. No treatment is available to prevent or delay disease progression. Friedreich ataxia is caused by intronic GAA trinucleotide repeat expansions in the frataxin-encoding FXN gene that reduce frataxin expression, impair iron-sulfur cluster biogenesis, cause oxidative stress, and result in mitochondrial dysfunction and apoptosis. Here we examined the metabolic, neuroprotective, and frataxin-inducing effects of glucagon-like peptide-1 (GLP-1) analogs in in vivo and in vitro models and in patients with Friedreich ataxia. The GLP-1 analog exenatide improved glucose homeostasis of frataxin-deficient mice through enhanced insulin content and secretion in pancreatic β cells. Exenatide induced frataxin and iron-sulfur cluster-containing proteins in β cells and brain and was protective to sensory neurons in dorsal root ganglia. GLP-1 analogs also induced frataxin expression, reduced oxidative stress, and improved mitochondrial function in Friedreich ataxia patients' induced pluripotent stem cell-derived β cells and sensory neurons. The frataxin-inducing effect of exenatide was confirmed in a pilot trial in Friedreich ataxia patients, showing modest frataxin induction in platelets over a 5-week treatment course. Taken together, GLP-1 analogs improve mitochondrial function in frataxin-deficient cells and induce frataxin expression. Our findings identify incretin receptors as a therapeutic target in Friedreich ataxia.

Deficient as well as excessive/prolonged endoplasmic reticulum (ER) stress signaling can lead to pancreatic β cell failure and the development of diabetes. Saturated free fatty acids (FFAs) such as palmitate induce lipotoxic ER stress in pancreatic β cells. One of the main ER stress response pathways is under the control of the protein kinase R-like endoplasmic reticulum kinase (PERK), leading to phosphorylation of the eukaryotic translation initiation factor 2 (eIF2α). The antihypertensive drug guanabenz has been shown to inhibit eIF2α dephosphorylation and protect cells from ER stress. Here we examined whether guanabenz protects pancreatic β cells from lipotoxicity. Guanabenz induced β cell dysfunction in vitro and in vivo in rodents and led to impaired glucose tolerance. The drug significantly potentiated FFA-induced cell death in clonal rat β cells and in rat and human islets. Guanabenz enhanced FFA-induced eIF2α phosphorylation and expression of the downstream proapoptotic gene C/EBP homologous protein (CHOP), which mediated the sensitization to lipotoxicity. Thus, guanabenz does not protect β cells from ER stress; instead, it potentiates lipotoxic ER stress through PERK/eIF2α/CHOP signaling. These data demonstrate the crucial importance of the tight regulation of eIF2α phosphorylation for the normal function and survival of pancreatic β cells.

The prevalence of type 2 diabetes is increasing dramatically worldwide. Type 2 diabetes is a major health and socio-economic burden. Genetic predisposition and the obesity epidemic, due to sedentary life style and high caloric food intake, are associated with development of type 2 diabetes. Circulating free fatty acids (FFAs), in particular saturated FFAs, are linked with insulin resistance and β cell dysfunction. Following this background we performed RNA sequencing of human pancreatic islets treated with the saturated FFA palmitate to acquire a global image of the islet response to this insult. We identified several stress pathways induced by palmitate with a major induction of the endoplasmic reticulum (ER) stress response. The ER stress response, in particular the PKR-like ER kinase (PERK) branch, has been shown to be induced by saturated FFA. It leads to increased β cell apoptosis both in fluorescence activated cell sorter (FACS) purified rat β cells and human islets. We further clarified the role of this pathway by studying the involvement of the constitutive repressor of eIF2α phosphorylation (CReP) in a monogenic form of diabetes. CReP is a repressor of eukaryotic translation initiation factor 2α (eIF2α) phosphorylation. A direct target of PERK, eIF2α is involved in translational attenuation and induction of apoptosis. We have shown that CReP loss-of-function leads to a new syndrome of young onset diabetes, intellectual disability and microcephaly. The identified R658C mutation abrogated CReP activity leading to increased eIF2α phosphorylation and β cell apoptosis. To further demonstrate the importance of eIF2α dysregulation in β cell demise, we used guanabenz, a chemical inhibitor of growth arrest DNA damage inducible 34 (GADD34). GADD34 is an ER stress-induced repressor of eIF2α phosphorylation. Guanabenz potentiated FFA-mediated ER stress and apoptosis in clonal and primary rat β cells and in human islets through the activation of CCAAT/enhancer binding protein homologous protein (CHOP), downstream of eIF2α. Guanabenz administration in mice impaired glucose tolerance and led to β cell dysfunction. In ex vivo experiments guanabenz also induced β cell dysfunction in mouse and rat islets.In conclusion our data demonstrate that the dysregulation of signaling in the PERK/eIF2α pathway is crucial for β cell demise. Together with previously reported monogenic diabetes caused by loss-of-function mutations in PERK in man and the eIF2αS51A mutation in mice, our findings suggest that a narrow regulation of PERK/eIF2α signaling is central for proper β cell function and survival.

Dysregulated endoplasmic reticulum stress and phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) are associated with pancreatic β-cell failure and diabetes. Here, we report the first homozygous mutation in the PPP1R15B gene (also known as constitutive repressor of eIF2α phosphorylation [CReP]) encoding the regulatory subunit of an eIF2α-specific phosphatase in two siblings affected by a novel syndrome of diabetes of youth with short stature, intellectual disability, and microcephaly. The R658C mutation in PPP1R15B affects a conserved amino acid within the domain important for protein phosphatase 1 (PP1) binding. The R658C mutation decreases PP1 binding and eIF2α dephosphorylation and results in β-cell apoptosis. Our findings support the concept that dysregulated eIF2α phosphorylation, whether decreased by mutation of the kinase (EIF2AK3) in Wolcott-Rallison syndrome or increased by mutation of the phosphatase (PPP1R15B), is deleterious to β-cells and other secretory tissues, resulting in diabetes associated with multisystem abnormalities.

Friedreich's ataxia (FRDA) is a neurodegenerative disorder associated with cardiomyopathy and diabetes. Effective therapies for FRDA are an urgent unmet need; there are currently no options to prevent or treat this orphan disease. FRDA is caused by reduced expression of the mitochondrial protein frataxin. We have previously demonstrated that pancreatic β-cell dysfunction and death cause diabetes in FRDA. This is secondary to mitochondrial dysfunction and apoptosis but the underlying molecular mechanisms are not known. Here we show that β-cell demise in frataxin deficiency is the consequence of oxidative stress-mediated activation of the intrinsic pathway of apoptosis. The pro-apoptotic Bcl-2 family members Bad, DP5 and Bim are the key mediators of frataxin deficiency-induced β-cell death. Importantly, the intrinsic pathway of apoptosis is also activated in FRDA patients' induced pluripotent stem cell-derived neurons. Interestingly, cAMP induction normalizes mitochondrial oxidative status and fully prevents activation of the intrinsic pathway of apoptosis in frataxin-deficient β-cells and neurons. This preclinical study suggests that incretin analogs hold potential to prevent/delay both diabetes and neurodegeneration in FRDA.

We describe a new syndrome of young onset diabetes, short stature and microcephaly with intellectual disability in a large consanguineous family with three affected children. Linkage analysis and whole exome sequencing were used to identify the causal nonsense mutation, which changed an arginine codon into a stop at position 127 of the tRNA methyltransferase homolog gene TRMT10A (also called RG9MTD2). TRMT10A mRNA and protein were absent in lymphoblasts from the affected siblings. TRMT10A is ubiquitously expressed but enriched in brain and pancreatic islets, consistent with the tissues affected in this syndrome. In situ hybridization studies showed that TRMT10A is expressed in human embryonic and fetal brain. TRMT10A is the mammalian ortholog of S. cerevisiae TRM10, previously shown to catalyze the methylation of guanine 9 (m(1)G9) in several tRNAs. Consistent with this putative function, in silico topology prediction indicated that TRMT10A has predominant nuclear localization, which we experimentally confirmed by immunofluorescence and confocal microscopy. TRMT10A localizes to the nucleolus of β- and non-β-cells, where tRNA modifications occur. TRMT10A silencing induces rat and human β-cell apoptosis. Taken together, we propose that TRMT10A deficiency negatively affects β-cell mass and the pool of neurons in the developing brain. This is the first study describing the impact of TRMT10A deficiency in mammals, highlighting a role in the pathogenesis of microcephaly and early onset diabetes. In light of the recent report that the type 2 diabetes candidate gene CDKAL1 is a tRNA methylthiotransferase, the findings in this family suggest broader relevance of tRNA methyltransferases in the pathogenesis of type 2 diabetes.