Once regarded as transcriptional noise, long non-coding RNAs (lncRNAs) are now recognized as pivotal regulators of inflammation and host immune responses. In this context, comprehensive profiling of lncRNAs is especially relevant in heterogeneous disorders like asthma, where biologically distinct endotypes often converge into similar clinical presentations. Deploying lncRNAs as endotype-specific biomarkers offers a promising strategy to address heterogeneity in asthma, refine patient stratification, and guide the development of targeted therapies beyond conventional phenotype-based disease management. This comprehensive review outlines the multifaceted roles of lncRNAs across all stages of asthma pathogenesis, highlighting their function as molecular conduits linking environmental triggers to airway inflammation, driving hyperresponsiveness, and promoting persistent tissue remodelling. In addition, it discusses systematic discovery-to-validation pipelines for asthma-associated lncRNAs and finally addressing current limitations and their emerging potential as diagnostic and therapeutic candidates.

Abstract [Background and Purpose] In the tumor environment, T cells chronically express PD-1, and its interaction with PD-L1 on tumor cells results in decreased T cell cytokine secretion and proliferation. Exon2 of PD-1 encodes the PD-L1-binding domain. There have been few studies targeting RNA rather than the protein of PD-1 to upregulate lymphocyte antitumor immunity, especially the pre-mRNA region involved in Exon 2 splicing. We have recently reported that the region of PD-1 pre-mRNA was identified using the CRISPR/dCas13 system and a human CD8+ T cell line, and cytokine secretion capacity was maintained in the RNA region-targeted CD8+ T cells (PMID: 40920775). These findings were revealed in the presence of the idea that disrupting the interaction of the Exon2 splice cis-trans element on PD-1 pre-mRNA prevents the expression of the extracellular domain of PD-1, allowing lymphocytes to exert their inherent. In this presentation, we report on the effects on lymphocytes using a newly designed antisense oligonucleotides (ASO) derived from the identified pre-mRNA region of PD-1. [Materials and Methods] The designed PD-1 ASO sequences were based on the concept of the screening workflow of CLOVERNA Inc., and the ASO was provided by CLOVERNA Inc.. The ASO targeting PD-1 pre-mRNA was transduced into the human CD8+ T cell line, EBT-8 cells. The cells were maintained in GIT medium supplemented with recombinant human IL-2. Five days after transfection, the cells were harvested, and cell surface PD-1 expression was measured by flow cytometry. [Results] The new, unpublished data showed a decrease in the percentages of PD-1-positive cells of CD8+ T cells by the transfection with the ASO targeting PD-1 pre-mRNA. [Conclusion] This study revealed that the designed ASOs derived from the specific sequences of pre-mRNA identified using CRISPR/dCas13 contribute to suppressing PD-1 expression on the cell surface of human CD8+ T cells. [Future Plans] To assess tumor clearance capacity, we are in the preparation stage to begin in vitro cell-killing assays or in vivo PDX model experiments. Citation Format: Yuto Tan, Naoko Kumagai-Takei, Shuya Yano, Yurika Shimizu, Akira Yamasaki, Mari Hara-Yamamoto, Shigeru Mitani, Tatsuo Ito. Effects of antisense oligonucleotides targeting PD-1 pre-mRNA identified by DIRAC-dCas13-based screening on PD-1-positive lymphocytes [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 4304.

The concept of immune reconstitution inflammatory syndrome (IRIS) has recently been applied to patients with non-HIV infection with immune fluctuations. However, quantitative criteria to diagnose non-HIV IRIS have not been established. Similarly, immune-related adverse events (irAEs) caused by immune checkpoint inhibitors (ICIs) are also caused by immune fluctuations. No study has directly compared the immunological indicators of non-HIV IRIS and irAEs. Thus, we investigated whether irAEs can be included in non-HIV IRIS. We aimed to search for diagnostic biomarkers for non-HIV IRIS and to compare the immunopathogenesis of non-HIV IRIS and irAEs based on immunological indicators. We selected drug-induced hypersensitivity syndrome/drug reaction with eosinophilia and systemic symptoms (DIHS/DRESS) and dipeptidyl peptidase-4 inhibitor-associated bullous pemphigoid (DPP4i-BP) as underlying diseases of non-HIV IRIS. Blood cell counts, cytokines or chemokines, and herpesvirus-derived DNA in saliva were quantified and compared between IRIS/irAE-positive and -negative as well as non-HIV IRIS and irAEs groups. The DPP4i-BP group had a shorter incubation time to IRIS onset than the DIHS/DRESS group; the irAE group had a longer incubation time than the DIHS/DRESS group. A higher neutrophil-to-lymphocyte ratio and serum interferon gamma inducible protein 10 levels could be potential biomarkers of IRIS and irAEs onset; however, no useful cut-off values for diagnosis were indicated. Meanwhile, the transition of  regulatory T cells (Tregs) from the baseline to the onset of IRIS or irAEs differed between IRIS in DIHS/DRESS and irAEs. Only the DIHS/DRESS group showed an increase of Epstein-Bar virus (EBV) (p < 0.0001) and human herpesvirus 6 (p < 0.05) positivity in saliva at the onset of IRIS compared to that at baseline. Although non-HIV IRIS and irAEs have a small number of common immunological indicators, the dynamics of Tregs, cytokines, or chemokines and positivity of herpesvirus-derived DNA in saliva differ, suggesting that non-HIV IRIS and irAEs should remain as separate entities.

Objective The incidence of cytomegalovirus (CMV) infection or disease in patients with rheumatic musculoskeletal diseases is reported to be 2%. Over half received pulsed methylprednisolone, and some experienced a fatal outcome. In this study, we aimed to explore predictive and diagnostic biomarkers for CMV infection or disease in such patients and compare them with biomarkers reported for immune reconstitution inflammatory syndrome (IRIS) in people with HIV. Methods In this multicentre prospective cohort study, we collected blood and saliva samples from 38 patients with rheumatic musculoskeletal disease before initiating high-dose glucocorticoid therapy, at the start of glucocorticoid tapering, at the onset of CMV infection, and 4 weeks later. Peripheral blood cell counts, flow cytometry for CD4, CD8, and Tregs, ELISA for cytokine/chemokine panels, and measurements of herpesvirus-derived DNA in saliva were performed. Results Lower white blood cells, CD4(+) cells, IL-6, and interferon-gamma levels and higher interferon-inducible protein (IP)-10 and granulysin levels at baseline could be predictive biomarkers for CMV infection. Furthermore, lower platelet counts and higher IL-10, IP-10, granulysin, TNF-a, IL-1ra, and IL-15 levels at the onset of CMV infection were found as diagnostic biomarkers for CMV infection. EBV, human herpes virus (HHV)-6, and HHV-7 DNA levels in the saliva were significantly increased after high-dose glucocorticoids, regardless of CMV infection. Conclusion We identified predictive and diagnostic biomarkers for CMV infection after high-dose glucocorticoid therapy for rheumatic musculoskeletal diseases. While similarities with IRIS biomarkers in patients living with HIV were observed, complete agreement could not be confirmed.

T-cell therapies have proven to be a promising treatment option for cancer patients in recent years, especially in the case of chimeric antigen receptor (CAR)-T cell therapy. However, the therapy is associated with insufficient activation of T cells or poor persistence in the patient's body, which leads to incomplete elimination of cancer cells, recurrence, and genotoxicity. By extracting the splice element of PD-1 pre-mRNA using biology based on CRISPR/dCas13 in this study, our ultimate goal is to overcome the above-mentioned challenges in the future. PD-1 plays an important role in controlling T cell responses and is expressed at the cell surface of T cells following activation. The receptor PD-1 interferes with T cell receptor (TCR) signaling following interaction with PD-L1. The outcome of stimulation via PD-1 leads to decreases in cytokine secretion and cell proliferation. We extracted the RNA region of PD-1 pre-mRNA using CD8+T cell lines and examined the effect of targeting the Exon2 splice cis-element on the production of cytokines in the present study. In particular, the production of IFN-γ, TNF-α, GM-CSF was lower in RNA-targeted cells than in non-targeted cells, but the cytokine secretion capacity and cell proliferation were maintained in RNA-targeted cells. These results suggested that the use of the RNA editing technology, CRISPR/dCas13 strategy offers a novel approach to mitigate genotoxicity in lymphocytes with cytokine production and cell proliferation.

BRCA1-associated protein 1 (BAP1) has emerged as a major tumor suppressor gene in diverse cancer types, notably in malignant pleural mesothelioma (DPM), and has also been identified as a germline cancer predisposition gene for DPM and other select cancers. However, its role in the response to DNA damage has remained unclear. Here, we show that BAP1 inactivation is associated with increased DNA damage both in Met-5A human mesothelial cells and human DPM cell lines. Through proteomic analyses, we identified PRKDC as an interaction partner of BAP1 protein complexes in DPM cells and 293 T human embryonic kidney cells. PRKDC encodes the catalytic subunit of DNA protein kinase (DNA-PKcs) which functions in the nonhomologous end-joining (NHEJ) pathway of DNA repair. Double-stranded DNA damage resulted in prominent nuclear expression of BAP1 in DPM cells and phosphorylation of BAP1 at serine 395. A plasmid-based NHEJ assay confirmed a significant effect of BAP1 knockdown on cellular NHEJ activity. Combination treatment with X-ray irradiation and gemcitabine (as a radiosensitizer) strongly suppressed the growth of BAP1-deficient cells. Our results suggest reciprocal positive interactions between BAP1 and DNA-PKcs, based on phosphorylation of BAP1 by the latter and deubiquitination of DNA-PKcs by BAP1. Thus, functional interaction of BAP1 with DNA-PKcs supports a role for BAP1 in NHEJ DNA repair and may provide the basis for new therapeutic strategies and new insights into its role as a tumor suppressor.

We herein elucidate the function of SARS-CoV-2derived 5'UTR in the human cells. 5'UTR bound host cellular RNAs were immunoprecipitated by gRNA-dCas13 (targeting luciferase RNA fused to SARS-CoV-2 5'UTR) in HEK293T and A549 cells. The 5'UTR bound RNA extractions were predominantly enriched for regulating lipid metabolism. Overexpression of SARS-CoV-2 5'UTR RNA altered the expression of factors involved in the process of the human Mevalonate pathway. In addition, we found that HMG-CoA reductase inhibitors were shown to suppress SARS-CoV-2 5'UTR-mediated translation activities. In conclusion, we deduce the array of host RNAs interacting with SARS-CoV-2 5'UTR that drives SARS-CoV-2 translation and influences host metabolic pathways.

PDF file - 308K, Complete list of target sequences for NanoString probes

PDF file - 76K, Examples of negative results with the NanoString assay for kinase fusions.

PDF file - 32K, Clinicopathological characteristics of study cohort

Silicosis (SIL) is a well-known typical lung fibrosis categorized as pneumoconiosis. Patients suffer from dyspnea, shortness of breath, cough and sputum, which can develop into respiratory failure. The main complications of silicosis are pulmonary diseases. However, SIL is often complicated with various autoimmune diseases such as rheumatoid arthritis, systemic sclerosis, and anti-neutrophil cytoplasmic antibody (ANCA)-related vasculitis. We have been investigating the cellular and molecular alterations of immune cells derived from SIL as well as silica particles in vitro with particular emphasis on the effects on human immune cells. Results showed continuous activation and long survival of CD4 + responder T (Tresp) cells. Additionally, CD4 + 25 + regulatory T (Treg) cells were lost by earlier apoptosis since CD95/Fas death receptor was overexpressed as a result of chronic activation induced by silica particles. The imbalance between Tresp and Treg cells may be the basis for the alteration of dysregulation in autoimmunity. Then, we developed an autoimmune score (AIS) by multiple regression analysis using 19 immune factors in plasma of 19 healthy volunteers (HV) and 20 SIL patients who did not show any autoimmune clinical symptoms. The formula generated is [AIS = (0.119 × sFas) + (1.063 × IgG4) + (0.059 × IL-6) + 0.063]. Using this formula, all values from the 19 HV and 20 SIL patients ranged between 0.90 and 2.71. If we set the cut off value as 1.3935, HV and SIL patients were clearly divided, with only one false-negative SIL patient. We could use this formula for early preclinical detection of autoimmune diseases among various populations predominantly comprising relatively young and female subjects. There are presently some limitations to this formula, such as age differences between two groups and the use of limited factors. Thus, an altered version of this formula could be proposed to be used in the fields of preventive medicine.

Feature Editor's Introduction––The recent decade has witnessed unprecedented research activity in the field of myocardial regeneration with particular enthusiasm displayed around cardiac stem cell therapy. This enthusiastic research resulted in a number of clinical studies, in which cardiac progenitor cells were delivered to the myocardium during heart surgery in children and adults, demonstrating improvement in heart function. The stem cell therapy appeared to be of great promise in children, particularly neonates, who are likely to have higher regenerative potential.

Background Asbestos fibers possess tumorigenicity and are thought to cause mesothelioma. We have previously reported that exposure to asbestos fibers causes a reduction in antitumor immunity. Asbestos exposure in the mixed lymphocyte reaction (MLR) showed suppressed induction of cytotoxic T lymphocytes (CTLs), accompanied by a decrease in proliferation of CD8 + T cells. Recently, we reported that asbestos-induced suppression of CTL induction is not due to insufficient levels of interleukin-2 (IL-2). In this study, we continue to investigate the mechanism responsible for the effect of asbestos fibers on the differentiation of CTLs and focus on interleukin-15 (IL-15) which is known to be a regulator of T lymphocyte proliferation. Methods For MLR, human peripheral blood mononuclear cells (PBMCs) were cultured with irradiated allogenic PBMCs upon exposure to chrysotile B asbestos at 5 μg/ml for 7 days. After 2 days of culture, IL-15 was added at 1 ng/ml. After 7 days of MLR, PBMCs were collected and analyzed for phenotypic and functional markers of CD8 + T cells with fluorescence-labeled anti-CD3, anti-CD8, anti-CD45RA, anti-CD45RO, anti-CD25, and anti-granzyme B antibodies using flow cytometry. To examine the effect of IL-15 on the expression level of intracellular granzyme B in proliferating and non-proliferating CD8 + lymphocytes, PBMCs were stained using carboxyfluorescein diacetate succinimidyl ester (CFSE) and then washed and used for the MLR. Results IL-15 addition partially reversed the decrease in CD3 + CD8 + cell numbers and facilitated complete recovery of granzyme B + cell percentages. IL-15 completely reversed the asbestos-induced decrease in percentage of granzyme B + cells in both non-proliferating CFSE-positive and proliferating CFSE-negative CD8 + cells. The asbestos-induced decrease in the percentage of CD25 + and CD45RO + cells in CD8 + lymphocytes was not reversed by IL-15. Conclusion These findings indicate that CTLs induced upon exposure to asbestos possess dysfunctional machinery that can be partly compensated by IL-15 supplementation, and that IL-15 is more effective in the recovery of proliferation and granzyme B levels from asbestos-induced suppression of CTL induction compared with IL-2.

The effects of asbestos on immunocompetent cells have been investigated. In particular, attention was paid to regulatory T cell function, which was observed using the HTLV-1 immortalized human polyclonal T cell line MT-2. Exposure to asbestos (approximately more than 25 mu g/mL for 1-3 day) induced apoptosis, and we observed an increase in regulatory T cell function and acceleration of the cell cycle with continuous exposure to low concentrations of asbestos (5-10 mu g/mL for more than eight months). Furthermore, cDNA microarray analysis in this study revealed that expression of matrix metalloproteinase-7 (MMP-7) was markedly higher in exposed sublines compared to original MT-2 cells. It was determined that MMP-7 had no effect on Treg function, as determined by examination of sublines and by addition of recombinant MMP-7 and neutralizing antibodies or inhibitors of MMP-7. However, when examining melting of the extracellular matrix (an MMP-7-mediated event) or the extent to which the MT-2 parent strain or long-term exposed subline cells pass through a fibronectin-coated filter, more filter passes were observed for the subline. These results suggest that the effect of asbestos fibers on Treg cells results in excessive migration of the tumor microenvironment through hypersecretion of MMP-7 together with an increase in suppressive function and enhancement of cell cycle progression. Therefore, one possible way to prevent the development of asbestos-induced cancer is to reduce the function (including MMP-7 production) or amount of Treg cells by physiologically active substances or food ingredients. Alternatively, it may be possible to invoke immune checkpoint treatments when carcinogenesis occurs.

Exposure of human immune cells to asbestos causes a reduction in antitumor immunity. The present study aimed to investigate the recovery of reduced antitumor immunity by several ingredients taken as supplements or foods, including trehalose (Treh) and glycosylated hesperidin (gHesp). Peripheral blood CD4+ cells were stimulated with IL‑2, anti‑CD3 and anti‑CD28 antibodies for 3 days, followed by further stimulation with IL‑2 for 7 days. Subsequently, cells were stimulated with IL‑2 for an additional 28 days. During the 28 days, cells were cultured in the absence or presence of 50 µg/ml chrysotile asbestos fibers. In addition, cells were treated with 10 mM Treh or 10 µM gHesp. Following culture for 28 days, reverse transcription‑quantitative PCR was performed to assess the expression levels of transcription factors, cytokines and specific genes, including matrix metalloproteinase‑7 (MMP‑7), nicotinamide nucleotide transhydrogenase (NNT) and C‑X‑C motif chemokine receptor 3, in unstimulated cells (fresh) and cells stimulated with PMA and ionomycin (stimuli). The results demonstrated that compared with the control group, chrysotile‑exposure induced alterations in MMP‑7, NNT and IL‑17A expression levels were not observed in the ‘Treh’ and ‘gHesp’ groups in stimulated cells. The results suggested that Treh and gHesp may reverse asbestos exposure‑induced reduced antitumor immunity in T helper cells. However, further investigation is required to confirm the efficacy of future trials involving the use of these compounds with high‑risk human populations exposed to asbestos, such as workers involved in asbestos‑handling activities.

The immune system functions to eliminate abnormal cells that may arise for a variety of reasons. This process can help prevent tumor formation and is referred to as anti-tumor immunity. Inhaled asbestos fibers can accumulate in the non-lymphoid organ of the lungs as well as draining lymph nodes, exposing immune cells to the inhaled asbestos and thereby triggering potential immunological effects. On the basis of that idea, we have been investigating various kinds of asbestos exposure-mediated functional alterations in natural killer (NK), CD4+ T helper (Th), CD8+ cytotoxic T lymphocyte (CTL), and macrophage cells by in vitro experiments. The findings obtained indicate that exposure to asbestos causes decreased cytotoxicity of NK and CTL cells and decreased expression of cell surface activating receptors (NKp46, NKG2D), intracellular perforin levels, and IFN- γ production. Furthermore, an enhanced immune-suppressive role of Th (regulatory T (Treg)) cell function results, with increases in cell surface CTLA-4, and increased production of IL-10 and TGF-β cells as well as fibrogenic/immune-suppressive macrophages with high and lasting production of TGF-β. Interestingly, patients with malignant mesothelioma also show similar characteristics with respect to findings relating to peripheral blood mononuclear cells. Taken together, those data suggest that asbestos fibers elicit immune-suppressive potential, which might contribute to immune escape of abnormal mesothelial cells arising transiently, and promote the development of malignant mesothelioma in people exposed to asbestos. Continued investigations of these events may facilitate the development of early intervention strategies from an immunological perspective to mitigate the development of mesothelioma.

Asbestos exposure causes malignant tumors such as lung cancer and malignant mesothelioma. The effects of asbestos fibers on immunocompetent cells, however, have not been well studied. Asbestos physically comprises a fibrous substance, which differs from silica particles which are a particulate substance, although chemically it is a mineral silicate. Since silicosis patients previously exposed to silica particles often suffer from lung and autoimmune diseases, it is clear that silica exposure impairs immune tolerance. Similarly, asbestos may alter the immune system in asbestos-exposed individuals. Given that malignant tumors can result following exposure to asbestos, the attenuation of anti-tumor immunity in cases of asbestos exposure is an important area of investigation. We observed the effect of asbestos fibers on T lymphocytes, such as CD8+ cytotoxic T lymphocytes (CTLs), CD4+ helper T (Th), and regulatory T (Treg) cells, and showed that anti-tumor immunity was attenuated, as demonstrated in a system that stimulates fresh cells isolated from peripheral blood in vitro and a system that is continuously exposed to a cell line. In this manuscript, we introduce the experiments and results of studies on CTLs, as well as Th and Treg cells, and discuss how future changes in immunocompetent cells induced by asbestos fibers can be clinically linked.

Cas13 endonuclease activity depends on the RNA local secondary structure with strong preference for single-stranded (SS) regions. Hence, it becomes indispensable to identify the SS regions for effective Cas13 mediated RNA knockdown. We herein present rational gRNA design by integrating experimental structure-seq data and predicted structural models. Utilizing structure-seq data for XIST transcript, we observed that gRNAs targeting the SS regions significantly induce transcript knockdown and cleavage than those targeting double-stranded (DS) regions. Further, we identified the "central seed region" in the gRNA that upon targeting the SS regions efficiently facilitates Cas13 mediated cleavage. In our following pursuits, we considered the scenario wherein experimental structure-seq data is not available, hence we used SS18-SSX2 fusion transcript indicated in synovial sarcomas and computationally predicted its structure. We observed that gRNAs targeting the SS regions predicted from the structure, efficiently induced necrosis compared to gRNAs that target the DS regions. In conclusion, for the effective RNA knockdown, the Cas13 mediated targeting strategy presented herein emphasizes the designing of gRNAs specifically targeting SS regions by utilizing structural information. Further, this strategy, in turn, can be anticipated to narrow the search space for gRNA design (by exclusively targeting SS regions) especially when lncRNAs are the targets.

Paired related homeobox 1 (PRRX1) is a marker of limb bud mesenchymal cells, and deficiency of p53 or Rb in Prrx1-positive cells induces osteosarcoma in several mouse models. However, the regulatory roles of PRRX1 in human osteosarcoma have not been defined. In this study, we performed PRRX1 immunostaining on 35 human osteosarcoma specimens to assess the correlation between PRRX1 level and overall survival. In patients with osteosarcoma, the expression level of PRRX1 positively correlated with poor prognosis or the ratio of lung metastasis. Additionally, we found PRRX1 expression on in 143B cells, a human osteosarcoma line with a high metastatic capacity. Downregulation of PRRX1 not only suppressed proliferation and invasion but also increased the sensitivity to cisplatin and doxorubicin. When 143B cells were subcutaneously transplanted into nude mice, PRRX1 knockdown decreased tumor sizes and rates of lung metastasis. Interestingly, forskolin, a chemical compound identified by Connectivity Map analysis using RNA expression signatures during PRRX1 knockdown, decreased tumor proliferation and cell migration to the same degree as PRRX1 knockdown. These results demonstrate that PRRX1 promotes tumor malignancy in human osteosarcoma.