Clinical and Translational Medicine

Cisplatin is a DNA targeting anticancer drug, yet its damaged gene loci have remained unclear. In the present work, combining affinity isolation and high throughput sequencing, we genome-widely mapped 17729 gene loci containing platination lesions, which mainly function as enzymes, transcription regulators, transporters and kinases, and of which 445 genes account for 71% of potential gene targets for cancer therapy reported in the literature. The most related core signaling pathway, disease and tissue toxicity of 7578 genes with an enrichment fold (EFG) of >12, where EFG refers to the ratio of total read counts of a gene detected in cells with and without cisplatin treatment, are sperm motility, cancer and hepatotoxicity with association P values of < 1x10-22. Among 616 kinase genes damaged by cisplatin, 427 are protein kinases which account for 82% of putative protein kinases, suggesting that cisplatin may act as broad-spectrum protein kinase inhibitor. Western Blot assays verified that expression of 8 important protein kinase genes was significantly reduced due to cisplatin damage. SPAG9 is closely related to 147 of 361 cancer diseases which the cisplatin damaged genes are associated with and was severely damaged by cisplatin. Given SPAG9 abundantly expresses JIP-4, a upstream mediator of protein kinase signaling, in testis, it may be responsible for the high sensitivity of testicular cancer to cisplatin, thus being a potential therapeutic target for precise treatment of testicular cancer. These findings provide novel insights into better understanding in molecular mechanism of anticancer activity and toxicity of cisplatin, more importantly inspire further studies in prioritizing gene targets for precise treatment of cancers.

BACKGROUNDCardiac arrest (CA) and successful cardiopulmonary resuscitation (CPR) cause post-CA brain injury (PCABI) and extracerebral multiple organ dysfunction (EMOD), leading to low survival and disability in resuscitated patients. The pathogenesis of PCABI is still poorly understood, and no therapeutic-related factors have been identified to improve survival and neurological outcomes to date. Bumetanide is a promising pharmaceutical intervention for some neurological disorders that have some common pathophysiology with PCABI, and it also exhibit systemic protective effects on vital organs under pathological conditions. This study aims to investigate the protective effects of bumetanide on PCABI and EMOD after CA/CPR, and uncover the pathogenesis and biomarkers of PCABI at protein level. METHODSWe generated a hyperkalemia-induced asystole CA/CPR mouse model with bumetanide/vehicle treatment after resuscitation. Survival, neurological outcome, functional outcome, key pathophysiological process underlying PCABI, and injury level of EMOD were evaluated. Proteomics analysis of cerebral cortex was performed for investigating mechanisms of PCABI. RESULTSBumetanide significantly improved outcomes after CA/CPR and reduced the main pathophysiological processes of PCABI, including seizures, neurodegeneration, neuroinflammation, decreased cerebral blood flow, blood-brain barrier disruption, and oxidative stress. CA/CPR-induced injury in heart, lung, liver, kidney, spleen, adrenal gland, spinal cord, pennis, and urinary bladder were also alleviated by bumetanide. Proteomic study and experimental verification identified LCN2/NGAL is a potential biomarker for early neuroprognostication and has association with PCABI severity. CONCLUSIONSSystemic administration of bumetanide improved outcomes and prevented multiple organ dysfunction after CA/CPR. LCN2/NGAL is a novel biomarker for early neuroprognostication at 24 hours after CA/CPR. Clinical PerspectiveO_LIWhat Is New? O_LIPost-resuscitation bumetanide treatment could improve outcomes and prevent brain injury and extracerebral multiple organ dysfunction after hyperkalemia-induced asystole cardiac arrest in mice. C_LIO_LINeuronal subpopulations in cerebral cortex were selectively vulnerable, and all major organs had obvious tissue damage with inflammatory cell infiltration and tissue edema after resuscitation. C_LIO_LIThis the first study to identify the pathogenesis and biomarkers of post-cardiac arrest brain injury with proteomic studies, and LCN2/NGAL had a strong and graded association with pathogenesis of PCABI, which could be a marker for monitoring and neuroprognostication. C_LI C_LIO_LIWhat Are the Clinical Implications? O_LIBumetanide may be a novel pharmacological therapy to improve survival and neurological outcomes in post-resuscitation care, and cerebral-specific quantification of LCN2/NGAL could be used for early neuroprognostication at 24 hours after cardiac arrest. C_LIO_LIExtracerebral multiple organ injury is common and severe after resuscitation, which needs to be given more attention in clinical management. C_LI C_LI

The comparison between traditional Chinese medicine Jinzhen Oral Liquid (JZOL) and western medicine in treating children with acute bronchitis (AB) showed encouraging outcomes. This trial evaluated the efficacy and safety of the JZOL for improving cough and expectoration in children with AB. 480 children were randomly assigned to take JZOL or Ambroxol Hydrochloride and Clenbuterol Hydrochloride Oral Solution for 7 days. The primary outcome was time-to-cough resolution. The median time-to-cough resolution in both groups was 5.0 days and the antitussive onset median time was only 1 day. This head to head randomized controlled trial showed that JZOL was not inferior to cough suppressant and phlegm resolving western medicine in treating cough and sputum and could comprehensively treat respiratory and systemic discomfort symptoms. Combined with clinical trials, the mechanism of JZOL against AB was uncovered by network target analysis, it was found that the pathways in TRP channels like IL-1{beta}/IL1R/TRPV1/TRPA1, NGF/TrkA/TRPV1/TRPA1 and PGE2/EP/PKA/TRPV1/TRPA1 might play important roles. Animal experiments further confirmed that inflammation and immune regulatory effect of JZOL in the treatment of AB were of vital importance and TRP channels was the key mechanism of action.

Diagnosing and managing intrahepatic cholangiocarcinoma (iCCA) poses a significant oncological hurdle as it is a deadly form of liver cancer.A significant role is played by nonapoptotic regulatory cell death (NRCD) in the tumor immune microenvironment (TME) of iCCA. Nevertheless, the precise functions of NRCD-associated genes (NRGs) in the tumor microenvironment (TME) are still not well understood. Transcriptomics, proteomic analysis, and single-cell RNA analysis were utilized to distinguish two NRG-related clusters in iCCA patients from the FU-iCCA cohort in this study. We have shown the clear disparities in immune traits and predictive categorization among two groups. To address the risk stratification and prognosis prediction, a prognostic signature model called NPS (NRG-related risks core prognostic signature model) was created using the FU-iCCA cohort. The validation of the NRG-associated risk score in prognosis and immunotherapy confirmed its predictive capabilities. In iCCA patients with high-risk, the secretion of CP and TGF-{beta} proteins strengthened the enriched TGF-{beta} signaling network between CD4+ T cells and erythroid cells. Patients exhibiting a low-risk score demonstrated improvement in the effector function of CD4+ T cells, resulting in a more favorable reaction to chemotherapy medications. The NPS-risk score showed a significant negative correlation with the IC50 values of four drugs (Trametinib, CI-1040, X17-ACC, and PD-0325901). From these findings, it can be inferred that a clear connection exists between the NRG and the TME in iCCA. Additionally, the risk score has the potential to act as a reliable prognostic indicator, offering advantageous outcomes for chemotherapy and immunotherapy. This could aid in making informed clinical decisions for patients with iCCA.

Immunomodulatory agents dexamethasone and colchicine, antiviral drugs remdesivir, favipiravir and ribavirin, as well as antimalarial drugs chloroquine phosphate and hydroxychloroquine are currently used in the combat against COVID-191-16. However, whether some of these drugs have clinical efficacy for COVID-19 is under debate. Moreover, these drugs are applied in COVID-19 patients with little knowledge of genetic biomarkers, which will hurt patient outcome. To answer these questions, we designed a screen approach that could employ genome-wide sgRNA libraries to systematically uncover genes crucial for these drugs action. Here we present our findings, including genes crucial for the import, export, metabolic activation and inactivation of remdesivir, as well as genes that regulate colchicine and dexamethasones immunosuppressive effects. Our findings provide preliminary information for developing urgently needed genetic biomarkers for these drugs. Such biomarkers will help better interpret COVID-19 clinical trial data and point to how to stratify COVID-19 patients for proper treatment with these drugs.

BackgroundAnti-N-methyl-D-aspartate receptor encephalitis (NMDAR-E) is a common and severe antibody-mediated autoimmune encephalitis. While the roles of B cells and NMDAR antibodies in NMDAR-E have been extensively studied, the involvement of T cell subpopulations in the disease progression remains unclear. MethodsThis study conducted single-cell RNA sequencing, single-cell TCR sequencing, and flow cytometry to analyze the T cell subpopulations and their transcriptomic characteristics in NMDAR-E patients and control individuals. Furthermore, it explored the interaction between CD8+T cells and B cells through in vitro cell co-culture and cell communication analysis. ResultsThe study found activated CD8+T cell subpopulations in the cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) of NMDAR-E patients, with some subpopulations exhibiting significant TCR clonal expansion. Differential expression gene analysis revealed upregulation of genes related to cytotoxicity, tissue residency, Th1, IFN, or TCR signaling in certain activated CD8+T cell and CD4+ memory T cell subpopulations. In vitro co-culture experiments demonstrated that CD8+T cells from the PBMCs of NMDAR-E patients could induce apoptosis of their own B cells. Cell interaction analysis revealed the existence of interactions between KIR+CD8+T cells and B cell subpopulations in NMDAR-E patients. ConclusionThis study explored the changes and transcriptomic characteristics of activated CD8+T cell subpopulations in the CSF and PBMCs of NMDAR-E patients. Additionally, it discovered the impact of CD8+T cells from NMDAR-E patients on their own B cells, providing new evidence for the interaction between CD8+T cells and B cells.

Primary central nervous system lymphoma (PCNSL) is a rare and aggressive brain tumor with a poor prognosis and is almost exclusively diffuse large B-cell lymphoma (DLBCL). Its genetic characteristics and molecular subtypes in Chinese patients remain poorly understood, which in turn makes developing effective new therapies challenging. By enrolling 176 newly diagnosed Chinese PCNSLs at five tertiary care centers with extensive follow-up, we performed a genomic study aimed at expanding the genomic landscape and developing new molecular subtypes. We first confirmed that the molecular subtyping of DLBCL, as previously published, is not applicable to Chinese PCNSLs. We then identified (n = 58) and validated (n = 82) three prominent genetic subtypes related to different clinical and molecular features of PCNSL, and further confirmed by an independent external Chinese PCNSL cohort (n = 36). We called these BMIs (from the co-occurrence of mutations in two genes among BTG1, MYD88, and IRF4), which are associated with favorable outcomes; E3s (so-called EP300 mutations), which are associated with unfavorable outcomes; and UCs (unclassified, without characteristic mutations). Importantly, EP300 was mutated in more Asians (16.98%) than in Western PCNSLs (< 4.53%), resulting in unfavorable outcomes independent of the specific mutation site. Our analysis comprehensively reveals the genomic landscape of Chinese PCNSL and emphasizes the clinical value of molecular classification for improving precision medicine strategies.

Hearing hypersensitivity (hyperacusis) is a common hearing stress and can cause many psychological diseases, e.g., anxiety, learning disabilities, and attention-deficit/hyperactivity disorder (ADHD). Here, we report an unexpected finding that the upregulation of P2x2 ATP-purinergic receptors in the cochlea links to hyperacusis generation. We found that P2x2 expression in the cochlea but not in auditory centers was upregulated in the hyperacusis generated by Cx26 deficiency. Overexpression of P2x2 in the cochlea also caused hyperacusis. Conversely, downregulation of P2x2 expression or administration of P2x2 antagonists attenuated hyperacusis. We further found that upregulation of P2x2 receptors in the cochlea increased outer hair cell (OHC) electromotility through the post-transcription functional modulation to potentiate active cochlear amplification leading to hearing hypersensitivity. Such enhancements in OHC electromotility and active cochlear amplification were also suppressed by P2x2 receptor antagonists. Overall, these findings demonstrate that P2x2-mediated ATP-purinergic signaling in the cochlea plays a critical role in hyperacusis generation; targeting P2x2 receptors can attenuate hyperacusis stress, which may also offer a therapeutic strategy for other related psychological comorbidities. Significance statementHearing hypersensitivity is a common hearing stress and can cause many other psychological disorders. However, little is known about the underlying genetic and cellular mechanisms. Also, it lacks efficient drugs for their treatments in the clinic. In this study, we found that upregulation of P2x2 ATP-purinergic receptors in the cochlea can potentiate outer hair cell electromotility, which is an active cochlear amplifier in mammals and can increase hearing sensitivity and frequency selectivity, through post-transcription functional modulation to enhance active cochlear amplification leading to hearing hypersensitivity. These enhancements can be inhibited by administrations of P2x2 receptor antagonists both in vitro and in vivo. These findings revealed a new genetic and cellular mechanism underlying hyperacusis generation and opened a new avenue to develop an efficient therapy for this common hearing stress and other associated psychological comorbidities.

Immune checkpoint inhibitors (ICIs), especially CTLA-4 inhibitors (CTLA-4), exhibit a high incidence of colitis as an immune-related adverse event (irAE) during cancer treatment, severely limiting patient benefit. Clinically, both treatment interruption and existing intervention drugs for ICI-mediated colitis may compromise antitumor efficacy. However, there is inadequate research on the pathogenesis of ICI-mediated colitis, with findings often conflicting. Here, we first established multiple clinically relevant animal models, including an immuno-humanized ICI-mediated colitis model. Through time-series transcriptomics, we discovered that CTLA-4-induced colonic toxicity exhibits characteristics ranging from early metabolic reprogramming represented by glycolysis to later immune disorders represented by Th17 responses. By targeting colonic CTLA-4+ T cells, CTLA-4 blocked CD80/CD86-CTLA-4 interaction, thereby activating the PI3K-AKT-mTOR pathway. Subsequently, mTOR mediated metabolic reprogramming in T cells, shifting them from Treg-biased oxidative phosphorylation to Th17-biased glycolysis. The colonic toxicity of CTLA-4 has also been demonstrated to depend on the PI3K-AKT-mTOR pathway, glycolysis, and Th17 responses. Notably, metformin significantly relieved ICI-mediated colitis by inhibiting mTOR without impeding antitumor efficacy. Collectively, these findings highlighted the metabolic-immune axis in the colonic toxicity of ICI and provided a clinically superior intervention strategy.

BackgroundImmunotherapy such as oncolytic virus has become a powerful cancer treatment but only a part of cancer patients can benefit from it, especially to advanced-stage cancer patients are required new therapeutic strategies to facilitate extended survival. Intestinal microbiota may contribute to colorectal cancer (CRC) carcinogenesis and response to immunotherapy. However, whether and how the modulating effect of intestinal microbiota on oncolytic virus vaccine (OVV) in CRC remains to be investigated. MethodsWe generated a MC38-gp33 CRC mouse model and treated with OVV-gp33 in early- and advanced-stages. Probiotics, fecal microbiota transplantation (FMT) and antibiotics (ABX) were treated to regulate the microbial composition of CRC mice of advanced stage. The tumor growth rate and survival time of mice were recorded. 16S rDNA sequencing analyzed the microbial composition and flow cytometry detected the T cells subsets activity. ResultsOVV-gp33 treatment led to inhibited tumor growth and prolonged survival in the early stage of CRC but did not have a significant effect on the advanced stage of CRC. Moreover, 16S rDNA sequence analysis and flow cytometry showed significant differences in intestinal microbiota composition, microbial metabolites and T-cell subsets in early- and advanced-stage CRC. Probiotic and FMT treatment significantly enhanced the antitumor effect of OVV in advanced stage of CRC with an increased abundance of activated CD8+ T cells and a decreased ratio of Treg cells, while depletion of the microbiota by ABX eliminated the antitumor activity of OVV with decreased CD8+ T-cell activation and upregulated Treg cells. ConclusionsThese results indicate that intestinal microbiota and microbial metabolites play an important role in the OVV antitumor effect in CRC, furthermore, altering the intestinal microbiota composition can modulate the antitumor and immunomodulatory effect of OVV in CRC.

Dyslipidemia is a hallmark of obstructive sleep apnea (OSA)-induced metabolic syndrome, yet the mechanisms remain poorly understood. We conducted a genome-wide association study on lipid traits in the OSA cohorts, identifying the SNP rs3745683 in ANGPTL8, significantly associated with reductions in multiple lipid traits. ANGPTL8, an essential lipogenic hormone and potential therapeutic target for metabolic syndrome, showed elevated expression in OSA patients compared to healthy controls, strongly correlated with increased insulin levels. Notably, ANGPTL8 expression can be upregulated by insulin stimulation, indicating it as an insulin-responsive hormone regulating dyslipidemia in OSA. Mechanistically, SNP rs3745683 attenuated ANGPTL8 transcription by inhibiting its binding to transcription factor YBX1. Insulin prompted AKT1 to phosphorylate YBX1 at Ser102, facilitating YBX1s nuclear translocation and subsequent regulation of ANGPTL8 expression and lipid synthesis. Specific knockdown of YBX1 in mouse liver confirmed its necessity for ANGPTL8 expression and hepatic lipid synthesis in vivo. Our findings highlight ANGPTL8 as a critical regulator of dyslipidemia in OSA patients, offering a promising therapeutic avenue for managing metabolic syndrome in OSA.

Interstitial lung disease is the primary cause of death in individuals who have systemic sclerosis, one of the autoimmune connective tissue diseases. Understanding the pathophysiology of the disease is crucial to developing treatment options. Here, we performed a single-cell multi-omic analysis on lung tissue samples from patients with systemic sclerosis-associated interstitial lung disease (SSC-ILD), profiling chromatin accessibility and gene expression in the same samples and discovering significant cellular heterogeneity. Systemic-venous endothelial cells (ECs) have been shown to be pro-inflammatory and highly active. In addition, it was shown that the transcription factor FOSL2 targets the genes involved in response to unfolded proteins in systemic-venous ECs. Furthermore, we prioritized functional risk variants for systemic sclerosis using a genome-wide association study. Ligand-receptor analysis revealed that ECs significantly increased interaction with B cells via CXCL10-CXCR3 in patients with SSC-ILD. Overall, our analysis emphasizes epigenetic and transcriptional patterns in systemic-venous ECs, which might be beneficial in understanding the pathogenesis of SSC-ILD.

Oculopharyngodistal myopathy is an adult-onset degenerative muscle disorder characterized by ptosis, ophthalmoplegia and weakness of the facial, pharyngeal and limb muscles. Trinucleotide repeat expansions in non-coding regions of LRP12, G1PC1and NOTCH2NLC were recently reported to be the etiologies for OPDM. However, a significant portion of OPDM patients still have unknown genetic causes. In this study, we performed long-read whole-genome sequencing in a large five-generation family of 156 individuals, including 22 patients diagnosed with typical OPDM and identified CGG repeat expansions in RILPL1 gene in all patients we tested while not in unaffected family members. Methylation analysis indicated that methylation levels of the RILPL1 gene were unaltered in OPDM patients, which was in consistent with previous reports. Our findings first provided evidences that RILPL1 were associated OPDM which we suggested as OPDM type 4.

Emerging evidence strongly supports a close relationship between age-related hearing loss and frailty, highlighting the importance of early detection and intervention. Recently, we invented a mitochondria-homing drug named mitochonic acid 5 (MA-5), that increases the adenosine triphosphate (ATP) levels, rescue mitochondrial function, and protect tissue damages. Currently, the phase I clinical trial has been finished in Japan (jRCT2031210495) and the phase 2 clinical trial has already been approved by PMDA. Here we show that MA-5 improved various types of hearing loss in mouse models. Structural chemical bioanalysis revealed that MA-5 is a mixture of equal amount of S- and R- enantiomer and both S- and R- enantiomer increase ATP by binding mitochondrial protein, mitofilin. However, S-enantiomer significantly increased the NAD+ levels by binding to the NAD+-producing key enzyme nicotinamide phosphoribosyltransferase (NAMPT). Moreover, the S-enantiomer increased the sirtuin 1 protein by suppressing polyubiquitination induced by tripartite motif containing 28 (TRIM28) phosphorylation which was triggered by DNA-dependent protein kinase (DNA-PK) activation in the absence of DNA damage. Transcriptomic signatures showed that the signature of MA-5 shows an inverse correlation with aging and mortality and is oriented in the same direction as the OSKM-related iPSCs, suggesting the modification of aging pathways. Oral administration of MA-5 to mitochondrial disease model mouse showed increased survival. Our findings suggest that, in addition to enhancing ATP levels, the coordinated regulation of NAD+ metabolism, SIRT protein expression, and DNA-PK activity-constituting a novel therapeutic triad may contribute to the amelioration of hearing impairment and mitochondrial dysfunction, thereby improving life prognosis.

Long-COVID-19 manifests as a multisystemic condition with varied symptoms lingering beyond three weeks of acute SARS-CoV-2 infection, though its underlying mechanisms remain elusive. Aiming to decipher the long-term molecular impacts of COVID-19, we conducted a transcriptomic analysis on PBMCs from 1-year post-covid patients, including individuals without pneumonia (NP, n=10), those with severe pneumonia (SP, n=11), and healthy controls (C, n=13). Our extensive RNA sequencing revealed 4843 differentially expressed genes (DEGs) and 1056 differentially expressed long non-coding RNAs (DElncRNAs) in "C vs NP," 1651 DEGs and 577 DElncRNAs in "C vs SP," 954 DEGs and 148 DElncRNAs in "NP vs SP," with 291 DEGs and 70 DElncRNAs shared across all groups. We identified 14 hub genes from 291 DEGs, with functional enrichment analysis showing upregulated DEGs mainly linked to inflammation and osteoclast differentiation, and downregulated DEGs to viral infections and immune responses. These hub genes play central roles in inflammatory and immune processes and are significantly associated with pneumonitis and diverse lung diseases. Investigations revealed unique immune cell signatures across DEG categories, associating upregulated DEGs with neutrophils and monocytes, and downregulated DEGs with CD4 memory effector T cells. Analysis of 14 hub genes showed notable upregulation in the no pneumonia group versus healthy controls, displaying complex patterns in the severe pneumonia group. Our study uncovered potential idiopathic pulmonary fibrosis signals in Long-COVID-19 patients PBMC transcriptome, highlighting the urgency for thorough monitoring and extended research to understand COVID-19s lasting effects. This study sheds light on COVID-19s transcriptomic changes and potential lasting effects, guiding future research and therapeutic approaches for Long-COVID-19.

The causal genes for a large proportion of hereditary colorectal adenomas and early-onset colorectal cancer (CRC) remain to be identified. Here, we identified a germline heterozygous stop-gain mutation p.Arg1953X (rs150312701) of the POLQ (DNA Polymerase Theta) gene, which is co-segregated with disease status, by whole-exome sequencing of twelve hereditary CRC pedigrees. The mutation was validated in an independent pedigree, resulting in ten p.Arg1953X carriers from two CRC families. Mechanically, the heterozygous nonsense mutation led to compensated overexpression of the mRNA with wild-type POLQ allele under DNA damage stress, resulting in hyperactivation of the error-prone theta mediated end-joining (TMEJ) DNA repair pathway, which enables the survival of mutation-enriched cells. Concordantly, tumor tissues from p.Arg1953X mutation carriers showed microsatellite instability and hypermutation, and were resistant to radiotherapy. We found that an FDA-approved antibiotic Novobiocin inhibits the POLQ-mediated TMEJ pathway, eliminates the p.Arg1953X mutation-related resistance to DNA damage, finally benefits tumor radiotherapy. Collectively, we defined a POLQ-mutated CRC type and suggested for a mutation-based potential target therapeutic strategy.

BACKGROUNDPulmonary hypertension (PH) represents a significant cardiovascular disorder marked by both functional and structural alterations within the pulmonary vasculature. Long non-coding RNAs (lncRNAs) have been closely associated with the pathogenesis and progression of PH. Nonetheless, the precise mechanisms by which lncRNAs interact with its downstream target molecules to modulate the disease remain inadequately elucidated. METHODSThe expression levels of LINC00599 were quantified in the lung tissues of mice and pulmonary arterial smooth muscle cells (PASMCs) under hypoxic conditions. The involvement of LINC00599 in the progression of PH and vascular remodeling was evaluated through in vivo studies. To investigate the mechanisms by which LINC00599 influences the proliferation of human PASMCs, small interfering RNA and overexpression plasmids were employed. RESUITSThe expression of LINC00599 is upregulated in the medial layer of pulmonary arteries in experimental models of PH and in hypoxic PASMCs. Administration of a single dose of lentivirus-mediated shRNA targeting LINC00599 effectively reverses hypoxic PH in murine models. LINC00599 plays a critical role in PASMC proliferation by modulating stress granule formation through N6-methyladenosine (m6A) modification and promoting proliferation via liquid-liquid phase separation with myosin heavy chain 9. Furthermore, the expression of LINC00599 is regulated by a super-enhancer, which is mediated by the transcription factor ZNF263. CONCLUSIONSThese findings demonstrate for the first time that LINC00599, involved in liquid-liquid phase separation, facilitates the progression of pulmonary hypertension by enhancing the proliferation of pulmonary artery smooth muscle cells. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/629439v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7ac192org.highwire.dtl.DTLVardef@13a88b3org.highwire.dtl.DTLVardef@1e4c761org.highwire.dtl.DTLVardef@ddd105_HPS_FORMAT_FIGEXP M_FIG C_FIG What Is New?This study identified LINC00599 as a critical regulator of liquid-liquid phase separation through m6A modification and as a pivotal target in promoting the progression of PH. What Is Relevant?LncRNAs are intricately associated with the pathogenesis and progression of PH through the modulation of downstream target molecules. However, it remains unclear whether lncRNAs contribute to PH by forming specific subcellular structures with these target molecules. Furthermore, some studies have suggested that the increased presence of stress granules in PASMCs is implicated in the pathogenesis of pulmonary arterial hypertension. In this study, we provide evidence that LINC00599 promotes the development of PH by forming stress granules with its target proteins. Our findings indicate that the binding of LINC00599, modified with m6A, to G3BP1 and MYH9 in PASMCs suggests that the regulation of liquid-liquid phase separation by lncRNA m6A modification may represent a significant pathological mechanism underlying PH. What Are the Pathophysiological Implications?We found that LINC00599 levels were elevated in hypoxic PASMCs and experimental PH models. Knockout LINC00599 effectively prevented PH, indicating its potential as both a bomarker and therapeutic target for PH.

Influenza remains a significant global health burden, with the potential for severe complications and mortality. This study investigates the genetic architecture of hospitalized influenza and explores its shared and distinct genetic factors with hospitalized COVID-19. A binary GWAS of hospitalized influenza using UK Biobank data, followed by meta-analysis with FinnGen, identified three risk loci: ST6GAL1, AASDHPPT, and SPATS2L. Additionally, a time-to-event GWAS revealed a novel susceptibility locus, UGT2B4. Further differentiation analysis with hospitalized COVID-19 identified 29 differentially associated loci, highlighting their distinct genetic architectures. Colocalization analysis uncovered shared genetic mechanisms, with ST6GAL1 and ICAM5 emerging as key candidates. These findings provide new insights into the genetic basis of influenza and its relationship with COVID-19, offering potential therapeutic targets and avenues for personalized medicine.

Resistance to platinum is the main challenge in the chemotherapy of ovarian cancer (OV). Therefore, developing a response signature to platinum is essential for the precision therapy of OV. Existing quantitative signatures of platinum are susceptible to batch effects and sequencing platform variations. To address this, we developed a transcriptome-based platinum signature, named PRSM, consisting of 15 genes, based on within-sample prognostic and relative expression ordering of genes, to predict individual responses to platinum in OV. The PRSM model demonstrated superior classification accuracy compared to previous quantitative signatures. Resistant samples classified by PRSM exhibited poorer overall survival, lower SNV neoantigen load, tumor mutational burden, and distinct methylation patterns compared to sensitive samples. Pathway analysis revealed the activation of MYC targets V2 and oxidative phosphorylation in resistant tumors. Single-cell analysis highlighted the roles of NK and epithelial cells in resistance. Among the 15 core genes, five (TFAP2B, KRT81, PAGE1, CRNN, UGT2B17) were linked to poor prognosis, with TFAP2B having the highest contribution to PRSM. Overexpression of TFAP2B in A2780 cells enhanced cisplatin sensitivity, while in A2780cis cells, it inhibited growth. In brief, our findings provide a multi-dimensional view of platinum resistance in ovarian cancer, introducing a robust predictive model and identifying potential therapeutic targets.

BackgroundGastric cancer (GC) continues to be among the most commonly identified cancers worldwide. This study integrates glycosylation and inflammation-related gene features for the first time to construct a prognostic model for gastric cancer, providing new theoretical basis for revealing immune escape mechanisms and personalized treatment strategies. MethodsTranscriptomic and clinical data derived from GC samples were meticulously examined, utilizing resources from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Through differential expression analysis, we successfully identified glycosylation and inflammatory-related differentially expressed genes (GANDIRDEGs). To construct a prognostic gene signature, we applied least absolute shrinkage and selection operator (LASSO) analysis in conjunction with Cox regression analysis. Additionally, we performed somatic mutation (SM) along with copy number variation (CNV) analyses, alongside gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, we conducted gene set enrichment analysis (GSEA) along with a comprehensive evaluation of immune infiltration and drug sensitivity. ResultsWe identified and validated a six-gene (INHBA, OLR1, ROS1, EPHA5, TACR1, and IL6) signature, termed GANDIRDEGs, which showed excellent performance in distinguishing overall survival (OS) between high-risk (HR) and low-risk (LR) cohorts. Moreover, we developed a prognostic nomogram utilizing this six-gene signature that provides highly accurate predictions of GC patient outcomes.SM and CNV analyses revealed that MSR1 had the highest mutation rate among the GANDIRDEGs, with a mutation rate of 5%. GO, KEGG, and GSEA revealed significant associations of each pivotal gene with pathways, including cytokine signaling, the inflammatory response, and apoptosis mediated by CDKN1A through TP53, among various biological functions and signal transduction pathways. Our findings offer a novel gene signature, GANDIRDEGs, that correlated with prognosis, immune infiltration, and therapeutic sensitivity in patients with GC. ConclusionThis study establishes a prognostic signature integrating glycosylation and inflammatory pathways in GC, providing valuable insights into the mechanisms of immune evasion and potential personalized treatment approaches.