Macrophage autophagy protects against acute kidney injury by inhibiting renal inflammation through the degradation of TARM1.

Macroautophagy/autophagy activation in renal tubular epithelial cells protects against acute kidney injury (AKI). However, the role of immune cell autophagy, such as that involving macrophages, in AKI remains unclear. In this study, we discovered that macrophage autophagy was an adaptive response during AKI as mice with macrophage-specific autophagy deficiency (atg5-/-) exhibited higher serum creatinine, more severe renal tubule injury, increased infiltration of ADGRE1/F4/80+ macrophages, and elevated expression of inflammatory factors compared to WT mice during AKI induced by either LPS or unilateral ischemia-reperfusion. This was further supported by adoptive transfer of atg5-/- macrophages, but not WT macrophages, to cause more severe AKI in clodronate liposomes-induced macrophage depletion mice. Similar results were also obtained in vitro that bone marrow-derived macrophages (BMDMs) lacking Atg5 largely increased pro-inflammatory cytokine expression in response to LPS and IFNG. Mechanistically, we uncovered that atg5 deletion significantly upregulated the protein expression of TARM1 (T cell-interacting, activating receptor on myeloid cells 1), whereas inhibition of TARM1 suppressed LPS- and IFNG-induced inflammatory responses in atg5-/- RAW 264.7 macrophages. The E3 ubiquitin ligases MARCHF1 and MARCHF8 ubiquitinated TARM1 and promoted its degradation in an autophagy-dependent manner, whereas silencing or mutation of the functional domains of MARCHF1 and MARCHF8 abolished TARM1 degradation. Furthermore, we found that ubiquitinated TARM1 was internalized from plasma membrane into endosomes, and then recruited by the ubiquitin-binding autophagy receptors TAX1BP1 and SQSTM1 into the autophagy-lysosome pathway for degradation. In conclusion, macrophage autophagy protects against AKI by inhibiting renal inflammation through the MARCHF1- and MARCHF8-mediated degradation of TARM1.

Enhancing immunity against Candida albicans infections through TIGIT knockout.

T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif (ITIM) domain (TIGIT) is an inhibitory receptor expressed by T and natural killer cells. Here, we used TIGIT knockout (KO) mice to demonstrate that mouse TIGIT directly interacts with Candida albicans. Reduced fungal growth and colonization were observed when TIGIT-KO splenocytes were co-cultured with C. albicans compared to the wild type (WT). In a systemic candidiasis model, TIGIT-KO mice exhibited improved survival and reduced body weight loss compared to WT mice. Organ-specific fungal burden assessment revealed significantly lower fungal loads in the kidneys, spleen, and lungs of TIGIT-KO mice. Finally, we show that the agglutinin-like sequence proteins ALS6, ALS7, and ALS9 of C. albicans are ligands for TIGIT and that the absence of these proteins abolishes the TIGIT effect in vivo. Our results identify the significance of TIGIT in modulating host defense against C. albicans and highlight the potential therapeutic implications for C. albicans infections. IMPORTANCE: Our results identify the significance of T cell immunoreceptor with immunoglobulin and ITIM domain in modulating host defense against Candida albicans and highlight the potential therapeutic implications for C. albicans infections.

Fusobacterium nucleatum subsp. nucleatum RadD binds Siglec-7 and inhibits NK cell-mediated cancer cell killing.

Fusobacterium nucleatum is an oral commensal bacterium that can colonize extraoral tumor entities, such as colorectal cancer and breast cancer. Recent studies revealed its ability to modulate the immune response in the tumor microenvironment (TME), promoting cancer progression and metastasis. Importantly, F. nucleatum subsp. animalis was shown to bind to Siglec-7 via lipopolysaccharides, leading to a pro-inflammatory profile in human monocyte-derived dendritic cells. In this study, we show that F. nucleatum subsp. nucleatum RadD binds to Siglec-7 on NK cells, thereby inhibiting NK cell-mediated cancer cell killing. We demonstrate that this binding is dependent on arginine residue R124 in Siglec-7. Finally, we determine that this binding is independent of the known interaction of RadD with IgA. Taken together, our findings elucidate the targeting of Siglec-7 by F. nucleatum subsp. nucleatum RadD as a means to modulate the NK cell response and potentially promoting immune evasion and tumor progression.

Recognition and management of stent malposition in the portal vein during endoscopic retrograde cholangiopancreatography: A case report.

BACKGROUND: Portal vein injury is an uncommon complication of endoscopic retrograde cholangiopancreatography (ERCP), for which stent malpositioning in the portal vein is very rare and can lead to fatal events. We report a case of biliary stent migration to the portal vein and a novel method for its safe removal under the guidance of portal angiography. Moreover, we reviewed the literature and summarized reports on the identification and management of this condition. CASE SUMMARY: A 59-year-old woman with pancreatic cancer presented with abdominal pain and a high fever 20 days after the placement of two plastic biliary stents under the guidance of ERCP. Blood cultures and laboratory tests revealed sepsis, which was treated with antibiotics. A contrast-enhanced computed tomography scan revealed that one of the biliary stents in the main portal vein was malpositioned. To safely remove the stent, portal angiography was performed to visualize the portal vein and to allow the management of any bleeding. The two stents were removed without obvious bleeding, and an uncovered self-expanding metal stent was placed in the common bile duct for drainage. The patient had an uneventful 6-month follow-up period, except for self-resolving portal vein thrombosis. CONCLUSION: The combination of endoscopic and angiographic techniques allowed uneventful management of stent malposition in the portal vein.

Three-dimensional architecture of ESCRT-III flat spirals on the membrane.

The endosomal sorting complexes required for transport (ESCRTs) are responsible for membrane remodeling in many cellular processes, such as multivesicular body biogenesis, viral budding, and cytokinetic abscission. ESCRT-III, the most abundant ESCRT subunit, assembles into flat spirals as the primed state, essential to initiate membrane invagination. However, the three-dimensional architecture of ESCRT-III flat spirals remained vague for decades due to highly curved filaments with a small diameter and a single preferred orientation on the membrane. Here, we unveiled that yeast Snf7, a component of ESCRT-III, forms flat spirals on the lipid monolayers using cryogenic electron microscopy. We developed a geometry-constrained Euler angle-assigned reconstruction strategy and obtained moderate-resolution structures of Snf7 flat spirals with varying curvatures. Our analyses showed that Snf7 subunits recline on the membrane with N-terminal motifs α0 as anchors, adopt an open state with fused α2/3 helices, and bend α2/3 gradually from the outer to inner parts of flat spirals. In all, we provide the orientation and conformations of ESCRT-III flat spirals on the membrane and unveil the underlying assembly mechanism, which will serve as the initial step in understanding how ESCRTs drive membrane abscission.

Melatonin ameliorates multiorgan injuries induced by severe acute pancreatitis in mice by regulating the Nrf2 signaling pathway.

Severe acute pancreatitis (SAP) is a complicated inflammatory reaction that impacts the pancreas, often resulting in damage to numerous organs. This disorder encompasses a range of processes such as inflammation, oxidative stress, and pancreatitis. The hormone melatonin (MT) is primarily secreted by the pineal gland and plays a crucial role in mitigating inflammation, countering the harmful effects of free radicals, and regulating oxidative stress. The aim of this research was to investigate the potential protective impact and the underlying mechanism of melatonin in mice afflicted with SAP. The biochemical and histological assessments unequivocally demonstrated that melatonin effectively inhibited necrosis, infiltration, edema and cell death in pancreatic tissues, thereby suppressing acute pancreatitis. Notably, melatonin also alleviated the consequent harm to distant organs, notably the lungs, liver, and kidneys. Furthermore, both preventive and therapeutic administration of melatonin prompted nuclear factor E2-related factor 2 (Nrf2) activation followed by Nrf2 target gene expression. Nrf2 initiates the activation of antioxidant genes, thereby providing defense against oxidative stress. Conversely, Nrf2 reduction may contribute to impaired antioxidant protection in SAP. The beneficial impact of Nrf2 on antioxidants was absent in Nrf2-knockout mice, leading to the accumulation of LDH and exacerbation of cell death. This deterioration in both pancreatitis and injuries in distant organs intensified significantly. The results indicate that melatonin has an enhanced ability to protect against multiorgan damage caused by SAP, which is accomplished through the increase in Nrf2 expression. Additionally, Nrf2 initiates the activation of antioxidant genes that offer defense against cell death.

Risk Factors and Clinical Significance of Ultra-Long-Term Microischemia After Intracranial Aneurysm Embolization.

INTRODUCTION: This study aimed to explore influencing factors and clinical significance of ultra-long-term microischemia following intracranial aneurysm (IA) embolization and establish a theoretical foundation for reducing both the incidence of ultra-long-term microischemia and cognitive dysfunction in patients post embolization. METHODS: A retrospective analysis was conducted on data from 147 patients who received endovascular treatment for IAs. Patients were categorized into microischemic and control (non-microischemic) groups on the based on the findings of high-resolution magnetic resonance vessel wall imaging (HR-VWI) examinations performed 3 days postoperatively and 6 months postoperatively. Risk factors for the occurrence of ultra-long-term microischemia were determined by univariate analysis and multivariate logistic regression analysis. RESULTS: Out of 147 patients included in the study, 51 (34.69%) developed microischemia while the remaining 96 (65.31%) did not experience this condition. Analysis revealed that factors such as sex, age, history of underlying diseases (hypertension, diabetes mellitus), aneurysmal site characteristics, the presence or absence of stenosis in the aneurysm-bearing artery, modified Fisher score at admission, Barthel's index at discharge, immunoinflammatory index at 3 days postoperatively and at the 6-month follow-up, the presence or absence of aneurysmal wall enhancement, and the presence or absence of aneurysmal lumen showed no statistically significant differences between the two groups (all P > 0.05). By contrast, variables like in operative time, rupture status of the aneurysm before surgery according to World Federation of Neurologic Surgeons (WFNS) grade, aneurysm size, number of stents used, number of guidewires and catheters used, and Evans index between the two groups were found to have statistically significant disparities between those who developed microischemia and those who did not (P < 0.05). A subsequent multivariate analysis revealed that aneurysm size, Evans index, and the number of stents used were independent risk factors for the occurrence of ultra-long-term microischemia after surgical intervention of aneurysms (P < 0.05). The receiver operating characteristic (ROC) curves of the patients were constructed on the basis of risk factors determined through multivariate logistic regression analysis. Results indicated that aneurysm size (area under ROC curve (AUC) 0.619, sensitivity 94.7%, specificity 17.1%, P = 0.049), Evans index (AUC 0.670, sensitivity 96.4%, specificity 26.8%, P = 0.004), and number of stents (AUC 0.639, sensitivity 44.6%, specificity 90.2%, P < 0.001) effectively predicted the occurrence of microischemia. The incidence of cognitive dysfunction was higher in the microischemic group than in the control group (P < 0.05), and a greater number of microischemic foci was associated with a higher incidence of cognitive dysfunction. The proportion of microschemia foci in the thalamus and basal ganglia in patients with cognitive dysfunction (60.87%) was significantly higher than that in patients without cognitive dysfunction (34.55%) (P < 0.05). CONCLUSION: Aneurysm size, Evans index > 0.3, and the quantity of stents were independent risk factors for the occurrence of ultra-long-term microischemia after aneurysm embolization and provided good predictive performance. Cognitive dysfunction was closely associated with microischemia, with its severity increasing with an increase in the number of ischemic foci.

Structures of the mumps virus polymerase complex via cryo-electron microscopy.

The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L-P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates.

Postponed endoscopic necrosectomy results in a lower rate of additional intervention for infected walled-off necrosis.

Although endoscopic necrosectomy (EN) is more frequently used to manage walled-off necrosis (WON), there is still debate over how much time should pass between the initial stent placement and the first necrosectomy. This study aims to determine the effect of performing EN within different timings after placing the initial stent on clinical outcomes for WON. A retrospective study on infected WON patients compared an early necrosectomy within one week after the initial stent placement with a necrosectomy that was postponed after a week. The primary outcomes compared the rate of clinical success and the need for additional intervention after EN to achieve WON resolution. 77 patients were divided into early and postponed necrosectomy groups. The complete resolution of WON within six months of follow-up was attained in 73.7% and 74.3% of patients in both the early and postponed groups. The early group tended to a greater need for additional intervention after EN (26.8% early necrosectomy vs. 8.3% postponed necrosectomy, P = 0.036). Our study does not demonstrate that early necrosectomy is superior to postponed necrosectomy in terms of clinical success rate, total count of necrosectomy procedures, procedure-related complications, length of hospitalization and prognosis. Conversely, patients in the postponed group received fewer additional interventions.

The signature of cuproptosis-related immune genes predicts the tumor microenvironment and prognosis of prostate adenocarcinoma.

Background: Cuproptosis plays a crucial role in cancer, and different subtypes of cuproptosis have different immune profiles in prostate adenocarcinoma (PRAD). This study aimed to investigate immune genes associated with cuproptosis and develop a risk model to predict prognostic characteristics and chemotherapy/immunotherapy responses of patients with PRAD. Methods: The CIBERSORT algorithm was used to evaluate the immune and stromal scores of patients with PRAD in The Cancer Genome Atlas (TCGA) cohort. Validation of differentially expressed genes DLAT and DLD in benign and malignant tissues by immunohistochemistry, and the immune-related genes of DLAT and DLD were further screened. Univariable Cox regression were performed to select key genes. Least absolute shrinkage and selection operator (LASSO)-Cox regression analyse was used to develop a risk model based on the selected genes. The model was validated in the TCGA, Memorial Sloan-Kettering Cancer Center (MSKCC) and Gene Expression Omnibus (GEO) datasets, as well as in this study unit cohort. The genes were examined via functional enrichment analysis, and the tumor immune features, tumor mutation features and copy number variations (CNVs) of patients with different risk scores were analysed. The response of patients to multiple chemotherapeutic/targeted drugs was assessed using the pRRophetic algorithm, and immunotherapy was inferred by the Tumor Immune Dysfunction and Exclusion (TIDE) and immunophenoscore (IPS). Results: Cuproptosis-related immune risk scores (CRIRSs) were developed based on PRLR, DES and LECT2. High CRIRSs indicated poor overall survival (OS), disease-free survival (DFS) in the TCGA-PRAD, MSKCC and GEO datasets and higher T stage and Gleason scores in TCGA-PRAD. Similarly, in the sample collected by the study unit, patients with high CRIRS had higher T-stage and Gleason scores. Additionally, higher CRIRSs were negatively correlated with the abundance of activated B cells, activated CD8+ T cells and other stromal or immune cells. The expression of some immune checkpoints was negatively correlated with CRIRSs. Tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH) and copy number variation (CNV) scores were all higher in the high-CRIRS group. Multiple chemotherapeutic/targeted drugs and immunotherapy had better responsiveness in the low-CRIRS group. Conclusion: Overall, lower CRIRS indicated better response to treatment strategies and better prognostic outcomes.

Melatonin alleviates intrarenal CaOx crystals deposition through inhibiting LPS-induced non-canonical inflammasome-mediated renal tubular epithelial cells pyroptosis.

Urinary tract infection has long been considered a complication rather than etiology of calcium oxalate (CaOx) nephrolithiasis. This study aimed to explore the role of lipopolysaccharide (LPS), an important component of Gram-negative bacteria, on CaOx nephrolithiasis formation and antagonistic effect of melatonin. Male C57BL/6 mice were intraperitoneally injected with glyoxylate acid (80 mg/kg) daily for 7 days to construct CaOx nephrolithiasis model. A single dose of LPS (2.0 mg/kg) was given 2 h before the second glyoxylate acid treatment in the presence or absence of melatonin (25 mg/kg). Our results found that LPS promoted adhesion of CaOx crystals to renal tubular epithelial cells (RTECs) and intrarenal CaOx crystals deposition. Protein levels of cleaved Caspase-11, N-terminal of cleaved GSDMD (GSDMD-N), NOD-like receptor thermal protein domain associated protein 3 (NLRP3) and cleaved Caspase-1, several markers of non-classical inflammasome activation were upregulated in LPS-treated mouse kidneys and HK-2 cells. Moreover, the number of GSDMD pores was increased in LPS-treated HK-2 cell membrane. Melatonin inhibited Caspase-11 cleavage and antagonized the subsequent LPS-mediated upregulation of GSDMD-N, NLRP3 and cleaved Caspase-1 in kidney tissues and HK-2 cells. In addition, melatonin reduced membrane localization of GSDMD-N and the number of GSDMD pores in LPS-treated HK-2 cells. Accordingly, melatonin inhibited LPS-induced IL-1ß and IL-18 in mouse serum and HK-2 culture supernatant. Importantly, melatonin alleviated LPS-induced crystal-cell interactions and intrarenal CaOx crystals deposition. We provide experimental evidence that LPS promoted CaOx nephrolithiasis formation by inducing non-canonical inflammasome-mediated RTECs pyroptosis. Melatonin alleviated CaOx nephrolithiasis formation through inhibiting LPS-induced non-canonical inflammasome-mediated RTECs pyroptosis.

Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection.

White spot syndrome virus (WSSV) is one of the largest DNA viruses and the major pathogen responsible for white spot syndrome in crustaceans. The WSSV capsid is critical for genome encapsulation and ejection and exhibits the rod-shaped and oval-shaped structures during the viral life cycle. However, the detailed architecture of the capsid and the structural transition mechanism remain unclear. Here, using cryo-electron microscopy (cryo-EM), we obtained a cryo-EM model of the rod-shaped WSSV capsid and were able to characterize its ring-stacked assembly mechanism. Furthermore, we identified an oval-shaped WSSV capsid from intact WSSV virions and analyzed the structural transition mechanism from the oval-shaped to rod-shaped capsids induced by high salinity. These transitions, which decrease internal capsid pressure, always accompany DNA release and mostly eliminate the infection of the host cells. Our results demonstrate an unusual assembly mechanism of the WSSV capsid and offer structural insights into the pressure-driven genome release.

Vitamin D deficiency aggravates growth and metastasis of prostate cancer through promoting EMT in two ß-catenin-related mechanisms.

Increasing evidence has demonstrated that vitamin D deficiency is associated with prostate cancer progression, but its mechanism remains unclear. This study investigated effects of vitamin D deficiency on growth and metastasis of prostate cancer. Nude mice and Transgenic adenocarcinoma of the mouse prostate (TRAMP) mice were fed with vitamin D-deficient (VDD) diets. Prostate cancer growth was aggravated in VDD diet-fed nude mice and TRAMP mice. Invasion and metastasis of prostate cancer were exacerbated in VDD diet-fed TRAMP mice. In vitro experiments showed that calcitriol, an active vitamin D3, inhibited migration and invasion in transforming growth factor (TGF)-ß1 -stimulated and -unstimulated PC-3 and DU145 cells. Mechanistically, calcitriol inhibited epithelial-mesenchymal transition (EMT) in TGF-ß1 -stimulated and -unstimulated DU145 cells. Unexpectedly, calcitriol did not inhibit Smad2/3 phosphorylation in TGF-ß1-stimulated DU145 cells. Instead, calcitriol downregulated expression of proliferation-, metastasis- and EMT-related genes, includes Cyclin D1, MMP7, and Zeb1, by inhibiting interaction between TCF4 and ß-catenin. In addition, calcitriol promoted interaction between cytoplasmic VDR and ß-catenin, reduced ß-catenin phosphorylation and elevated ß-catenin/E-cadherin adherens junction complex formation. We provide novel evidence that vitamin D deficiency aggravates growth and metastasis of prostate cancer possibly through promoting EMT in two ß-catenin-related mechanisms.

Distinct impact of IgG subclass on autoantibody pathogenicity in different IgG4-mediated diseases.

IgG4 is the least potent human IgG subclass for the FcγR-mediated antibody effector function. Paradoxically, IgG4 is also the dominant IgG subclass of pathogenic autoantibodies in IgG4-mediated diseases. Here, we show that the IgG subclass and Fc-FcγR interaction have a distinct impact on the pathogenic function of autoantibodies in different IgG4-mediated diseases in mouse models. While IgG4 and its weak Fc-FcγR interaction have an ameliorative role in the pathogenicity of anti-ADAMTS13 autoantibodies isolated from thrombotic thrombocytopenic purpura (TTP) patients, they have an unexpected exacerbating effect on anti-Dsg1 autoantibody pathogenicity in pemphigus foliaceus (PF) models. Strikingly, a non-pathogenic anti-Dsg1 antibody variant optimized for FcγR-mediated effector function can attenuate the skin lesions induced by pathogenic anti-Dsg1 antibodies by promoting the clearance of dead keratinocytes. These studies suggest that IgG effector function contributes to the clearance of autoantibody-Ag complexes, which is harmful in TTP, but beneficial in PF and may provide new therapeutic opportunity.

A transistor-like pH-sensitive nanodetergent for selective cancer therapy.

Plasma membrane rupture is a promising strategy for drug-resistant cancer treatment, but its application is limited by the low tumour selectivity of membranolytic molecules. Here we report the design of 'proton transistor' nanodetergents that can convert the subtle pH perturbation signals of tumour tissues into sharp transition signals of membranolytic activity for selective cancer therapy. Our top-performing 'proton transistor' nanodetergent, P(C6-Bn20), can achieve a >32-fold change in cytotoxicity with a 0.1 pH input signal. At physiological pH, P(C6-Bn20) self-assembles into neutral nanoparticles with inactive membranolytic blocks shielded by poly(ethylene glycol) shells, exhibiting low toxicity. At tumour acidity, a sharp transition in its protonation state induces a morphological transformation and an activation of the membranolytic blocks, and the cation-π interaction facilitates the insertion of benzyl groups-containing hydrophobic domains into the cell membranes, resulting in potent membranolytic activity. P(C6-Bn20) is well tolerated in mice and shows high anti-tumour efficacy in various mouse tumour models.

Annealing synchronizes the 70S ribosome into a minimum-energy conformation.

Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70S ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.

Prediction of prognosis and immunotherapy response with a robust immune-related lncRNA pair signature in lung adenocarcinoma.

The tumor immune microenvironment plays essential roles in regulating inflammation, angiogenesis, immune modulation, and sensitivity to therapies. Here, we developed a powerful prognostic signature with immune-related lncRNAs (irlncRNAs) in lung adenocarcinoma (LUAD). We obtained differentially expressed irlncRNAs by intersecting the transcriptome dataset for The Cancer Genome Atlas (TCGA)-LUAD cohort and the ImmLnc database. A rank-based algorithm was applied to select top-ranking altered irlncRNA pairs for the model construction. We built a prognostic signature of 33 irlncRNA pairs comprising 40 unique irlncRNAs in the TCGA-LUAD cohort (training set). The immune signature significantly dichotomized LUAD patients into high- and low-risk groups regarding overall survival, which is likewise independently predictive of prognosis (hazard ratio = 3.580, 95% confidence interval = 2.451-5.229, P < 0.001). A nomogram with a C-index of 0.79 demonstrates the superior prognostic accuracy of the signature. The prognostic accuracy of the signature of 33 irlncRNA pairs was validated using the GSE31210 dataset (validation set) from the Gene Expression Omnibus database. Immune cell infiltration was calculated using ESTIMATE, CIBERSORT, and MCP-count methodologies. The low-risk group exhibited high immune cell infiltration, high mutation burden, high expression of CTLA4 and human leukocyte antigen genes, and low expression of mismatch repair genes, which predicted response to immunotherapy. Interestingly, pRRophetic analysis demonstrated that the high-risk group possessed reverse characteristics was sensitive to chemotherapy. The established immune signature shows marked clinical and translational potential for predicting prognosis, tumor immunogenicity, and therapeutic response in LUAD.

Development of immune gene pair-based signature predictive of prognosis and immunotherapy in esophageal cancer.

BACKGROUND: Esophageal cancer (EC) is one of the deadliest solid malignancies, mainly consisting of esophageal squamous cell carcinoma (ESCC) and adenocarcinoma (EAC). Robust biomarkers that can improve patient risk stratification are needed to optimize cancer management. We sought to establish potent prognostic signatures with immune-related gene (IRG) pairs for ESCC and EAC. METHODS: We obtained differentially expressed IRGs by intersecting the Immunology Database and Analysis Portal (ImmPort) with the transcriptome data set of The Cancer Genome Atlas (TCGA)-ESCC and EAC cohorts. A novel rank-based pairwise comparison algorithm was applied to select effective IRG pairs (IRGPs), followed by constructing a prognostic IRGP signature via the least absolute shrinkage and selection operator (LASSO) regression model. We assessed the predictive power of the IRGP signatures on prognosis, tumor-infiltrating immune cells, and immune checkpoint inhibitor (ICI) efficacy in EC. Kaplan-Meier survival analysis and receiver operating characteristic curves (ROC) were used to evaluate the clinical significance of IRGPs. Univariate and multivariate Cox regression analyses were performed to investigate the association of overall survival (OS) with IRGPs and clinical characteristics. RESULTS: We built a 19-IRGP signature for ESCC (n=75) and a 17-IRGP signature for EAC (n=78), with an area under the ROC curve (AUC) of 0.931 and 0.803, respectively. IRGP signature-derived risk scores stratified patients into low- and high-risk groups with significantly different OS in ESCC and EAC (P<0.001). Nomogram and decision curve analysis were used to evaluate the clinical relevance of the prognostic signatures, achieving a C-index of 0.973 in ESCC and 0.880 in EAC. The risk scores were associated with immune and ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) scores and the composition of immune cells in the tumor microenvironment. The association between risk score and human leukocyte antigens (HLAs), mismatch repair (MMR) genes, and immune checkpoint molecules demonstrated its predictive value for ICI response. Differential immune characteristics and predictive value of the risk score were observed in EAC. CONCLUSIONS: The established immune signatures showed great promise in predicting prognosis, tumor immunogenicity, and immunotherapy response in ESCC and EAC.