Human Protein Research Articles

High-affinity VNARs targeting human hemoglobin: Screening, stability and binding analysis.

Hemoglobin, composed of α- and β-chains, is essential for oxygen transport and is key in diagnosing and treating gastrointestinal and blood disorders. It also aids in detecting blood contamination and estimating transfusion volumes. Immunological methods, based on antigen-antibody interactions, are distinguished by their high sensitivity and accuracy. Consequently, it is necessary to develop hemoglobin-specific antibodies characterized by high specificity and affinity to enhance detection accuracy. The variable domain of the new antigen receptor (VNAR) from sharks, the smallest antigen-binding unit, is ideal for disease diagnosis and treatment due to its small size, stability, and high affinity. In this study, Chiloscyllium plagiosum was immunized with human hemoglobin protein. Nine VNAR immune libraries with sizes ranging from 1 × 108 to 1.82 × 109 colony-forming units (CFU) were constructed and biopanned using phage display, resulting in three hemoglobin-specific VNAR sequences (5-10C, 7-11 A, T-12-4D). These sequences were inserted into pTT5-TEV-Fc vectors and transfected into HEK 293F cells. The resulting VNAR-Fc fusion proteins were purified from the cell culture supernatants. Binding activity, cross-reactivity, physicochemical stability, and epitope competition were evaluated using non-competitive enzyme-linked immunosorbent assay (ELISA) and biolayer interferometry (BLI). T-12-4D-Fc exhibited the highest affinity with a KD value of 7.59 nM and superior physicochemical stability. It maintained over 80 % binding activity at 90 °C, over 51 % in extreme pH conditions (pH 2 and 12), and above 65 % in urea concentrations up to 8 mol/L. Its binding activity remained largely unaffected after 6 h of incubation in human plasma-like medium (HPLM). The binding epitope competition results showed that 5-10C-Fc and T-12-4D-Fc targeted the same hemoglobin epitope. Molecular dynamics simulations revealed hydrogen bonds as the primary interaction force between VNARs and hemoglobin. Furthermore, a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) method was established for the detection of human hemoglobin, utilizing T-12-4D-Fc as the coating antibody. This technique demonstrated high accuracy, reproducibility and specificity when applied to human whole blood samples. Hence, the identified VNARs, particularly T-12-4D, demonstrated good stability, specificity, and high affinity, filling the gap of hemoglobin-targeting shark-derived single-domain antibodies and offering a foundation for diagnosing and monitoring hemoglobin-related diseases.

Anti-proliferative and photodynamic activities of Senna didymobotrya (Fresen.) leaf alkaloid-rich extracts against breast cancer cells

BackgroundAmongst all neoplastic diseases, breast cancer represents a major cause of death among the female population in developed and developing countries. Since alkaloid drugs are commonly used in chemotherapy to manage this disease, this study investigated the anti-proliferative effectiveness of alkaloid-rich fractions of Senna didymobotrya leaves only and with laser irradiation against MCF-7 breast cancer cells.Method and materialsA powdered sample of the plant leaves was extracted with 50% ethanol, filtered and their pH was adjusted with acid and base solution followed by partitioning with chloroform and ethyl acetate solvents. Cells were treated with 240 μg/mL of the respective extracts, while those in the photodynamic therapy groups, cells were exposed to laser (405 nm wavelength and 10 Jcm−2) irradiation 6 h post extracts' administration.ResultsTreatment with the S. didymobotrya leaves alkaloid extracts significantly decreased the ATP concentration and overall viability of the MCF-7 cells. Reactive oxygen species (ROS) levels in cell groups treated with the extracts and laser light were considerably higher than in experimental groups treated with only the extracts. Moreover, the molecular docking analysis revealed the involvement of only hydrophobic bonds in the interactions of the plant’s alkaloid-derived phytoconstituents’ with selected cancer protein biomarkers.ConclusionAlthough the in silico analysis suggests that the plant-identified alkaloid phytoconstituents inhibition of estrogen receptor-alpha, human epidermal growth factor receptor-2 and progesterone receptor proteins involved in breast cancer pathogenesis could explain a possible mechanism for the observed anticancer effect, more detailed in vitro molecular experiments are necessary to confirm these findings.

ARTN and CCL23 predicted chemosensitivity in acute myeloid leukemia: an Olink® proteomics approach

BackgroundThe standard “7 + 3” induction results in 30% of de novo acute myeloid leukemia (AML) patients not achieving complete remission (CR). We aimed to utilize the Olink® platform to compare the bone marrow plasma proteomic profiles of newly diagnosed de novo AML patients who did and did not achieve CR following “7 + 3” induction treatment.MethodsThis prospective study included 43 untreated AML patients, stratified into CR (n = 29) and non-CR (n = 14) groups based on their response to “7 + 3” induction therapy. We employed the Olink® Explore-384 Inflammation platform for proteomic analysis to investigate differences in bone marrow plasma protein levels between the CR and non-CR groups.ResultsProteomic analysis demonstrated that the CR group exhibited significantly higher bone marrow plasma levels of ARTN and CCL23 than did the non-CR group. Immunohistochemical staining confirmed a higher proportion of tissue samples with intense staining for ARTN (25.40% vs. 7.05%, p = 0.013) and CCL23 (24.14% vs. 14.29%, p = 0.039) in the CR group. These findings were corroborated by bulk-RNA-seq, which indicated significantly elevated mRNA expression levels of ARTN (1.93 vs. -0.09; p = 0.003) and CCL23 (1.50 vs. 0.12; p = 0.021) in the CR group. The Human Protein Atlas provided external support for our findings.ConclusionsThe results suggest that ARTN and CCL23 may serve as biomarkers for predicting responsiveness to the “7 + 3” induction in untreated AML. Using an enzyme-linked immunosorbent assay to identify the roles of ARTN and CCL23 in predicting AML chemosensitivity may enhance clinical applicability in the future.

Human epididymis protein 4-annexin II binding promotes aberrant epithelial-fibroblast crosstalk in pulmonary fibrosis

Invasive lung myofibroblasts are the main cause of tissue remodeling in idiopathic pulmonary fibrosis (IPF). A key mechanism contributing to this important feature is aberrant crosstalk between the abnormal/injured lung epithelium and pulmonary fibroblasts. Here, we demonstrate that lungs from patients with IPF and from mice with bleomycin (BLM)-induced pulmonary fibrosis (PF) are characterized by the induction of human epididymis protein 4 (HE4) overexpression in epithelial cells. HE4 knockdown primarily in epithelial cells attenuates BLM-induced PF in mice, whereas the administration of recombinant mouse HE4 exacerbates fibrosis after BLM stimulation. Mechanistic analysis shows that HE4 and annexin II (ANXA2) specific binding enhances the profibrotic phenotype in epithelial cells, and directly promotes lung fibroblast activation, leading to aberrant epithelial-fibroblast crosstalk and the persistent myofibroblast phenotype. The HE4 and ANXA2 binding site is located after the 30th amino acid at the N terminus of the HE4 molecule. Finally, intratracheal administration of HE4 shRNA lentivirus protects mice against BLM-induced PF. These data suggest that HE4 can serve as a potential therapeutic target in the treatment of IPF.

Fructose-derived glycation and immune function: Effects on antigen binding in human IgG and lymphocytes.

Diabetes Mellitus (DM), one of the oldest known metabolic disorders, dates back to 3000 BC and continues to have a profound impact on health and the economy. Nutrition plays a critical role in managing diabetes and enhancing overall quality of life. It is also vital for immune system function, as well as in the prevention and treatment of aging-related diseases. A key factor contributing to the global rise in obesity is the excessive consumption of fructose/glucose (corn) syrup, which leads to various metabolic complications. Uncontrolled intake of carbohydrates, particularly sugars like fructose, triggers the Maillard Reaction, a chemical process that occurs between sugars and proteins, resulting in advanced glycation end-products (AGEs). This process is accelerated in diabetic patients due to hyperglycemia, leading to increased glycation of plasma proteins such as immunoglobulins, which play an essential role in the immune system. Studies show that individuals with Diabetes Mellitus experience a higher susceptibility to infections due to increased viral entry, impaired immune responses, reduced viral clearance, and dysregulated inflammatory cytokine production. In this study, human IgG proteins were glycated in vitro using fructose, simulating the damaging effects seen in diabetic conditions. A mixture containing antioxidants like glutathione, oleuropein, and selenium was prepared and incubated with the glycated IgG to assess its protective properties. Lymphocyte cells from healthy volunteers were also treated with fructose and subjected to similar experiments. Results demonstrated that fructose significantly compromises immune function by damaging key proteins, but the antioxidant mixture effectively mitigates this damage, offering a protective mechanism against glycation in the immune system.

Health Risk Assessment of Potentially Toxic Metals in Differently Processed Catfish (Clarias gariepinus) from Selected Markets from Abeokuta Southwestern Nigeria.

Fish is a significant source of animal protein for humans; however, it has a tendency to bioaccumulate toxicants from the environment. The present study assessed the health risks associated with potential toxic metals (PTMs) in differently processed catfish (Clarias gariepinus) from four markets in Abeokuta metropolis, southwestern Nigeria. A total of 60 samples were collected and analyzed for PTMs using an Atomic Absorption Spectrophotometer. The health risk assessment was evaluated based on the hazard quotient (HQ), hazard index (HI), and cancer risk (CR). Iron concentrations ranged from 8.10 ± 6.80 to 70.7 ± 30.8mg/kg, making it the highest measured metal in the fish samples. The mean chromium (Cr) levels (0.25 ± 0.25 to 28.4 ± 14.5mg/kg), and lead concentrations (< 0.08 to 0.80 ± 0.70mg/kg) exceeded the permissible limits set by the joint FAO/WHO, in most of the differently processed fish samples. Principal component analysis identified two likely sources of metal contamination in the fish samples as pond/river runoff and vehicular emissions. The health risk assessment revealed a HQ for Cr exceeding the permissible limit of 1.0 across all processed catfish consumed by both adults and children. Similarly, the CR values for Cr surpassed the threshold of 1.0 × 10⁻4 in both age groups. Chromium accounted for 43% to 98% of the contributions to both carcinogenic and non-carcinogenic health risks. The findings indicated that children are more susceptible to the adverse health effects of PTMs than adults through the consumption of variously processed catfish.

Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds

BackgroundChickens and ducks are vital sources of animal protein for humans. Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species, highlighting the need for more comprehensive genomes. The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. We aim to complete the chicken and duck genomes, recover missing genes, and reveal common and unique chromosomal features between birds.ResultsThe near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies, with quality values of 36.65 and 44.17 for Silkie and Mallard, respectively; and BUSCO scores of 96.55% and 96.97% for Silkie and Mallard, respectively; the mapping rates reached over 99.52% for both assembled genomes, these evaluation results ensured high completeness and accuracy. We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard, respectively, and assembled gap-free sex chromosomes in Mallard for the first time. Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content, repetitive sequence abundance, gene density, and levels of 5mC methylation. Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes, with Mallard centromeres being invaded by CR1. The highly heterochromatic W chromosome, which serves as a refuge for ERVs, contains disproportionately long ERVs. Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes, and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome. Finally, we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time, revealing conserved protein structures and tissue-specific expression.ConclusionsThe near telomere-to-telomere assemblies in Mallard and Silkie, with the first gap-free sex chromosomes in ducks, significantly enhanced our understanding of genetic structures in birds, specifically highlighting the distinctive chromosome features between the chicken and duck genomes. This foundational work also provides a series of newly identified missing genes for further investigation.

Binding of ligands to the aryl hydrocarbon receptor: An overview of methods.

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor, which plays numerous and pivotal roles in human physiology and pathophysiology. Therefore, pharmacotherapeutic targeting of the AhR is a highly pertinent issue. The identification of new AhR ligands and the characterization of the interactions between the AhR ligands and AhR protein requires appropriate methodology. In spite the AhR is monomeric intracellular soluble receptor, the full-length human AhR protein has not been crystallized so far, and its isolation in a form applicable in the binding assays is highly challenging. Recent advances, including crystallization of AhR fragments, recombinant protein technologies, and cryogenic electron microscopy, allowed for exploitation of diverse experimental techniques for studying interactions between ligands and the AhR. In the current paper, we review existing AhR ligand binding assays, including their description, applicability and limitations.

Relationship between inherited genetic variation and survival from colorectal cancer stratified by tumour location

The location of a patient’s colorectal cancer (CRC) influences their outcome but inherited factors may also be involved. We studied 1899 patients with advanced CRC (514 had proximal colonic, 493 distal colonic and 892 rectal tumours) and carried out genome-wide association studies for survival. Single nucleotide polymorphisms (SNPs) suggestive of association (P < 1.0 × 10–5) were tested for replication in 5078 CRC patients from the UK Biobank. We investigated the relationship between Phosphatidylinositol 4-Kinase Type 2 Beta (PI4K2B) expression in colorectal tumours and survival in 597 patients from The Human Protein Atlas (THPA). We also analysed 3 SNPs previously associated with survival by anatomical site. We found that SNPs at 54 independent loci were suggestive of an association with survival when stratified by tumour location. rs76011559 replicated in patients with proximal tumours (COIN, COIN-B and UK Biobank combined Hazard Ratio [HR] = 1.53, 95% Confidence Intervals [CI] = 1.19–1.86, P = 7.5 × 10–7) and rs12273047 replicated in patients with rectal tumours (combined HR = 1.27, 95% CI = 1.09–1.46, P = 4.1 × 10–7). In gene analyses, PI4K2B associated with survival in patients with distal cancers (P = 2.1 × 10–6) and increased PI4K2B expression in colorectal tumours was associated with improved survival (P = 9.6 × 10–5). No previously associated SNPs were replicated. Our data identify novel loci associated with survival when stratified by tumour location.

Supervised learning approaches for predicting Ebola-Human Protein-Protein interactions.

The goal of this research work is to predict protein-protein interactions (PPIs) between the Ebola virus and the host who is at risk of infection. Since there are very limited databases available on the Ebola virus; we have prepared a comprehensive database of all the PPIs between the Ebola virus and human proteins (EbolaInt). Our work focuses on the finding of some new protein-protein interactions between humans and the Ebola virus using some state- of-the-arts machine learning techniques. However, it is basically a two-class problem with a positive interacting dataset and a negative non-interacting dataset. These datasets contain various sequence-based human protein features such as structure of amino acid and conjoint triad and domain-related features. In this research, we have briefly discussed and used some well-known supervised learning approaches to predict PPIs between human proteins and Ebola virus proteins, including K-nearest neighbours (KNN), random forest (RF), support vector machine (SVM), and deep feed-forward multi-layer perceptron (DMLP) etc. We have validated our prediction results using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Our goal with this prediction is to compare all other models' accuracy, precision, recall, and f1-score for predicting these PPIs. In the result section, DMLP is giving the highest accuracy along with the prediction of 2655 potential human target proteins.

Comparative proteomic landscapes elucidate human preimplantation development and failure.

Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility.

Structural basis for metal ion transport by the human SLC11 proteins DMT1 and NRAMP1

Iron and manganese are essential nutrients whose transport across membranes is catalyzed by members of the SLC11 family. In humans, this protein family contains two paralogs, the ubiquitously expressed DMT1, which is involved in the uptake and distribution of Fe2+ and Mn2+, and NRAMP1, which participates in the resistance against infections and nutrient recycling. Despite previous studies contributing to our mechanistic understanding of the family, the structures of human SLC11 proteins and their relationship to functional properties have remained elusive. Here we describe the cryo-electron microscopy structures of DMT1 and NRAMP1 and relate them to their functional properties. We show that both proteins catalyze selective metal ion transport coupled to the symport of H+, but additionally also mediate uncoupled H+ flux. Their structures, while sharing general properties with known prokaryotic homologs, display distinct features that lead to stronger transition metal ion selectivity.

A novel basement membrane-related gene signature for predicting prognosis of HNSCC.

In recent years, a notably heterogeneous malignant tumor, squamous cell carcinoma of the head and neck (HNSCC), has received increasing attention, with no significant improvement in its survival rate. The rapid increase in the number of prognostic models associated with HNSCC has been observed due to its accuracy, which offers crucial clinical benefits. The 10 genes were selected from 222 human genes associated with the basement membrane in the analysis of this article. The gene pool was narrowed through different classifications and intersections, followed by univariate Cox regression analysis. Genes with statistical significance underwent further Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis, resulting in the final selection of 10 genes. The data and images extracted from the Human Protein Atlas database were utilized to confirm the differential expression of the corresponding genes. Multivariate Cox regression analysis was employed to develop a nomogram, and the nomogram was assessed by additional decision curve analysis (DCA). The Gene Expression Omnibus validation set was used to validate the established model. Finally, between the high- and low-risk score groups, Gene Set Enrichment Analysis, immune correlation analysis, and drug sensitivity analysis were conducted in this paper. ITGA5, SPOCK1, EVA1C, TINAGL1, LAMB4, ADAMTS1, EGFL6, GPC2, BGN, and ITGA2B were successfully developed as basement membrane-associated risk models. The time-dependent receiver operating characteristic (timeROC) curve illustrated that the risk score prediction accuracy outperformed indicators, which were commonly adopted in clinical practice, consisting of age, stage, gender, T-staging, and N-staging. The 3-year risk score timeROC area under the curve value was 0.679. This model demonstrates a reliable ability to assess the prognosis of HNSCC patients. In addition, the specific potential biomarkers associated with the basement membrane were explored in this research.

Glycosylation Pathways Targeted by Deregulated miRNAs in Autism Spectrum Disorder.

Autism Spectrum Disorder (ASD) is a complex condition with a multifactorial aetiology including both genetic and epigenetic factors. MicroRNAs (miRNAs) play a role in ASD and may influence metabolic pathways. Glycosylation (the glycoconjugate synthesis pathway) is a necessary process for the optimal development of the central nervous system (CNS). Congenital Disorders of Glycosylation (CDGs) (CDGs) are linked to over 180 genes and are predominantly associated with neurodevelopmental disorders (NDDs) including ASD. From a literature search, we considered 64 miRNAs consistently deregulated in ASD patients (ASD-miRNAs). Computational tools, including DIANA-miRPath v3.0 and TarBase v8, were employed to investigate the potential involvement of ASD-miRNAs in glycosylation pathways. A regulatory network constructed through miRNet 2.0 revealed the involvement of these miRNAs in targeting genes linked to glycosylation. Protein functions were further validated through the Human Protein Atlas. A total of twenty-five ASD-miRNAs were identified, including nine miRNAs that were differentially expressed in cells or brain tissue in ASD patients and associated with glycosylation pathways, specifically protein N- and O-glycosylation and glycosaminoglycan biosynthesis (heparan sulfate). A number of CDG genes and/or ASD-risk genes, including DOLK, GALNT2, and EXT1, were identified as targets, along with validated interactions involving four key miRNAs (hsa-miR-423-5p, hsa-miR-30c-5p, hsa-miR-195-5p, and hsa-miR-132-5p). B4GALT1, an ASD susceptibility gene, emerged as a central regulatory hub, reinforcing the link between glycosylation and ASD. In sum, the evidence presented here supports the hypothesis that ASD-miRNAs mediate the epigenetic regulation of glycosylation, thus unveiling possible novel patho-mechanisms underlying ASD.

Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential.

The fungal Bromodomain and Extra-Terminal (BET) protein Bdf1 is a potential antifungal target against invasive fungal infections. However, the need to selectively inhibit both Bdf1 bromodomains (BDs) over human orthologs and the lack of molecular tools to assess on-target antifungal efficacy hamper efforts to develop Bdf1 BD inhibitors as antifungal therapeutics. This study reports a phenyltriazine compound that inhibits both Bdf1 BDs from the human fungal pathogen Candida glabrata with selectivity over the orthologous BDs from the human BET protein Brd4. On-target antifungal activity is established by devising two yeast-based inhibition assays: a growth assay using humanized Candida strains in which the Bdf1 BDs are replaced by their Brd4 counterparts, and a NanoBiT assay that evaluates the BD-mediated association of Bdf1 with chromatin. These assays additionally enable the discovery that BET inhibitor I-BET726 targets both Bdf1 BDs, inhibits the growth of a broad spectrum of Candida species, including antifungal-resistant clinical isolates, and displays efficacy in an invertebrate animal model of infection. These collective findings highlight the promising potential of Bdf1 BD inhibitors as an innovative class of antifungal therapeutics and the pivotal role of yeast-based assay development toward achieving this end.

Pan-cancer secreted proteome and skeletal muscle regulation: insight from a proteogenomic data-driven knowledge base.

Large-scale, pan-cancer analysis is enabled by data driven knowledge bases that link tumor molecular profiles with phenotypes. A debilitating cancer-related phenotype is skeletal muscle loss, or cachexia, which occurs partly from tumor products secreted into circulation. Using the LinkedOmicsKB knowledge base assembled from the Clinical Proteomics Tumor Analysis Consortium proteogenomic analysis, along with catalogs of human secretome proteins, ligand-receptor pairs and molecular signatures, we sought to identify candidate pan-cancer proteins secreted to blood that could regulate skeletal muscle phenotypes in multiple solid cancers. Tumor proteins having significant pan-cancer associations with muscle were referenced against secretome proteins secreted to blood from the Human Protein Atlas, then verified as increased in paired tumor vs. normal tissues in pan-cancer manner. This workflow revealed seven secreted proteins from cancers afflicting kidneys, head and neck, lungs and pancreas that classified as protein-binding activity modulator, extracellular matrix protein or intercellular signaling molecule. Concordance of these biomarkers with validated molecular signatures of cachexia and senescence supported relevance to muscle and cachexia disease biology, and high tumor expression of the biomarker set associated with lower overall survival. In this article, we discuss avenues by which skeletal muscle and cachexia may be regulated by these candidate pan-cancer proteins secreted to blood, and conceptualize a strategy that considers them collectively as a biomarker signature with potential for refinement by data analytics and radiogenomics for predictive testing of future risk in a non-invasive, blood-based panel amenable to broad uptake and early management.

Serum Biomarkers of Pulmonary Damage and Risk for Progression of Rheumatoid Arthritis-Associated Interstitial Lung Disease.

To investigate baseline and change of pulmonary damage biomarkers (serum Krebs von den Lungen 6 [KL-6], human surfactant protein D [hSP-D], and matrix metalloproteinase 7 [MMP-7]) with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) progression. In the Korean Rheumatoid Arthritis Interstitial Lung Disease (KORAIL) cohort, a prospective cohort, we enrolled patients with RA and ILD confirmed by chest computed tomography imaging and followed annually. ILD progression was defined as worsening in physiological and radiological domains of the 2022 American Thoracic Society, European Respiratory Society, Japanese Respiratory Society, and Latin American Thoracic Society guideline for progressive pulmonary fibrosis (PPF). Associations between biomarkers and RA-ILD progression were analyzed using multivariable Cox regression, adjusting for potential confounders. We analyzed 136 patients with RA-ILD (mean age 66.5 yrs, 30% male, 60.3% with usual interstitial pneumonia pattern). During a median 3.0 years of follow-up, 47 patients (34.6%) experienced progression. Higher baseline KL-6 and hSP-D levels were associated with higher risk of ILD progression (multivariable hazard ratios [HRs] 1.37 [95% CI 1.03-1.82] and 1.51 [95% CI 1.09-2.08], respectively), whereas only the highest quartile of MMP-7 showed an increased risk (multivariable HR 2.60 [95% CI 1.07-6.33]). Increasing levels of serum KL-6 at 1 year showed the strongest association with progression (ΔKL-6: multivariable HR 2.00 [95% CI 1.29-3.11]), additionally adjusting for baseline biomarker levels. In this first prospective study to apply PPF criteria to RA-ILD, 34.6% progressed over 3 years. Higher baseline KL-6 and hSP-D were associated with progression. In follow-up, greater change in KL-6 was associated with progression. Serial measurement of pulmonary damage biomarkers may predict RA-ILD progression and may be helpful in monitoring patients and treatment decisions.

IL-33-activated ILC2s induce tertiary lymphoid structures in pancreatic cancer.

Tertiary lymphoid structures (TLSs) are de novo ectopic lymphoid aggregates that regulate immunity in chronically inflamed tissues, including tumours. Although TLSs form due to inflammation-triggered activation of the lymphotoxin (LT)-LTβ receptor (LTβR) pathway1, the inflammatory signals and cells that induce TLSs remain incompletely identified. Here we show that interleukin-33 (IL-33), the alarmin released by inflamed tissues2, induces TLSs. In mice, Il33 deficiency severely attenuates inflammation- and LTβR-activation-induced TLSs in models of colitis and pancreatic ductal adenocarcinoma (PDAC). In PDAC, the alarmin domain of IL-33 activates group 2 innate lymphoid cells (ILC2s) expressing LT that engage putative LTβR+ myeloid organizer cells to initiate tertiary lymphoneogenesis. Notably, lymphoneogenic ILC2s migrate to PDACs from the gut, can be mobilized to PDACs in different tissues and are modulated by gut microbiota. Furthermore, we detect putative lymphoneogenic ILC2s and IL-33-expressing cells within TLSs in human PDAC that correlate with improved prognosis. To harness this lymphoneogenic pathway for immunotherapy, we engineer a recombinant human IL-33 protein that expands intratumoural lymphoneogenic ILC2s and TLSs and demonstrates enhanced anti-tumour activity in PDAC mice. In summary, we identify the molecules and cells of a druggable pathway that induces inflammation-triggered TLSs. More broadly, we reveal a lymphoneogenic function for alarmins and ILC2s.

The Atlas of Protein-Protein Interactions in Cancer (APPIC)-a webtool to visualize and analyze cancer subtypes.

Cancer is a complex disease with heterogeneous mutational and gene expression patterns. Subgroups of patients who share a phenotype might share a specific genetic architecture including protein-protein interactions (PPIs). We developed the Atlas of Protein-Protein Interactions in Cancer (APPIC), an interactive webtool that provides PPI subnetworks of 10 cancer types and their subtypes shared by cohorts of patients. To achieve this, we analyzed publicly available RNA sequencing data from patients and identified PPIs specific to 26 distinct cancer subtypes. APPIC compiles biological and clinical information from various databases, including the Human Protein Atlas, Hugo Gene Nomenclature Committee, g:Profiler, cBioPortal and Clue.io. The user-friendly interface allows for both 2D and 3D PPI network visualizations, enhancing the usability and interpretability of complex data. For advanced users seeking greater customization, APPIC conveniently provides all output files for further analysis and visualization on other platforms or tools. By offering comprehensive insights into PPIs and their role in cancer, APPIC aims to support the discovery of tumor subtype-specific novel targeted therapeutics and drug repurposing. APPIC is freely available at https://appic.brown.edu.

A Comprehensive Analysis of the Role of PAX9 in Head and Neck Squamous Cell Carcinoma.

Paired box 9 (PAX9) has been linked to several human disorders; however, its relevance in Head And Neck Squamous Cell Carcinoma (HNSCC) remains unknown. The difference in PAX9 mRNA expression in pan-cancer was analyzed utilizing The Cancer Genome Atlas (TCGA), and the level of PAX9 protein expression across various types of cancer was assessed utilizing the Human Protein Atlas (HPA) and UALCAN databases, as well as the cellular localization of PAX9. UALCAN studied the methylation levels of PAX9 in pan-cancer. The predictive significance of PAX9 in pan-cancer was assessed utilizing the Kaplan-Meier Plotter website. Functional enrichment analysis was carried out with the "cluster Profiler" program. By employing CCK8 and colony formation methods, the influence of PAX9 on the growth of HNSCC cells was evaluated. By conducting a transwell experiment, we assessed the influence of PAX9 on the migration of HNSCC cells. Western blotting was used to determine the levels of Bax and Bcl-2, two proteins involved in the regulation of apoptosis. A nude mouse model was established to study the impact of PAX9 overexpression on the growth of subcutaneous HNSCC tumors. In HNSCC, the expression of PAX9 was found to be low, while levels of promoter methylation rose considerably. Low PAX9 expression has been linked to a decrease in overall survival (OS) rates among individuals with HNSCC. Furthermore, overexpressing the PAX9 gene decreased HNSCC cell proliferation, migration, and invasion while boosting apoptosis rates. The abnormal expression of PAX9 is linked to various cancers. In HNSCC, PAX9 is a potential tumor suppressor, inhibiting tumor invasion and migration. The results reveal a potentially significant new therapeutic target for HNSCC.