Tissue-based map of the human proteome

The genetic basis of male and female infertility

This review provides a comprehensive overview of the genetic factors underlying male and female infertility. Infertility affects an estimated one in six couples worldwide, with both male and female factors contributing equally to its prevalence. Approximately, 50% of infertility cases are attributed to genetic causes. We explore three main categories of genetic causes: chromosomal abnormalities, monogenic disorders, and syndromic conditions. Chromosomal causes, including numerical and structural aberrations, are discussed with a focus on their impact on gametogenesis and reproductive outcomes. We review key monogenic causes of infertility, highlighting recent discoveries in genes critical for gonadal development, gametogenesis, and hormonal regulation. Syndromic conditions affecting fertility are examined, highlighting their impact on reproductive function. Throughout the review, we address the challenges in identifying genetic mechanisms of infertility, particularly focusing on the intricate processes involved in oogenesis and spermatogenesis. We also discuss how advancements in genetic testing, such as next-generation sequencing (NGS) and genome-wide association studies (GWAS), have significantly enhanced our understanding of idiopathic infertility and promise further insights in the future. We also discuss the clinical implications of genetic diagnoses, including the role of preimplantation genetic testing (PGT) and genetic counseling in reproductive medicine. This review synthesizes current knowledge on the genetic basis of infertility, providing a comprehensive overview of chromosomal, monogenic, and syndromic causes. It aims to offer readers a solid foundation for understanding the complex genetic factors underlying reproductive disorders.

The physiological limits of bispecific monoclonal antibody tissue targeting specificity

Bispecific monoclonal antibodies (bsmAbs) are expected to provide targeted drug delivery that overcomes the dose-limiting toxicities often accompanying antibody-drug conjugates (ADC) in clinical practice. Much attention has been paid in the past to target selection, mAb affinities and the payload linker design, but challenges remain. Here, we demonstrate, by physiologically based pharmacokinetic (PBPK) in silico modeling and simulation, that the tissue-targeting accuracy of mono- and bispecific antibody therapeutics is substantially limited by normal physiological characteristics like organ volumes, blood flow rates, lymphatic circulation, and rates of extravasation. Only a small fraction of blood flows through solid tumor, where the diffusion-driven extravasation is relatively slow compared with many other organs. EGFR and HER2 are used as model antigens based on their experimentally measured tissue and tumor expression levels, but the approach is generic and can account for the cellular expression variation of targets. The model confirms experimental observations that only about 0.1-1% of the dosed mAb is likely to reach the tumor, while the rest ends up in healthy tissues due to target-mediated internalization and nonspecific uptake. The model suggests that the dual-positive tumor cell targeting specificity with bispecific antibodies is likely to be higher at lower drug concentrations and doses. However, this can be offset by elevated drug exposure in more accessible healthy tissues, primarily endothelium. The balance of exposure can be shifted toward tumor cells by using higher doses, albeit at the expense of more extensive target engagement elsewhere in the body, suggesting the need to adapt the toxicity of the payload if ADCs are considered. We suggest that PBPK modeling can guide and support biologics and bsmAb development, from target evaluation and drug optimization to therapeutic dose selection.

Pan-cancer analysis reveals PRRT4 is a potential prognostic factor of AML

BACKGROUND

Proline-rich transmembrane protein 4 (PRRT4) has been infrequently studied, with limited literature suggesting its potential as a prognostic marker for gastric cancer. This study aims to investigate the prognostic value of the PRRT4 gene in pan-cancer.

METHODS

We acquired and analyzed data from several platforms, including The Cancer Genome Atlas (TCGA), Genotype Tissue Expression Project (GTEx), Cancer Cell Line Encyclopedia (CCLE), cBioPortal, HPA, and TIMER 2.0. In addition, we have further analyzed the data using multivariate analyzes and RT-qPCR. In vitro experiments were performed to detect the proliferation and apoptosis of AML cells before and after PRRT4 knockdown.

RESULTS

PRRT4 exhibited low expression in 10 types of cancers and high expression in 3 types, and this expression was significantly correlated with tumor stage, age, and gender across various cancer types. PRRT4, identified as a potential independent prognostic factor for overall survival (OS) in several cancers including LAML, PAAD, SKCM, STAD, THYM, and UVM, and exhibited a high frequency of mutation in UCEC. Moreover, PRRT4 was found to be correlated with DNA methylation and immune infiltration in various cancers. Ultimately, in the multivariate analysis model, PRRT4 was discerned as an independent prognostic biomarker for AML, predicated on the statistics based from our institution. After PRRT4 knockdown, the proliferation ability of THP1 cells was significantly enhanced, and the apoptosis ratio was significantly decreased.

CONCLUSION

PRRT4 may serve as a potential therapeutic target and prognostic marker for various malignancies.

EphA2 and phosphoantigen-mediated selective killing of medulloblastoma by γδT cells preserves neuronal and stem cell integrity

Medulloblastoma (MB) is a pediatric brain tumor that develops in the cerebellum, representing one of the most common malignant brain cancers in children. Standard treatments include surgery, chemotherapy, and radiation, but despite a 5-y survival rate of approximately 70%, these therapies often lead to significant neurological damage in the developing brain. This underscores the urgent need for less toxic, more effective therapeutic alternatives. Recent advancements in cancer immunotherapy, including immune checkpoint inhibitors and CAR-T cell therapy, have revolutionized cancer treatment. One promising avenue is the use of Gamma Delta (γδ)T cells, a unique T cell population with potential advantages, such as non-alloreactivity, potent tumor cell lysis, and broad antigen recognition. However, their capacity to recognize and target MB cells remains underexplored. To investigate the therapeutic potential of γδT cells against MB, we analyzed the proportion and status of MB-infiltrated γδT cells within patient datasets. We next investigated the expression of γδT cell ligands on MB cells and identified the EphA2 receptor and the phosphoantigen/Butyrophilin complex as key ligands, activating Vγ9 Vδ1 and Vγ9 Vδ2 T cells, respectively, leading to significant MB cell lysis in both monolayer and spheroid models. Importantly, preliminary safety data showed that γδT cells did not target differentiated neurons or neuroepithelial stem cells derived from induced pluripotent stem cells, underscoring the selectivity and safety of this approach. In conclusion, γδT cells trigger an efficient and specific killing of MB and would offer a promising novel therapeutic strategy.

Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer

Most high-grade serous ovarian cancers (OC) do not respond to current immunotherapies. To identify potential new actionable tumor antigens in OC, we performed immunopeptidomics on a human OC cell line expressing the HLA-A02:01 haplotype, which is commonly expressed across many racial and ethnic groups. From this dataset, we identified TTLL8, POTEE, and PKMYT1 peptides as candidate tumor antigens with low expression in normal tissues and upregulated expression in OC. Using tissue microarrays, we assessed the protein expression of TTLL8 and POTEE and their association with patient outcomes in a large cohort of OC patients. TTLL8 was found to be expressed in 56.7% of OC and was associated with a worse overall prognosis. POTEE was expressed in 97.2% of OC patients and had no significant association with survival. In patient TILs, increases in cytokine production and tetramer-positive populations identified antigen-specific CD8 T cell responses, which were dependent on antigen presentation by HLA class I. Antigen-specific T cells triggered cancer cell killing of antigen-pulsed OC cells. These findings suggest that TTLL8, POTEE, and PKMYT1 are potential targets for the development of antigen-targeted immunotherapy in OC.

Screening potential diagnostic biomarkers for PLA2R‑associated idiopathic membranous nephropathy by WGCNA analysis and LASSO algorithm

Adult nephrotic syndrome is primarily caused by membranous nephropathy (MN), with idiopathic membranous nephropathy (IMN) being a prominent subtype. The onset of phospholipase A2 receptor (PLA2R1)-associated IMN is critically linked to M-type PLA2R1 exposure, yet the mechanism underlying glomerular injury remains unclear. In this study, membranous nephropathy datasets (GSE115857, GSE200828) were retrieved from GEO. Differential gene expression was analyzed using the 'limma' R package. WGCNA filtered PLA2R-related modules and intersected genes. LASSO regression, evaluated by ROC analysis, identified characteristic genes. Binomial logistic regression assessed their association with IMN. Validation was performed in the GSE133288 dataset. IHC and qRT-PCR detected characteristic gene expression in PLA2R-positive patients. This study identified elevated PLA2R expression in IMN patients among 117 DEGs. PPI analysis suggested enrichment in Golgi membranes, co-regulation, and glucocorticoid responsiveness, implicating the PPAR pathway by KEGG. WGCNA revealed a 440-gene brown module associated with IMN-PLA2R, with ECM1, SLC19A2, RASD1, FOSB, KDELR3, ZFP36, and ELF4 highlighted as diagnostic markers by ROC analysis. Clinical validation confirmed ECM1 upregulation increased IMN risk, while upregulation of SLC19A2, ZFP36, RASD1, and FOSB decreased it. ECM1 positively correlated with PLA2R, whereas SLC19A2, ZFP36, and FOSB negatively correlated. IHC analysis demonstrated consistent gene expression patterns in IMN tissues, with podocyte exposure to PLA2R-positive serum reducing viability and increasing apoptosis. Functional studies, prompted by RASD1 downregulation, revealed enhanced cell activity and reduced apoptosis upon RASD1 overexpression compared to the Serum + Ov-NC control. Collectively, this study identified diagnostic markers for PLA2R-related IMN, offering novel therapeutic targets for the treatment of IMN.

Discovery of specific protein markers in multiple body fluids and their application in forensic science

Identification of multiple body fluids is crucial for the reconstruction and corroboration of crime event. However, for the body fluids with high component similarities, such as peripheral blood and menstrual blood, reliable distinguishing markers are still lacking. Furthermore, a comprehensive protein marker assay for multiple body fluids is urgently necessary for complex crime events. Herein, we established a highly specific and detectable method for discovering protein markers in peripheral blood, menstrual blood, saliva, semen and vaginal fluid through integrating in-depth discovery proteomics and a two-step targeted screening approach. Four menstrual blood markers with high endometrial specificities were identified for differentiation from peripheral blood and exhibited moderate protein concentrations for reproducible analysis with a protein quantitation CV value of 8.66%. Finally, a targeted discrimination method with 16 protein markers was established. We successfully identified 47 blind samples with 100% specificity and detection rate, sourced from five types of body fluids and presented on matrices such as cotton, tissues, slides or fluid. Overall, this work developed an effective method for discovering body fluid biomarkers, obtained specific protein markers to identify five kinds of body fluids and their targeted monitoring will show great significance for forensic science.

DDX24 inhibits clear cell renal cell carcinoma progression by directly regulating AKR1B10

Clear cell renal cell carcinoma (ccRCC) is one of the most common malignancies worldwide, but only a few markers have been used to diagnose ccRCC. Here, we report the critical roles of DEAD-box helicase 24 (DDX24), a member of the DEAD-box RNA helicase family, in ccRCC. The DDX24 expression level and its prognostic value were initially detected in public data and then verified in a ccRCC tissue microarray. Subsequent in vitro and in vivo experiments were conducted on representative ccRCC cell lines. RNA sequencing and experimental studies were performed to explore the underlying mechanisms, and the associations between DDX24 expression and immune characteristics were evaluated. DDX24 levels were significantly lower in ccRCC tissues and negatively correlated with advanced clinical stage and overall survival. Functional analyses showed that DDX24 overexpression inhibited ccRCC cell proliferation, migration, and invasion, while DDX24 knockdown enhanced these phenotypes. Mechanistic studies revealed that DDX24 regulated the expression of aldo-keto reductase family 1 member B10 (AKR1B10) and epithelial-mesenchymal transition (EMT)-related transcription factors. Given the low expression of DDX24, ccRCC patients may benefit more from immunotherapies. In conclusion, these findings demonstrate that DDX24 suppresses ccRCC progression through direct regulation of AKR1B10, potentially mediated by EMT-related pathways, which provides potential therapeutic targets for ccRCC.

ATF4:p52 complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1

Multiple myeloma (MM) is a B-cell malignancy accounting for 20 % of all blood-associated cancers. MM patients with a poorer prognosis and high-risk stratification were previously observed to be causally linked to the constitutive activation of non-canonical NF-κB (ncNF-κB) pathway. Consistent with this, the ncNF-κB p52 transcription factor was earlier found to regulate the enhancer landscape of MM to potentiate oncogenic transcription. However, the mechanism by which aberrant p52 expression is involved in coordinating enhancer activity has not been well explored. In this study, we analysed H3K27ac ChIP-seq and ATAC-seq data from MM cell lines and patient samples to screen for putative transcription factors that cooperate with p52 to regulate enhancers activated in MM. We report that ATF4 interacts with p52 and together, this complex mediates the activity of a subset of MM-associated enhancers through the recruitment of histone acetyltransferases (HATs), p300 and CBP (CREB-binding protein). We also identified a ATF4:p52 regulated target gene BACH1 under the regulation of a proximal super-enhancer, which was found to drive oncogenesis in MM by promoting cell cycle progression and proliferation. Together, our findings provide further mechanistic insights into how aberrant enhancer activation observed in MM tumours could lead to disease progression.

Open-source antibodies as a path to enhanced research reproducibility and transparency

Antibodies are important tools with diverse uses in biomedical research. However, open access to reliable sources of well-characterized antibodies with unambiguous molecular identities remains an obstacle to research transparency and reproducibility. We propose here a community shift towards open-source antibodies, analogous to open-source computer software. The tenets of such antibodies are that 1) they are available to researchers in a ready to use form, 2) the renewable source of the antibody (e.g., hybridoma cells or plasmid) is also widely available ensuring reproducible and cost-effective access to the same antibody, and 3) the antibody sequence is publicly available. With these criteria met, the antibody can be widely used with the transparent assurance associated with a molecularly defined reagent, and the code can be edited to generate antibody variants to meet researchers' specific needs. We (the UC Davis/NIH NeuroMab Facility, the Development Studies Hybridoma Bank, and Addgene) have established a consortium to provide open-source access to a large collection of well characterized antibodies. As open-source software has benefitted both users and developers, we suggest open-source antibodies will have a similar positive impact on antibody based biomedical research. We encourage funding agencies to support initiatives to expand access to open-source antibody resources, and researchers to both utilize and to contribute to them, with a goal of enabling more reliable and cost-effective pursuit of research.

Germline-specific deletion of testis-highly expressed Lrwd1 reveals nonessential roles in male fertility

Genetic etiologies constitute a major contributor to male factor infertility, a global health concern impacting over 7% of the reproductive-aged male population. Comprehensive transcriptomic profiling has identified more than 2300 mouse testicular-predominant genes, with knockout models functionally validating the critical role of numerous loci in preserving fertility. However, the biological significance of large portions of the male germ cell genes remains unclear. The present study aimed to investigate the function of leucine-rich repeats and WD40 repeat domain-containing protein 1 (Lrwd1) in male reproduction. Here we generated germ cell-specific Lrwd1 knockout mice with Stra8-Cre (Lrwd1-sKO) using CRISPR/Cas9 technology and assessed their fertility. Our results demonstrated that the absence of Lrwd1 did not affect the fertility of male mice, and no significant differences in sperm morphology were observed between Lrwd1-sKO and control mice. Histological analysis of testicular and epididymal tissues revealed that seminiferous tubules contained all stages of germ cell development, including mature spermatozoa, without noticeable alterations. Additionally, the progression of spermatocytes through prophase I was not impaired in ablation of Lrwd1 in germ cell. These findings suggest that Lrwd1 is not essential for spermatogenesis or male fertility in mice, indicating that it does not play a critical role in reproductive function under normal physiological conditions.

Regnases play a crucial role in guarding against cancer development

Transcript turnover, a fundamental process in maintaining cellular homeostasis, involves intricate interactions between cis-acting sequences and trans-acting factors. Recent advancements in RNA decay research have illuminated novel ribonucleases (RNases) and regulatory elements within mRNA untranslated regions (UTRs), shedding light on the complexity of this process. Members of the Regnase/ZC3H12/MCPIP family (Regnase-1-4) emerge as multifaceted regulators in inflammation and cancer biology. Here, we focused on studies discussing the role of Regnases in cancer. Understanding the intricate roles of Regnase family proteins provides insights into cellular homeostasis and disease pathology, offering promising avenues for targeted therapeutic interventions in inflammation-related disorders and cancer.

Gene co-expression patterns shared between chemobrain and neurodegenerative disease models in rodents

Chemotherapy-related cognitive impairment (CRCI), is a well-recognized phenomenon in cancer patients who have undergone chemotherapy but the exact molecular mechanisms underpinning CRCI remain elusive. Symptoms reported by people with CRCI resemble those experienced by people with age-related neurodegenerative disorders (ARNDDs), yet no clear connection between CRCI and ARNDDs has been reported to date. The existence of shared mechanisms between these conditions offers opportunities for repurposing drugs already approved for the treatment of ARNDDs to improve symptoms of CRCI. Given that there is no available microarray or RNA-Seq data from the brains of people who have experienced CRCI, we investigated to what extent brain gene expression perturbations from validated rodent models of CRCI induced by chemotherapy compared with validated rodent models of Alzheimer's disease and Parkinson's disease. We utilized multiple bioinformatic analyses, including functional enrichment, protein-protein interaction network analyses, gene ontology analyses and identification of hub genes to reveal connections between comparable gene expression perturbations observed in these conditions. Collectively 165 genes overlapped between CRCI and Parkinson's disease and/or Alzheimer's disease, and 15 overlapped between all three conditions. The joint genes between Alzheimer's disease, Parkinson's disease and CRCI demonstrate an average of 83.65% nucleotide sequence similarity to human orthologues. Gene ontology and pathway enrichment analyses suggest mechanisms involved in neural activity and inflammatory response as the key components of the studied neuropathological conditions. Accordingly, genes in which expression was comparably affected in all three condition models could be attributed to neuroinflammation, cell cycle arrest, and changes in physiological neural activity.

Role of the SPI1/CDKN2A/p53 signaling pathway in cuproptosis of lung adenocarcinoma cells

Lung adenocarcinoma (LUAD) is among the most prevalent malignancies worldwide. Cuproptosis, a copper-induced form of cell death, has been identified as a key process in LUAD progression; however, the molecular mechanisms underlying cuproptosis in LUAD and potential therapeutic targets remain unclear. The present study utilized The Cancer Genome Atlas database to retrieve mRNA expression profiles and clinical information of LUAD, identifying 10 candidate genes from differentially expressed genes associated with cuproptosis. Protein-protein interaction analysis indicated that CDK inhibitor 2A (CDKN2A), an upregulated gene in LUAD, may function as a hub gene. Furthermore, multiple online databases were used to analyze Spi-1 proto-oncogene (SPI1), a transcription factor upstream of CDKN2A, which was downregulated in LUAD cuproptosis. The LinkedOmics database identified the p53-mediated cuproptosis-related pathway regulated by CDKN2A. Gene expression patterns were examined through Gene Expression Profiling Interactive Analysis, the Human Protein Atlas and reverse transcription-quantitative polymerase chain reaction. Prognostic significance was assessed using the UALCAN and Kaplan-Meier plotter databases. In vitro experiments demonstrated that CDKN2A knockdown and SPI1 overexpression inhibited the proliferation and migration of the H1975 cell line. After copper-induced cuproptosis in H1975 cells, SPI1 expression was upregulated, whereas CDKN2A expression was downregulated. When H1975 cells were pretreated with tetrathiomolybdate, the upregulation of SPI1 was inhibited and the downregulation of CDKN2A was also suppressed. Cell Counting Kit-8 assays indicated that SPI1 overexpression and CDKN2A knockdown facilitated elesclomol-CuCl2-induced cuproptosis. Western blot analysis revealed an inverse association between SPI1 overexpression and CDKN2A/p53 levels. In conclusion, the present study demonstrated the role of the SPI1/CDKN2A/p53 axis in LUAD cuproptosis, providing insights into potential therapeutic targets and contributing to clinical research on treatment strategies.

Vestigial-like family member 1 (VGLL1): An emerging candidate in tumor progression

Vestigial-like family member 1 (VGLL1), a product of an X-linked gene (VGLL1), belongs to a family of transcriptional co-activators including VGLL2, VGLL3 and VGLL4. These proteins are called vestigial-like because of the structural and functional similarities with the Drosophila ortholog vestigial (vg). VGLL1 is usually expressed in human placenta, and has also been detected in many aggressive cancers. For this reason, it is called an onco-placental protein. It can bind and activate the TEA-domain containing transcription factors TEAD1-4, and the interaction is mediated through a conserved 'valine-x-x-histidine-phenylalanine' domain (VxxHF, x denotes any amino acid) present in VGLL1 protein. Prior studies indicate a pro-tumorigenic role for this protein in several cancers including carcinoma of the breast. This review aims at summarizing our present knowledge about the functions of VGLL1, and the mechanisms that regulate its expression in cancer.

Advancements in delivery Systems for Proteolysis-Targeting Chimeras (PROTACs): Overcoming challenges and expanding biomedical applications

PROTAC (Proteolysis-Targeting Chimera), an emerging drug development strategy based on small molecule technology, has garnered widespread attention due to its high efficiency, broad applicability, low resistance, and dosage advantages. However, PROTAC molecules still exhibit certain limitations that require urgent resolution. Although significant progress has been made in designing PROTACs that target various disease-related proteins, research on drug delivery systems (DDS) for PROTACs remains relatively limited. This review aims to explore the critical role of delivery system design in addressing the inherent challenges associated with PROTAC molecules from a novel perspective. Beginning with five major challenges-insufficient targeting, poor pharmacokinetic properties, low cell permeability, limited accessibility, and the Hook effect-this article introduces formulation strategies to mitigate these deficiencies. It discusses potential solutions through targeted modifications, nano-delivery systems, intelligent response systems, and membrane biomimetic technologies, among others. Furthermore, it elucidates the mechanisms and principles underlying these approaches and analyzes the advantages of various delivery strategies. The insights provided in this review offer insights for designing delivery systems tailored to PROTACs with diverse characteristics for different disease applications.

Omentin-1 attenuates atrial fibrillation via Src/PI3K/Akt signaling-mediated anti-fibrotic effects in cardiac fibroblasts

BACKGROUND

Atrial fibrillation (AF) is characterized by progressive atrial fibrosis, leading to increased morbidity and mortality. While the novel adipokine Omentin-1 demonstrates anti-fibrotic potential across organ systems, its role in AF pathogenesis remains unclear. This study investigates Omentin-1's therapeutic effects and the underlying mechanisms in angiotensin II (Ang II)-induced atrial fibrosis and AF.

METHODS

Atrial fibrosis was induced in C57BL/6 mice via continuous Ang II infusion for 4 weeks. Omentin-1 overexpression was achieved using adeno-associated virus serotype 2/9 (AAV2/9). AF susceptibility was assessed by programmed electrical stimulation, and atrial fibrosis was quantified using histological staining and Western blot analysis. Immunofluorescence co-localization assessed cell-type specific expression of Omentin-1, and proteomic analysis of atrial fibroblasts was conducted to explore molecular pathways involved. In vitro studies using primary fibroblasts were conducted to validate Omentin-1's effects.

RESULTS

Omentin-1 levels were significantly decreased in both serum and atrial tissue of Ang II-treated mice. Omentin-1 overexpression reduced AF inducibility, decreased atrial fibrosis, and improved left atrial strain parameters. Immunofluorescence showed that Omentin-1 predominantly localized to atrial fibroblasts. Mechanistically, Omentin-1 regulated collagen metabolism by targeting fibroblasts, with Src kinase acting as a critical mediator of fibroblast activation through the PI3K/Akt signaling pathway.

CONCLUSION

Omentin-1 attenuates atrial fibrosis and AF susceptibility through regulation of the Src/PI3K/Akt signaling pathway in atrial fibroblasts. These findings suggest that Omentin-1 may represent a potential therapeutic target for the prevention and treatment of AF.

Identifying Hepsin as a novel biomarker for human esophageal squamous cell carcinoma (ESCC) and its application in fluorescence imaging

Human Esophageal squamous cell carcinoma (ESCC) represents a type of malignant tumor characterized by a high mortality rate and a generally poor surgical prognosis. The accurate labeling and high-specificity visualization of ESCC cells is extremely importance for its precise diagnosis and effective treatment. Fluorescence molecular imaging has emerged as one of the most critical modalities for cancer detection and therapeutic guidance, owing to its superior sensitivity, cost-effectiveness, portability, real-time imaging, and no damage. In this study, we initially verified that Hepsin, a protease, is highly expressed in ESCC through high-throughput immunocapture (HIC) and Western blot (WB) assays. Subsequently, we designed and synthesized an innovative activatable fluorescent probe, Ac-KQLR Rhodamine 110. It is specifically identified and cleaved by Hepsin, which is over-expressed in ESCC cells. Consequently, the Ac-KQLR Rhodamine 110 could be utilized for the activation fluorescence imaging of ESCC cells, providing a method for their precise visualization. In conclusion, this research highlights that the overexpression of Hepsin serves as a novel biomarker for ESCC. Based on Hepsin's high expression in ESCC, our team has developed a distinctive activation fluorescence imaging strategy that can be employed for the tracking and identification of ESCC. The implementation of this strategy could potentially revolutionize the current methodologies used for monitoring and treating cancer, thereby offering new hope and improved outcomes for patients diagnosed with ESCC.

Membrane-Bounded Intracellular E3 Ubiquitin Ligase-Targeting Chimeras (MembTACs) for Targeted Membrane Protein Degradation

Targeted protein degradation (TPD) represents a potent therapeutic strategy aimed at dismantling disease-associated target proteins. PROTAC is the most widely developed technique for intracellular protein degradation, while its degradation ability on membrane proteins has been hindered by the need for complex synthetic processes and limited permeability. In this study, we developed the membrane-bounded intracellular E3 ubiquitin ligase-targeting chimeras (MembTACs) that simultaneously recruit intracellular E3 ubiquitin ligase and bind to the desired membrane proteins for targeted degradation of membrane proteins. We demonstrate that the MembTACs can effectively utilize intracellular E3 ubiquitin ligase to degrade the therapeutically relevant membrane proteins of EpCAM and Met via the proteasome pathway. We anticipate that the new platform will expand the range of PROTAC applications and provide a new dimension for targeted membrane protein degradation.

Pan-Cancer Analysis and Experimental Validation of CEND1 as a Prognostic and Immune Infiltration-Associated Biomarker for Gliomas

Cell cycle exit and neuronal differentiation 1 (CEND1), highly expressed in the brain, is a specific transmembrane protein which plays a tumor suppressor role. This study is performed to investigate the role of CEND1 in various cancers through pan-cancer analysis, and further investigate its functions in gliomas by cell experiments. The expression and subcellular localization of CEND1 in different cancer types were analyzed utilizing the data from the GEPIA, UCSC, UALCAN and HPA databases. Relationships of CEND1 expression with prognosis, immunomodulation-related genes, immune checkpoint genes, microsatellite instability (MSI), tumor mutation burden (TMB) and RNA modifications were analyzed based on the TCGA database. The ESTIMATE algorithm was utilized to evaluate tumors' StromalScore, Immune Score, and ESTIMATES Score. The cBioPortal database was employed to analyze the categories and frequencies of CEND1 gene alterations. Biological functions and co-expression patterns of CEND1 in gliomas were explored using the LinkedOmics database, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. The interactions between CEND1 and drugs were explored employing the Comparative Toxicogenomics Database and molecular docking technology. Cell experiments were conducted to analyze triptonide's effects on glioma cells through CCK-8, flow cytometry and qRT-PCR. CEND1 was lowly expressed in gliomas, and high CEND1 expression was correlated to better overall survival of glioma patients (HR = 0.65, P = 0.02). Deep deletion was the main type of hereditary change of CEND1 mutation. CEND1 expression was markedly associated with immune infiltration, TMB, MSI, and RNA modification in various tumors (r > 0.3, P < 0.05). CEND1 co-expressed genes in gliomas were markedly correlated with immune responses and cell cycle (FDR < 0.05). Triptonide could bind well to CEND1 (-5.0 kcal/mol), and triptonide could facilitate CEND1 expression in glioma cells and cell apoptosis, and block the cell cycle progression (P < 0.05). CEND1 serves as a potential biomarker for pan-cancer. Particularly in gliomas, CEND1 is a key regulator of cell apoptosis and cell cycle, and a potential target for glioma treatment.

Defining diverse spike-receptor interactions involved in SARS-CoV-2 entry: Mechanisms and therapeutic opportunities

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped RNA virus that caused the Coronavirus Disease 2019 (COVID-19) pandemic. The SARS-CoV-2 Spike glycoprotein binds to angiotensin converting enzyme 2 (ACE2) on host cells to facilitate viral entry. However, the presence of SARS-CoV-2 in nearly all human organs - including those with little or no ACE2 expression - suggests the involvement of alternative receptors. Recent studies have identified several cellular proteins and molecules that influence SARS-CoV-2 entry through ACE2-dependent, ACE2-independent, or inhibitory mechanisms. In this review, we explore how these alternative receptors were identified, their expression patterns and roles in viral entry, and their impact on SARS-CoV-2 infection. Additionally, we discuss therapeutic strategies aimed at disrupting these virus-receptor interactions to mitigate COVID-19 pathogenesis.

NDR2 kinase: A review of its physiological role and involvement in carcinogenesis

The Hippo kinase, NDR2, plays a key role in the natural history of several human cancers, particularly lung cancer, by regulating processes such as proliferation, apoptosis, migration, invasion, vesicular trafficking, autophagy, ciliogenesis and immune response. To examine the specificity of NDR2's action, interaction and function in physiological or tumoral contexts, we first focus on the structural differences in the amino-acid sequence between NDR1 and NDR2. We then establish a correlation between these NDR1/2 differences and specific post-translational regulation, as well as the distinct action, interactions, and functions of NDR2 in physiological or tumoral paradigms, such as lung cancer. Furthermore, the full set of NDR2 partners and/or substrates remains to be identified. Given that it is hypothesized that NDR2 and its partners may offer new perspectives for anticancer therapies, we emphasize potential clustering or functional enrichment networks among the NDR2-specific interactants. Additionally, we provide an unpublished proteomic comparison of the NDR1 versus NDR2 interactome, focusing on human bronchial epithelial cells (HBEC-3), lung adenocarcinoma cells (H2030), and their brain metastasis-derived counterparts (H2030-BrM3). In conclusion, this study underscores the pivotal role of NDR2 in cancer progression, particularly lung cancer, and helps to better understand their specific functions and interactions in both normal and tumor contexts. The identification of NDR2 partners and substrates remains essential, with the potential to open new avenues for anticancer therapies.

Total plasma cfDNA methylation in pediatric kidney transplant recipients provides insight into acute allograft rejection pathophysiology

Cell-free DNA (cfDNA) is a marker of organ injury and immune response. DNA methylation is an epigenetic regulator of gene expression. Here, we elucidate total plasma cfDNA methylation from kidney transplant recipients in presence versus absence of rejection. In doing so, we exploit cfDNA as a real-time biomarker to define molecular pathways of rejection. Twenty plasma cfDNA samples from pediatric kidney transplant recipients were collected at allograft biopsy. Differentially methylated cytosine residues (>20 % methylation difference, q-value <0.05) were identified in presence (N = 7) versus absence (N = 9) of acute rejection. Separate analyses were performed comparing borderline rejection (N = 4) to rejection and non-rejection. In rejection versus non-rejection, there were 1269 differentially methylated genes corresponding to 533 pathways. These numbers were 4-13× greater than comparisons against borderline samples. Enriched pathways between rejection and non-rejection samples were related to immune cell/inflammatory response, lipid metabolism, and tryptophan-kynurenine metabolism, suggesting differential methylation of these pathways contributes to rejection.

Trim38 attenuates pressure overload‑induced cardiac hypertrophy by suppressing the TAK1/JNK/P38 signaling pathway

Pathological cardiac hypertrophy is a major contributor to heart failure (HF), resulting in high mortality rates worldwide; therefore, identifying key molecules in pathological cardiac hypertrophy is of critical importance for preventing or reversing HF. Tripartite motif 38 (Trim38) is an E3 ubiquitin ligase that serves a pivotal role in various diseases. The present study aimed to elucidate the regulatory role of Trim38 in pressure overload‑induced pathological cardiac hypertrophy and to explore its underlying molecular mechanisms. The expression of Trim38 was decreased in hypertrophic heart tissues from a murine model of transverse aortic constriction (TAC) and in neonatal rat cardiomyocytes (NRCMs) treated with phenylephrine (PE). Furthermore, Trim38 knockout (Trim38‑KO) aggravated cardiac hypertrophy after TAC, and Trim38 knockdown in cardiomyocytes increased cell cross section area, and upregulated the expression of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) following treatment with PE. Ubiquitinomics analysis revealed that the MAPK signaling pathway was regulated by Trim38. Furthermore, western blotting confirmed that Trim38‑KO activated TAK1 and JNK/P38. By contrast, Trim38 overexpression in NRCMs suppressed the JNK/P38 signaling pathway and inhibited the phosphorylation of TAK1. Furthermore, Trim38 knockdown resulted in a marked enhancement of TAK1 phosphorylation, concomitant with an augmentation of cardiomyocyte area and a significant upregulation of the hypertrophic biomarkers ANP and BNP. By contrast, infection with an adenovirus containing dominant‑negative TAK1 inhibited TAK1 activity, which attenuated Trim38 knockdown‑induced cardiomyocyte hypertrophy, confirming that TAK1 is a key molecule involved in the protective effects of Trim38 on cardiomyocytes. In conclusion, to the best of our knowledge, the present study is the first to reveal that Trim38 confers protection against pathological cardiac hypertrophy by inhibiting the TAK1/JNK/P38 signaling pathway; therefore, Trim38 may be a promising target for treating cardiac hypertrophy.

Differences in the role of Gper1 in colorectal cancer progression depending on sex

To evaluate the role of 17β-oestradiol (E2) in the sex-dependent progression of colorectal cancer (CRC), the present study focused on E2 signalling mediated via the nuclear receptors [oestrogen receptor (ESR)1 and ESR2] and the membrane G protein-coupled oestrogen receptor 1 (Gper1) in males and females diagnosed with CRC. This study also investigated Gper1 signalling in the CRC cell lines DLD1 and LoVo, which differ in the p53 pathway. In cancer tissue, Gper1 becomes by far the most abundant E2 receptor due to an increase in Gper1 and a decrease in ESR2 expression. These changes are more prominent in males than in females. More pronounced differences in Gper1 expression between cancer and adjacent tissues were observed in males in lower stages compared with those in higher stages of disease and females. High expression of Gper1 was associated with worse survival in males without nodal involvement but not in females. The expression of E2 receptors in the CRC cell lines DLD1 and LoVo resembles that of human cancer tissue. Silencing of Gper1 (siGper1) caused an increase in the rate of metabolism in LoVo cells with wild-type tp53. In DLD1 cells with the mutated form of tp53, siGper1 did not exert this effect. High levels of Gper1 were associated with worse survival and could contribute to sex-dependent changes in the CRC prognosis. Tumour suppressor effects of Gper1 were, at least to some extent, dependent on signalling downstream of p53, which was more frequently deficient in males than in females. Overall, this suggests that up-regulation of Gper1 (or administration of a Gper1 agonist) would be more beneficial for patients with wild-type tp53.

Using gene and gene-set association tests to identify lethal prostate cancer genes

BACKGROUND

Recent advances in the detection and treatment of prostate cancer (PCa) have reduced morbidity and mortality from this common cancer. Despite these improvements, PCa remains the second leading cause of cancer death in men in the United States. Further understanding of the genetic underpinnings of lethal PCa is required to drive risk detection and prevention and ultimately reduce mortality. We therefore set out to identify germline variants associated with cases of lethal prostate cancer (LPCa).

METHODS

Using a two-stage study design, we compared whole-exome sequencing data of 550 LPCa patients to 488 healthy male controls. Men were classified as having LPCa based on medical record review. Candidate genes were identified using gene- and gene-set-based rare truncating variant association tests. Case-control burden testing through Firth's penalized logistic regression and case-gnomAD allelic burden testing through a one-sided mid-p Fisher's exact test were conducted. Each gene's p-values from these tests were combined into an omnibus p-value for candidate gene selection. In the subsequent validation stage, genes were assessed using the UK Biobank and Firth's penalized logistic regression for each ancestry, combined through meta-analysis.

RESULTS

Gene-based rare variant association tests identified 12 genes nominally associated with LPCa. Rare-variant association tests identified a gene set with a significantly higher burden of truncating germline mutations in LPCa patients than controls. Combining gene- and gene-set test results, four nominally significant genes (PPP1R3A, TG, PPFIBP2, and BTN3A3) were selected as candidates. Subsequent validation using the UK Biobank found that PPP1R3A was significantly associated with LPCa risk (odds ratio 2.34, CI 1.20-4.59). Specifically, pGln662ArgfsTer7 was identified as the predominant variant in PPP1R3A among LPCa patients in our dataset.

CONCLUSIONS

Both individual gene and gene-set analyses identified candidates associated with LPCa. The novel association of PPP1R3A and LPCa risk merits further investigation.

S, Dolma S, Kaur R, Kapoor HS, Goyal LD, Khetarpal P. Xenobiotic metabolizing gene variants and the risk of male infertility - A systematic review, meta-analysis and in silico analysis

Many studies have been performed to explore the role of xenobiotic metabolizing gene variants and male infertility risk. However, the results remain inconclusive and contradictory. Therefore, the objective of the present study was to investigate the association among 16 genes and its 24 variants (CAT rs1001179, rs7943316, SOD2 rs4880, GPX1 rs1050450, CYP1A1 rs1048943, rs4646903, GSTP1 rs1695, MTHFR rs1801133, rs1801131, rs2274976, rs2066472, MTHFD1 rs2236225, MTRR rs1801394, CYP2D6 rs3892097, PON1 rs854560, rs662, PON2 rs7493, NAT2 rs1799930, NRF2 rs6721961, AHR rs2066853, rs1476080, rs6960165, null GSTM1, null GSTT1) involved in xenobiotic metabolism and their correlation with male infertility. A literature search was done using PubMed, Google Scholar, and Science Direct. Meta-analysis was conducted using Review Manager 5.3 software. Genotype-tissue expression (GTEx) portal and RegulomDB were used to determine genotype and tissue expression. Pathogenicity of significant gene variants was determined using I-Mutant 2.0, PolyPhen 2, SNP & GO, SIFT, and CADD tools. A total of 106 studies were selected for the present study to analyze 16 genes and their variants. SOD2 rs4880, CYP1A1 rs4646903, MTHFR rs1801133, rs1801131, rs2274976, PON1 rs854560, NRF2 rs6721961, and null GSTM1 gene variants are associated with increased risk of male infertility. SOD2 rs4880 and MTHFR rs1801133, rs1801131, rs2274976 are found to decrease the stability of the protein. However, no significant association was observed between CAT rs1001179, rs7943316, GPX1 rs1050450, CYP1A1 rs1048943,GSTP1 rs1695,MTHFR rs2066472, MTHFD1 rs2236225, MTRR rs1801394, CYP2D6 rs3892097, PON1 rs662, PON2 rs7493, NAT2 rs1799930, AHR rs2066853, rs1476080, rs6960165, null GSTT1 gene polymorphisms and the risk of male infertility.

Haematometabolism rewiring in atherosclerotic cardiovascular disease

Atherosclerotic cardiovascular diseases are the most frequent cause of death worldwide. The clinical complications of atherosclerosis are closely linked to the haematopoietic and immune systems, which maintain homeostatic functions and vital processes in the body. The nodes linking metabolism and inflammation are receiving increasing attention because they are inextricably linked to inflammatory manifestations of non-communicable diseases, including atherosclerosis. Although metabolism and inflammation are essential to survival and involve all tissues, we still know little about how these processes influence each other. In an effort to understand these mechanisms, in this Review we explore whether and how potent cardiovascular risk factors and metabolic modifiers of atherosclerosis influence the molecular and cellular machinery of 'haematometabolism' (metabolic-dependent haematopoietic stem cell skewing) and 'efferotabolism' (metabolic-dependent efferocyte reprogramming). These changes might ultimately propagate a quantitative and qualitative drift of the macrophage supply chain and affect the clinical manifestations of atherosclerosis. Refining our understanding of the different metabolic requirements of these processes could open the possibility of developing therapeutics targeting haematometabolism that, in conjunction with improved dietary habits, help rebalance and promote efficient haematopoiesis and efferocytosis and decrease the risk of atherosclerosis complications.

Integrated analysis of single‑cell and bulk RNA sequencing data to construct a risk assessment model based on plasma cell immune‑related genes for predicting patient prognosis and therapeutic response in lung adenocarcinoma

Plasma cells serve a crucial role in the human immune system and are important in tumor progression. However, the specific role of plasma cell immune-related genes (PCIGs) in tumor progression remains unclear. Therefore, the present study aimed to establish a risk assessment model for patients with lung adenocarcinoma (LUAD) based on PCIGs. The data used in the present study were obtained from The Cancer Genome Atlas and the Gene Expression Omnibus databases. After identifying nine PCIGs, a risk assessment model was constructed and a nomogram was developed for predicting patient prognosis. To explore the molecular mechanism and clinical significance, gene set enrichment analysis (GSEA), tumor mutational burden (TMB) analysis, tumor microenvironment (TME) analysis and drug sensitivity prediction were performed. Furthermore, the accuracy of the model was validated using reverse transcription-quantitative PCR (RT-qPCR). The present study constructed a risk assessment model consisting of nine PCIGs. Kaplan-Meier survival curves indicated a worse prognosis in the high-risk subgroup (risk score ≥0.982) compared with that in the low-risk subgroup. The nomogram exhibited predictive value for survival prediction (area under the curve=0.727). GSEA enrichment analysis revealed enrichment of the focal adhesion and extracellular matrix-receptor interaction pathways in the high-risk group. Moreover, the high-risk group exhibited a higher TMB, as demonstrated by the TME analysis showing lower ESTIMATE scores. Drug sensitivity prediction facilitated potential drug selection. Subsequently, differential gene expression was validated in multiple LUAD cell lines using RT-qPCR. In conclusion, the risk assessment model based on nine PCIGs may be used to predict the prognosis and drug selection in patients with LUAD.

ProLoc-IHS: Multi-label protein subcellular localization based on immunohistochemical images and sequence information

Immunohistochemistry (IHC) imaging is a powerful technique to study the subcelluar localization (SCL) of human proteins in both normal and pathological tissues. As the manual annotation of localization for IHC images is time-consuming and the number of annotated is limited, a computational tool is necessary to analyze IHC images. However, existing prediction models rarely incorporate protein sequences. In this paper, a novel protein SCL prediction model for IHC images, ProLoc-IHS, is proposed by combining with sequence features. First, a bimodal dataset is curated including IHC images and protein sequences, which are derived from the Human Protein Atlas (HPA) and UniProt respectively. Then, ProLoc-IHS extracts embeddings from IHC images and protein sequences using a visual language model, Vision Transformer (Vit), and a protein language model, ProtT5, respectively. Subsequently, these embeddings are fused using a cross-attention module, and the fused features are input into the feature learning module of ProLoc-IHS, which contains a multi-head attention mechanism, a feedforward neural network and a residual connection. Finally, binary cross entropy (BCE) and Focal loss function are incorporated into the feature learning module to solve multi-label classification tasks. Experimental results show that ProLoc-IHS outperforms other prediction models. The newly curated dataset and ProLoc-IHS code are available at https://github.com/xinshuaiiii/ProLoc-IHS.

NKAP: A new m6A RNA binding protein predicts prognosis and immunotherapy response in head and neck squamous cell carcinoma

OBJECTIVE

This study aimed to investigate whether NKAP (nuclear factor κB activating protein) serves as a prognostic marker and predictive biomarker for immunotherapy response in head and neck squamous cell carcinoma (HNSCC).

METHODS

A retrospective cohort study combined with in vitro analyses was conducted. NKAP mRNA expression levels were assessed in 520 HNSCC tumor tissues and 44 normal tissues from the TCGA dataset and validated in a clinical cohort (n = 32). Clinical correlations with overall survival and immunotherapy outcomes were analyzed. The key pathological variables included tumor stage, grade, HPV status, and TP53 mutation. Appropriate statistics were calculated at a significant level (P<0.05).

RESULTS

In this study, we have collected tissue samples from HNSCC patients (mean age: 52.65 ± 7.76; males 66%, females 34%). NKAP was upregulated in HNSCC tissues compared to adjacent normal tissues (P < 0.001). The high expression of NKAP correlated with advanced tumor stage, grade, and reduced survival (P < 0.05). High expression levels of NKAP were also associated with anti-PD-L1 therapy response (P < 0.05). Functional enrichment analysis revealed NKAP involvement in cell cycle regulation, mRNA processing, and chromatin remodeling pathways critical for cancer progression.

CONCLUSION

NKAP represents a promising prognostic marker and therapeutic target for immunotherapy in HNSCC. Prospective studies are warranted to confirm these findings.

Alpha-Synuclein as a Potential Biomarker for Inclusion Body Myositis in Blood and Muscle

AIMS

Diagnosis of inclusion body myositis (IBM) is difficult and currently based on a combination of clinical and (immuno)histological findings. Biomarkers facilitating the diagnostic process are needed. Alpha-synuclein (αSN) aggregates are a known histological feature of IBM, but there is a lack of information on their diagnostic relevance. Furthermore, serum αSN concentrations in IBM have not been investigated.

METHODS

Immunohistochemical staining for αSN was performed on 63 biopsies (19 IBM, 21 other inflammatory myopathies, 20 other myopathies and 3 healthy controls), and αSN reactive fibres were quantified. The serum concentration of αSN was determined by ELISA in 156 serum samples (11 IBM, 25 other inflammatory myopathies, 53 hereditary myopathies, 30 mitochondriopathies and 37 healthy controls).

RESULTS

The proportion of fibres with αSN immunoreactivity was significantly higher in IBM compared to all groups (p < 0.001) and discriminated IBM against all other neuromuscular disorders with a sensitivity of 79% and a specificity of 85%, which further improved when only non-regenerating fibres were examined. In serum, αSN concentrations in IBM were generally not different from healthy controls. However, serum concentrations were inversely correlated with disease duration (r = -0.62, p = 0.04) and positively correlated with the IBM functional rating scale (r = 0.74, p = 0.01). Consequently, stratification according to these clinical parameters showed significantly lower serum αSN concentrations in late-stage, more severely affected patients.

CONCLUSIONS

αSN reactivity may serve as an additional immunohistochemical marker for IBM diagnosis. Furthermore, this study indicates that αSN serum concentrations decrease with disease duration and clinical deterioration. Therefore, serum αSN may be provisionally considered a monitoring biomarker in IBM, pending further studies.

Refining antipsychotic treatment strategies in schizophrenia: discovery of genetic biomarkers for enhanced drug response prediction

Schizophrenia (SCZ) is a severe mental disorder affecting around 1% of individuals worldwide. The variability in response to antipsychotic drugs (APDs) among SCZ patients presents a significant challenge for clinicians in determining the most effective medication. In this study, we investigated the biological markers and established a predictive model for APD response based on a large-scale genome-wide association study using 3269 Chinese schizophrenia patients. Each participant underwent an 8-week treatment regimen with one of five mono-APDs: olanzapine, risperidone, aripiprazole, quetiapine, or amisulpride. By dividing the response into ordinal groups of "high", "medium", and "low", we mitigated the bias of unclear treatment outcome and identified three novel significantly associated genetic loci in or near CDH12, WDR11, and ELAVL2. Additionally, we developed predictive models of response to each specific APDs, with accuracies ranging from 79.5% to 98.0%. In sum, we established an effective method to predict schizophrenia patients' response to APDs across three categories, integrating novel biomarkers to guide personalized medicine strategies.

Spexin expression in the human bile duct and perihilar cholangiocarcinoma

The bile duct transports bile fluid from the liver to the gallbladder and small intestine. It contains bioactive peptides, including galanin (GAL) and its receptors (GAL1-3-R). Spexin (SPX), a member of the GAL peptide family, activates GAL2-R and GAL3-R. Its expression in perihilar bile ducts or in perihilar cholangiocarcinoma (pCCA), the most common biliary cancer, is largely unknown. This study investigated SPX expression in healthy, cholestatic, and malignant bile duct tissues. Immunohistochemistry was used to evaluate SPX in healthy (n = 4), peritumoral (PIT) (n = 23) and pCCA (n = 34) tissues. Score values of SPX expression were calculated and statistically analyzed. In healthy and PIT tissues with or without cholestasis, SPX expression was predominantly observed in cholangiocytes and nerve fibers. In pCCA, tumor cells also expressed SPX. SPX levels were similar across healthy, peritumoral, and cholangiocytes/tumor cells. In a small pCCA patient cohort (n = 19), SPX expression did not correlate with tumor grade or patient survival (p = 0.0838). The substantial expression of SPX in cholangiocytes and nerve fibers in the bile duct indicates that SPX contributes via galaninergic signaling to gall bladder function. The presence of SPX in submucosal nerve fibers suggests a neuromodulatory role, possibly involving bile duct motility. SPX expression did not correlate with survival in pCCA, whereas previous findings on GAL suggest a prognostic value. This highlights the need for joint studies of SPX and GAL in larger cohorts.

A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome

The complex genotype-to-phenotype relationships in Mendelian diseases can be elucidated by mutation-induced disturbances to the networks of molecular interactions (interactomes) in human cells. Missense and nonsense mutations cause distinct perturbations within the human protein interactome, leading to functional and phenotypic effects with varying degrees of severity. Here, we structurally resolve the human protein interactome at atomic-level resolutions and perform structural and thermodynamic calculations to assess the biophysical implications of these mutations. We focus on a specific type of missense mutation, known as "quasi-null" mutations, which destabilize proteins and cause similar functional consequences (node removal) to nonsense mutations. We propose a "fold difference" quantification of deleteriousness, which measures the ratio between the fractions of node-removal mutations in datasets of Mendelian disease-causing and non-pathogenic mutations. We estimate the fold differences of node-removal mutations to range from 3 (for quasi-null mutations with folding ΔΔG ≥2 kcal/mol) to 20 (for nonsense mutations). We observe a strong positive correlation between biophysical destabilization and phenotypic deleteriousness, demonstrating that the deleteriousness of quasi-null mutations spans a continuous spectrum, with nonsense mutations at the extreme (highly deleterious) end. Our findings substantiate the disparity in phenotypic severity between missense and nonsense mutations and suggest that mutation-induced protein destabilization is indicative of the phenotypic outcomes of missense mutations. Our analyses of node-removal mutations allow for the potential identification of proteins whose removal or destabilization lead to harmful phenotypes, enabling the development of targeted therapeutic approaches, and enhancing comprehension of the intricate mechanisms governing genotype-to-phenotype relationships in clinically relevant diseases.

Peptidylglycine alpha-amidating monooxygenase is important in mice for beta-cell cilia formation and insulin secretion but promotes diabetes risk through beta-cell independent mechanisms

OBJECTIVES

Carriers of PAM (peptidylglycine alpha-amidating monooxygenase) coding variant alleles have reduced insulinogenic index, higher risk of developing type 2 diabetes (T2D), and islets from heterozygous carriers of the PAM p.Asp563Gly variant display reduced insulin secretion. Exactly how global PAM deficiency contributes to hyperglycemia remains unclear. PAM is the only enzyme capable of converting glycine-extended peptide hormones into amidated products. Like neuropeptide Y (NPY), α-melanocyte stimulating hormone (αMSH), and glucagon-like peptide 1 (GLP-1), islet amyloid polypeptide (IAPP), a beta cell peptide that forms islet amyloid in type 2 diabetes, is a PAM substrate. We hypothesized that Pam deficiency limited to beta cells would lead to reduced insulin secretion, prevent the production of amidated IAPP, and reveal the extent to which loss of Pam in β-cells could accelerate the onset of hyperglycemia in mice.

METHODS

PAM activity was assessed in human islets from donors based on their PAM genotype. We generated beta cell-specific Pam knockout (Ins1Cre/+, Pamfl/fl; βPamKO) mice and performed islet culture, histological, and metabolic assays to evaluate the physiological roles of Pam in beta cells. We analyzed human IAPP (hIAPP) amyloid fibril forming kinetics using synthetic amidated and non-amidated hIAPP peptides, and generated hIAPP knock-in beta cell-specific Pam knockout (hIAPPw/w βPamKO) mice to determine the impact of hIAPP amidation on islet amyloid burden, islet graft survival, and glucose tolerance.

RESULTS

PAM enzyme activity was significantly reduced in islets from donors with the PAM p. Asp563Gly T2D-risk allele. Islets from βPamKO mice had impaired second-phase glucose- and KCl-induced insulin secretion. Beta cells from βPamKO mice had larger dense-core granules and fewer and shorter cilia. Interestingly, non-amidated hIAPP was less fibrillogenic in vitro, and high glucose-treated hIAPPw/w βPamKO islets had reduced amyloid burden. Despite these changes in beta cell function, βPamKO mice were not more susceptible to diet-induced hyperglycemia. In vitro beta cell death and in vivo islet graft survival remained comparable between hIAPPw/w βPamKO and hIAPPw/w islets. Surprisingly, aged hIAPPw/w βPamKO mice had improved insulin secretion and glucose tolerance.

CONCLUSIONS

Eliminating Pam expression only in beta cells leads to morphological changes in insulin granules, reduced insulin secretion, reduced hIAPP amyloid burden and altered ciliogenesis. However, in mice beta-cell Pam deficiency has no impact on the development of diet- or hIAPP-induced hyperglycemia. Our data are consistent with current studies revealing ancient, highly conserved roles for peptidergic signaling in the coordination of the diverse signals needed to regulate fundamental processes such as glucose homeostasis.

A FAM8A1 frameshift variant is associated with REM sleep behavior disorder, urinary retention, and mydriasis in Russian Blue cats

REM sleep behavior disorder (RBD) is a disease characterized by the loss of lower motor neuron inhibition responsible for skeletal muscle atonia during REM sleep. It has been reported in humans, dogs and cats, and can be idiopathic or secondary to a neurodegenerative disease. Five young adult Russian Blue cats from two related families were presented for progressively worsening RBD episodes frequently associated with urinary loss. Three of these cats also suffered urinary retention with overflow incontinence between RBD episodes. Neurological examination revealed a large bladder in three cats and a bilateral mydriasis with absent pupillary light reflexes in two cats; further examinations were unremarkable. Treatment attempts were unsatisfactory, with four cats being euthanized. Histopathology of the brain did not reveal any abnormalities. A disease-associated 23-bp deletion in exon 1 of FAM8A1 (NC_058372.1:g.11622168_11622190del), introducing a frameshift at codon 162 and a premature stop codon at codon 276 (XM_019831563.3:c.485_507del p.(Gln162Profs*115)), was identified by whole genome sequencing. The variant segregated in the affected families with a recessive mode of inheritance, showed an allele frequency of 1.5% in West-European Russian Blue cats (N = 68) and was not present in 276 cats belonging to 32 other breeds (including the closely related Nebelung breed). The variant FAM8A1 isoform is predicted to affect the assembly and activity of the endoplasmic reticulum-associated protein degradation pathway, which plays an important role in cell homeostasis. RBD and urinary retention syndrome is a hereditary encephalopathy affecting Russian Blue cats. A genetic test now allows diagnosis and prevention of this debilitating disease.

BRCA1 influences whole body metabolism in humanized mice

The role of BRCA1 in cellular metabolism is not fully characterized and what we do understand has been primarily demonstrated in vitro. Our studies aimed to characterize the role of BRCA1 in metabolic pathways in a whole body system. In vivo studies using C57BL/6 wild-type and transgenic humanized BRCA1 mice demonstrate the effect of human BRCA1 on the whole body metabolic phenotype and start to elucidate the mechanism by which this occurs. Promethion metabolic chambers and glucose tolerance tests measured a number of metabolic outputs of male and female mice that were either wild-type (normal mouse Brca1 gene) or humanized BRCA1 mice (knockout Brca1/knock-in human BRCA1 gene). Humanized BRCA1 mice are more lean, hyperactive, display higher energy expenditure, and demonstrate a sexual dimorphism in lean mass and glucose tolerance when compared with wild-type mice on the same genetic background. To begin to elucidate the mechanisms behind the observed metabolic phenotype, we performed mass spectrometry, SuperArray, and Western blot analysis using skeletal muscle, a metabolic organ that significantly impacts energy metabolism. Proteomic and genomic analysis revealed changes in a number of metabolic pathways that may be implicated in the observed whole body metabolic phenotype. We concluded that substituting BRCA1 for Brca1 in an in vivo model altered the overall metabolic profile of humanized BRCA1 mice. Thus, the Brca1/BRCA1 gene appears to have a significant impact on metabolic pathways, and these effects differ from mouse to human.NEW & NOTEWORTHY This is the first in vivo evidence demonstrating the complex effects of BRCA1 expression in whole body metabolism.

Endolysosomal processing of neuron-derived signaling lipids regulates autophagy and lipid droplet degradation in astrocytes

Dynamic regulation of metabolic activities in astrocytes is critical to meeting the demands of other brain cells. During neuronal stress, lipids are transferred from neurons to astrocytes, where they are stored in lipid droplets (LDs). However, it is not clear whether and how neuron-derived lipids trigger metabolic adaptation in astrocytes. Here, we uncover an endolysosomal function that mediates neuron-astrocyte transcellular lipid signaling. We identify Tweety homolog 1 (TTYH1) as an astrocyte-enriched endolysosomal protein that facilitates autophagic flux and LD degradation. Astrocyte-specific deletion of mouse Ttyh1 and loss of its Drosophila ortholog lead to brain accumulation of neutral lipids. Computational and experimental evidence suggests that TTYH1 mediates endolysosomal clearance of ceramide 1-phosphate (C1P), a sphingolipid that dampens autophagic flux and LD breakdown in mouse and human astrocytes. Furthermore, neuronal C1P secretion induced by inflammatory cytokine interleukin-1β causes TTYH1-dependent autophagic flux and LD adaptations in astrocytes. These findings reveal a neuron-initiated signaling paradigm that culminates in the regulation of catabolic activities in astrocytes.

YTHDF3 regulates IL32 mRNA stability to promote osteogenic differentiation of bone mesenchymal stem cells in ankylosing spondylitis

BACKGROUND

As a member of the family of the YTH domain and a an m6A reader, YTHDF3 is implicated in cancer and inflammatory diseases. However, its function in ankylosing spondylitis (AS)-a chronic inflammatory disease marked by aberrant bone formation-is still mysterious. The research set out to study how YTHDF3 may promote osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) in AS and delineate the underlying mechanism.

METHODS

BMSCs were separated from AS and healthy controls patients. YTHDF3 expression was manipulated using lentiviral transduction. Alkaline phosphatase (ALP) activity and Alizarin Red staining were utilized to assess osteogenic differentiation. This work employed quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blot (WB) analysis, and enzyme-linked immunosorbent assay to determine the expression of osteogenic markers, including RUNX2, SP7, BMP2, and OCN. Furthermore, RNA sequencing (RNA-seq), m6A sequencing (m6A-seq), and RNA immunoprecipitation were performed to identify downstream targets, particularly focusing interleukin 32 (IL32). Additionally, RNA stability assays and fluorescence in situ hybridization were used to evaluate the role of YTHDF3 in stabilizing IL32.

RESULTS

YTHDF3 expression was notably increased in AS-BMSCs in comparison with the control group. YTHDF3 overexpression promoted osteogenic differentiation, as shown by the rise in ALP activities, boosted calcium deposition, and upregulation of osteogenic markers. In contrast, the YTHDF3 knockdown inhibited these processes. IL32 was identified as a key downstream target using RNA-seq and m6A-seq, whose mRNA stability was directly regulated by YTHDF3 via m6A modifications. Notably, increased IL32 expression in AS contributed to osteogenesis.

CONCLUSION

YTHDF3 prevents IL32 mRNA degradation and promotes osteogenic differentiation of AS-BMSCs in an m6A-dependent manner. The results shed light on previous questions regarding the molecular mechanisms behind ectopic bone formation in AS, identifying YTHDF3 as a potential therapeutic target for controlling pathological bone formation.

Deep palaeoproteomic profiling of archaeological human brains

Palaeoproteomics leverages the persistence, diversity, and biological import of ancient proteins to explore the past, and answer fundamental questions about phylogeny, environment, diet, and disease. These insights are largely gleaned from hard tissues like bone and teeth, as well-established protocols exist for extracting ancient proteins from mineralised tissues. No such method, however, exists for the soft tissues, which are underexplored in palaeoproteomics given permission for destructive analysis routinely depends on a proven methodology. Considering less than one-tenth of all human proteins are expressed in bone, compared to three-quarters in the internal organs, the amount of biological information presently inaccessible is substantial. We address this omission with an optimised LC-FAIMS-MS/MS workflow yielding the largest, most diverse palaeoproteome yet described. Using archaeological human brains, we test ten protocols with varied chemistries and find that urea lysis effectively disrupts preserved membrane regions to expose low-abundant, intracellular analytes. Further, we show that ion mobility spectrometry improves unique protein identification by as much as 40%, and represents a means of "cleaning" dirty archaeological samples. Our methodology will be useful for improving protein recovery from a range of ancient tissues and depositional environments.

CD81 is a receptor for equine arteritis virus (family: Arteriviridae)

Arteriviruses are a family of single-stranded, positive-sense RNA (+ssRNA) viruses that infect diverse animal hosts. Many arteriviruses are macrophage-tropic, consistent with their utilization of the macrophage-specific molecule CD163 as a receptor. However, the horse arterivirus (equine arteritis virus, EAV), which infects additional cell types beyond macrophages, does not utilize CD163 in its entry mechanism. Here, we use a genome-wide CRISPR knockout screen to identify alternative receptors that could explain this discrepancy in arterivirus receptor utilization and tropism, identifying the plasma membrane tetraspanin CD81 as a required host factor for EAV infection. Genetic knockout of CD81 or pre-incubation with soluble CD81 protected cells from infection with EAV, but had no impact on susceptibility to other arteriviruses. Bypassing the entry step of the viral life cycle by transfecting the EAV genome into CD81-knockout cells produced infectious EAV, implicating CD81 in the EAV entry process. Screening of CD81 orthologs from natural arterivirus hosts identified the brushtail possum CD81 as unsupportive of EAV entry, indicating that CD81 incompatibility can serve as a barrier to cross-species infection. Horse/possum CD81 chimeras were then used to map the structural domains of CD81 engaged by EAV, identifying alpha helix "D" on the large extracellular loop of CD81 as critical for EAV entry. This study identifies the first example of receptor switching in the Arteriviridae family and, given the broad tissue distribution of CD81 expression, suggests that the adoption of CD81 enabled an expansion of EAV tropism.IMPORTANCEArteriviruses are a family of diverse positive-sense RNA viruses that can infect a wide range of animal hosts, but many details regarding how arteriviruses gain entry into cells remain unclear. Most arteriviruses are thought to utilize the macrophage-specific molecule CD163 as a receptor; however, the horse arterivirus (equine arteritis virus, EAV) infects additional cell types beyond macrophages and does not utilize CD163. In this study, we identified the host factor CD81 as a significant player in EAV entry. Beyond the implications that this discovery holds for equine health, this study adds to the increasingly complex picture of arterivirus entry and demonstrates that these viruses are capable of adopting new host molecules as receptors, with consequences for the types of cells these viruses infect, the disease they cause, and their mode(s) of transmission.

Refining Drug-Induced Cholestasis Prediction: An Explainable Consensus Model Integrating Chemical and Biological Fingerprints

Effective drug safety assessment, guided by the 3R principle (Replacement, Reduction, Refinement) to minimize animal testing, is critical in early drug development. Drug-induced liver injury (DILI), particularly drug-induced cholestasis (DIC), remains a major challenge. This study introduces a computational method for predicting DIC by integrating PubChem substructure fingerprints with biological data from liver-expressed targets and pathways, alongside nine hepatic transporter inhibition models. To address class imbalance in the public cholestasis data set, we employed undersampling, a technique that constructs a small and robust consensus model by evaluating distinct subsets. The most effective baseline model, which combined PubChem substructure fingerprints, pathway data and hepatic transporter inhibition predictions, achieved a Matthews correlation coefficient (MCC) of 0.29 and a sensitivity of 0.79, as validated through 10-fold cross-validation. Subsequently, target prediction using four publicly available tools was employed to enrich the sparse compound-target interaction matrix. Although this approach showed lower sensitivity compared to experimentally derived targets and pathways, it highlighted the value of incorporating specific systems biology related information. Feature importance analysis identified albumin as a potential target linked to cholestasis within our predictive model, suggesting a connection worth further investigation. By employing an expanded consensus model and applying probability range filtering, the refined method achieved an MCC of 0.38 and a sensitivity of 0.80, thereby enhancing decision-making confidence. This approach advances DIC prediction by integrating biological and chemical descriptors, offering a reliable and explainable model.

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments

Macromolecular protein complexes carry out most cellular functions. Unfortunately, we lack the subunit composition for many human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify >15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing nearly 70% of human proteins into their physical contexts. We globally characterize our complexes using mass spectrometry based protein covariation data (ProteomeHD.2) and identify covarying complexes suggesting common functional associations. hu.MAP3.0 generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 5871 mutually exclusive proteins in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI's Complex Portal ( https://www.ebi.ac.uk/complexportal/home ) and provide complexes through our hu.MAP3.0 web interface ( https://humap3.proteincomplexes.org/ ). We expect our resource to be highly impactful to the broader research community.

Importin-alpha transports Norrin to the nucleus to promote proliferation and Notch signaling in glioblastoma stem cells

Norrin, a secreted protein encoded by NDP gene, is recognized for its established role as a paracrine canonical Frizzled-4/Wnt ligand that mediates angiogenesis and barrier function in the brain. However, emerging evidence suggests that Norrin possesses Frizzled-4-independent functions, notably impacting Notch activation and proliferation of cancer stem cells. We conducted a BioID protein-proximity screen to identify Norrin-interacting proteins. Surprisingly, a significant proportion of the proteins we identified were nuclear. Through comprehensive tagging and proximity ligation assays, we demonstrate that Norrin is transported to the nucleus through KPNA2 (member of the Importin-alpha family). Subsequently, we demonstrate that KPNA2 loss of function in patient-derived primary glioblastoma stem cells results in a nuclear to cytoplasmic shift of Norrin distribution, and a complete abrogation of its function in stimulating Notch signaling and cellular proliferation. These results indicate that Norrin is actively transported into the nucleus to regulate vital signaling pathways and cellular functions.

Alternative Splicing Regulation in Metabolic Disorders

Alternative splicing (AS) is a fundamental mechanism for enhancing transcriptome diversity and regulating gene expression, crucial for various cellular processes and the development of complex traits. This review examines the role of AS in metabolic disorders, including obesity, weight loss, dyslipidemias, and metabolic syndrome. We explore the molecular mechanisms underlying AS regulation, focusing on the interplay between cis-acting elements and trans-acting factors, and the influence of RNA-binding proteins (RBPs). Advances in high-throughput sequencing and bioinformatics have unveiled the extensive landscape of AS events across different tissues and conditions, highlighting the importance of tissue-specific splicing in metabolic regulation. We discuss the impact of genetic variants on AS, with a particular emphasis on splicing quantitative trait loci (sQTLs) and their association with cardiometabolic traits. The review also covers the regulation of spliceosome components by phosphorylation, the role of m6A modification in AS, and the interaction between transcription and splicing. Additionally, we address the clinical relevance of AS, illustrating how splicing misregulation contributes to metabolic diseases and the potential for therapeutic interventions targeting splicing mechanisms. This comprehensive overview underscores the significance of AS in metabolic health and disease, advocating for further research to harness its therapeutic potential.

Click-constructed modular signal aptamer chimeras enable receptor-independent degradation of membrane proteins

Cell-membrane proteins are critical mediators of signal transduction, playing essential roles in disease occurrence and progression. The emerging LYTACs (Lysosome-targeting chimeras) technology combines drug-targeting strategies with lysosomal degradation, providing a novel approach to drug development and offering new possibilities for disease therapy. However, the clinical applicability of current LYTAC degraders is limited by the variable expression of lysosome-targeting receptors (LTRs) in tissues. To overcome this limitation, we herein hijacked a YXXØ sorting signal that derived from lysosome-associated membrane protein 2a (LAMP-2a) to develop a signal aptamer platform (SApt), which exhibits high specificity for targeting membrane proteins and inducing efficient lysosomal degradation. SApts were synthesized by conjugating the YXXØ signal peptide to the aptamer's terminus through a click reaction. Our study demonstrated that SApts efficiently degrade disease-associated membrane proteins, such as PTK7, Met, and NCL, based on the inherent signals rather than specific LTR. The potent antitumor efficacy of SApts was further confirmed in a xenograft tumor model, where in vivo degradation of PTK7 was observed. Collectively, our work provides insights into the development of a simple and universal lysosomal degradation platform with potential translational value in clinical treatment.

NXPE1 alters the sialoglycome by acetylating sialic acids in the human colon

Mild periodic acid Schiff staining (mPAS) of human colonic tissue has been used to answer a variety of fundamental questions in germline and somatic genetics. mPAS stains sialic acids except when these glycans are modified by O-acetylation, but a full accounting of the genes contributing to sialoglycan acetylation is incomplete. Using haplotypes derived from whole genome sequencing, we identify a region on chromosome 11 that is associated with inherited differences in mPAS staining. Of the genes in this region, only haplotypes containing NXPE1 correlate perfectly with mPAS staining in the original cohort used for whole genome sequencing, as well as in a validation cohort. Transcriptomic analysis indicates that linked haplotypes are associated with altered expression of NXPE1 suggesting a possible genetic mechanism. Genetic manipulation of a common single nucleotide polymorphism observed in the haplotype region and located in NXPE1's promoter alters expression and causes changes to modified sialic acid levels supporting this mechanism. Finally, high-performance liquid chromatography (HPLC) confirms that enzymatically active NXPE1 is capable of transferring an acetyl group from acetyl coenzyme A to sialic acid in vitro. These findings suggest that NXPE1 is the long-sought gene responsible for differences in colon mPAS staining and may be the prototype of a new family of sialic acid O-acetylation-modifying genes.

Comprehensive analysis of FAM83B in pan-cancer and preliminary exploration in esophageal squamous cell carcinoma

FAM83B is a novel oncogene that mediates transformation. Despite emerging evidence supporting an association between FAM83B and cancer, a holistic view of FAM83B's correlation with pan-cancer is limited and its carcinogenic and radioresistant roles in esophageal squamous cell carcinoma (ESCC) remain to be explored. Using data from the TCGA project, GTEx database, and other online resources, we comprehensively examined FAM83B expression, genetic mutation, copy number variations (CNV), methylation, prognosis, function, immune-associated analyses, and drug sensitivity in pan-cancer. In addition, the biological function of FAM83B in ESCC was verified by CCK-8, colony formation assays, and flow cytometry. We discovered aberrant expression of FAM83B affected prognosis in various malignant tumors. Abnormal FAM83B mRNA expression was associated with CNV and methylation. Significant correlations were also observed between FAM83B expression and immune cell infiltration, immune checkpoints, tumor mutational burden (TMB), and microsatellite instability (MSI) in malignancies. In vitro experiments indicated that FAM83B mRNA and protein were upregulated in ESCC, and knockdown of FAM83B significantly inhibited the proliferation while promoting apoptosis and radiosensitivity of ESCC. These results suggest the multiple functional roles of FAM83B in pan-cancer and provide an attractive diagnostic and therapeutic biomarker for certain cancer types, especially ESCC.

Can the co-localization of CD8+, PD-1, PD-L1 AND PD-L2 patterns provide guidance in clinical evolution of patients with head and neck cutaneous squamous cell carcinoma?

OBJECTIVE

Cutaneous Squamous Cell Carcinoma (cSCC) incidence has increased almost 200% in recent years. Blockade of immune checkpoint axes is an effective way to reactivate the host anti-tumor immune response across a variety of cancer types. We aimed to assess the presence of the Programmed cell Death-1 (PD-1):PD-L1/PD-L2 axis and associated CD8+ infiltration in head and neck cSCC, establish the co-localization criteria.

METHODS

This retrospective, cross-sectional study included 46samples of patients with high-risk cSCC. Multiplex staining for PD-1, PD-L1, PD-L2, and CD8 was performed, and images were captured by an epifluorescence microscope. 1%, 20% and 50% expression cutoff values were used, as well as the COX regression method to calculate the Hazard Ratio (HR) and 95% Confidence Interval (95% CI).

RESULTS

PD-1/PD-L1, PD-1/PD-L2 and PD-L1/PD-L2 co-localized in 80.4%, 45.7% and 47.8% of the patients, respectively. All patients exhibited CD8+ infiltration to some extent, with PD-1/PD-L1, PD-1/PD-L2 and PD-1/PD-L1/PD-L2 co-localized in 97.8%, 82.6% and 82.6% of the patients, respectively. There was no statistically significant relationship regarding the co-localization of immune checkpoint and the outcomes evaluated.

CONCLUSION

This study has evidenced significant expression and co-localization of immune checkpoint axes in whole tissues and tumor infiltrate, emphasizing the potential application of co-localization as a valuable tool in the clinical management of cSCC. These findings provide important insights for understanding and optimizing therapeutic strategies in head and neck cSCC.

LEVEL OF EVIDENCE: 4