Molecular biology of BPIFB1 and its advances in disease

Label-free-based proteomics analysis reveals differential proteins of sheep, goat and cow milk

Regarding the limited information on species protein differences between sheep, goat, and cow milk, the differentially expressed proteins in sheep, goat, and cow milk and their functional differences are analyzed using label-free proteomics technology to identify potential biomarkers. 770 proteins and 2914 peptide segments were identified. The statistical analysis showed significant differences in the relative abundances of the 74 proteins among the sheep, goat, and cow milk. CSN3 and LALBA can be used as potential biomarkers for goat milk, XDH can be used as potential biomarkers for cow milk, and CTSB and BPIFB1 can be used as potential biomarkers for sheep milk. The functional analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes showed that these significantly different proteins were enriched by different pathways including thyroid hormone synthesis and glycerol phospholipid metabolism. The data revealed differences in the amounts and physiological functions of the milk proteins of different species, which may provide an important basis for research on the nutritional composition of dairy products and adulteration identification technology.

Quantitative proteomics revealed protein biomarkers to distinguish malignant pleural effusion from benign pleural effusion

To identify protein biomarkers capable of early prediction regarding the distinguishing malignant pleural effusion (MPE) from benign pleural effusion (BPE) in patients with lung disease. A four-dimensional data independent acquisition (4D-DIA) proteomic was performed to determine the differentially expressed proteins in samples from 20 lung adenocarcinoma MPE and 30 BPE. The significantly differential expressed proteins were selected for Gene Ontology (GO) enrichment and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. Protein biomarkers with high capability to discriminate MPE from BPE patients were identified by Random Forest (RF) algorithm prediction model, whose diagnostic and prognostic efficacy in primary tumors were further explored in public datasets, and were validated by ELISA experiment. 50 important proteins (30 up-regulated and 20 down-regulated) were selected out as potential markers to distinguish the MPE from BPE group. GO analysis revealed that those proteins involving the most important cell component is extracellular space. KEGG analysis identified the involvement of cellular adhesion molecules pathway. Furthermore, the Area Under Curve (AUC) of these proteins were ranged from 0.717 to 1.000，with excellent diagnostic properties to distinguish the MPE. Finally, significant survival and gene and protein expression analysis demonstrated BPIFB1, DPP4, HPRT1 and ABI3BP had high discriminating values. SIGNIFICANCE: We performed a 4D-DIA proteomics to determine the differentially expressed proteins in pleural effusion samples from MPE and BPE. Some potential protein biomarkers were identified to distinguish the MPE from BPE patients., which may provide helpful diagnostic and therapeutic insights for lung cancer. This is significant because the median survival time of patients with MPE is usually 4-12 months, thus, it is particularly important to diagnose MPE early to start treatments promptly. The most common causes of MPE are lung cancers, while pneumonia and tuberculosis are the main causes of BPE. If more diagnostic markers could be identified periodically, there would be an important significance to clinical diagnose and treatment with drugs in lung cancer patients.

Use of the traditional Chinese medicine "compound healthy ear agent" to protect against age-related hearing loss in mice: A proteomics study

Background

Previous studies have shown that the traditional Chinese medicine (TCM) called "compound healthy ear agent" (CHEA) had anti-apoptosis effects in cochlear hair cells and spiral ganglion neurons, and could protect mice hearing against presbycusis or age-related hearing loss (AHL), as well as aminoglycoside antibiotic-induced ototoxicity. Because its mechanisms of action are still unclear, we investigated the mechanism of action of CHEA against AHL in mice using proteomics techniques.

Methods

Eighteen C57BL/6J mice at 1 month of age were randomly divided into three groups: (A) drinking water until 2 months of age, K2M); (B) drinking water until 7 months of age to induce AHL, K7M; (C) drinking water containing CHEA daily until 7 months of age as treatment group, Z7M. At 2 or 7 months mice were sacrificed and their cochleae were removed for proteomics analysis.

Results

The numbers of proteins with a false discovery rate (FDR) < 1% were respectively 5873 for qualitative and 5492 for quantitative statistics. The numbers of proteins with differential enrichment at least 1.5-fold (p < 0.05) were respectively 351 for K7M vs K2M groups, 52 for Z7M vs K7M groups, 264 for Z7M vs K2M groups. The differentially expressed proteins in the Z7M group were involved in synaptic molecular transmission, energy metabolism, immune response, antioxidant defenses, and anti-apoptosis.

Conclusion

The TCM CHEA played a protective role against AHL in mice by regulating the expression of specific proteins and genes in cochlear hair cells and spiral ganglion neurons. Besides the pathways expected to be involved (antioxidant and anti-apoptosis), proteins related to immune response is a new finding of the present study.

BPIFB1, Serving as a Downstream Effector of EBV-miR-BART4, Blocks Immune Escape of Nasopharyngeal Carcinoma via Inhibiting PD-L1 Expression

Nasopharyngeal carcinoma (NPC) is one of the most common tumors of head and neck in the Southeast Asia. PD-L1-dependent immune escape plays a critical role involved in NPC development. BPIFB1 has previously reported to take tumor-suppressive actions on NPC cell proliferation and migration. Nonetheless, the function of BPIFB1 in immune escape remains largely elusive. Expression pattern on mRNA and protein levels of target genes in NPC patients' samples and cell lines were examined by qRT-PCR, western blot, and immunohistochemistry staining, respectively. The assessment of CD8+ T-cell apoptosis and expression was determined by flow cytometry. Molecular interactions were verified using chromatin immunoprecipitation (ChIP) and luciferase reporter assay. BPIFB1 was downregulated in NPC tumor tissues, exhibiting a negative correlation of PD-L1. Overexpression of BPIFB1 significantly inhibited the expression of PD-L1, suppressing the apoptosis and enhancing the expression of CD8+ T cells. Mechanistically, BPIFB1 was found to repress the expression of STAT1, which was identified to be an upstream activator of PD-L1. Furthermore, the EBV-encoded miR-BART4 overexpressed in NPC cells could directly target and inhibit BPIFB1. This study provided a comprehensive understanding of the molecular mechanism for the upstream and downstream pathway of BPIFB1 related with immune escape, indicating a novel approach for the treatment of NPC.

Differences in Immune Characteristics and Related Gene Expression in Spleen among Ningxiang, Berkshire Breeds and Their Hybrid Pigs

To investigate the differential immunology in Ningxiang and Berkshire pigs and their F1 offspring (F1 offspring), physiological and biochemical indicators in the plasma and spleen were analyzed. Then, transcriptomic analysis of the spleen identified 1348, 408, and 207 differentially expressed genes (DEGs) in comparisons of Ningxiang vs. Berkshire, Berkshire vs. F1 offspring, and Ningxiang vs. F1 offspring, respectively. In Ningxiang vs. Berkshire pigs, the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs included CD163, MARCO, CXCL14, CCL19, and PPBP, which are associated with immunity. GO and KEGG analyses were also conducted comparing F1 offspring and their parents. The DEGs, including BPIFB1, HAVCR2, CD163, DDX3X, CCR5, and ITGB3, were enriched in immune-related pathways. Protein-protein interaction (PPI) analysis indicated that the EGFR and ITGA2 genes were key hub genes. In conclusion, this study identifies significant immune DEGs in different pig breeds, providing data to support the exploration of breeding strategies for disease resistance in local and crossbred pig populations.

Allergenic Activity of Individual Cat Allergen Molecules

More than 10% of the world's population suffers from an immunoglobulin E (IgE)-mediated allergy to cats which is accompanied mainly by respiratory symptoms such as rhinitis and asthma. Several cat allergen molecules have been identified, but their allergenic activity has not been investigated in depth. Purified cat allergen molecules (Fel d 1, Fel d 2, Fel d 3, Fel d 4, Fel d 6, Fel d 7 and Fel d 8) were characterized via mass spectrometry and circular dichroism spectroscopy regarding their molecular mass and fold, respectively. Cat-allergen-specific IgE levels were quantified via ImmunoCAP measurements in IgE-sensitized subjects with (n = 37) and without (n = 20) respiratory symptoms related to cat exposure. The allergenic activity of the cat allergens was investigated by loading patients' IgE onto rat basophils expressing the human FcεRI receptor and studying the ability of different allergen concentrations to induce β-hexosaminidase release. Purified and folded cat allergens with correct masses were obtained. Cat-allergen-specific IgE levels were much higher in patients with a respiratory allergy than in patients without a respiratory allergy. Fel d 1, Fel d 2, Fel d 4 and Fel d 7 bound the highest levels of specific IgE and already-induced basophil degranulation at hundred-fold-lower concentrations than the other allergens. Fel d 1, Fel d 4 and Fel d 7 were recognized by more than 65% of patients with a respiratory allergy, whereas Fel d 2 was recognized by only 30%. Therefore, in addition to the major cat allergen Fel d 1, Fel d 4 and Fel d 7 should also be considered to be important allergens for the diagnosis and specific immunotherapy of cat allergy.

BPIFB1 promotes metastasis of hormone receptor-positive breast cancer via inducing macrophage M2-like polarization

Metastasis is an important factor affecting the prognosis of hormone receptor-positive breast cancer (BC). However, the molecular basis for migration and invasion of tumor cells remains poorly understood. Here, we identify that bactericidal/permeability-increasing-fold-containing family B member 1 (BPIFB1), which plays an important role in innate immunity, is significantly elevated in breast cancer and associated with lymph node metastasis. High expression of BPIFB1 and its coding mRNA are significantly associated with poor prognosis of hormone receptor-positive BC. Using enrichment analysis and constructing immune infiltration evaluation, we predict the potential ability of BPIFB1 to promote macrophage M2 polarization. Finally, we demonstrate that BPIFB1 promotes the metastasis of hormone receptor-positive BC by stimulating the M2-like polarization of macrophages via the establishment of BC tumor cells/THP1 co-culture system, qPCR, Transwell assay, and animal experiments. To our knowledge, this is the first report on the role of BPIFB1 as a tumor promoter by activating the macrophage M2 polarization in hormone receptor-positive breast carcinoma. Together, these results provide novel insights into the mechanism of BPIFB1 in BC.

A Proteomics Investigation of Salivary Profiles as Potential Biomarkers for Autism Spectrum Disorder (ASD)

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that affects approximately 1/68 children, with a more recent study suggesting numbers as high as 1/36. According to Diagnostic and Statistical Manual of Mental Disorders, the etiology of ASD is unknown and diagnosis of this disorder is behavioral. There is currently no biomarker signature for ASD, however, identifying a biomarker signature is crucial as it would aid in diagnosis, identifying treatment targets, monitoring treatments, and identifying the etiology of the disorder. Here we used nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) to investigate the saliva from individuals with ASD and matched controls in a 14 vs 14 study. We found numerous proteins to have statistically significant dysregulations, including lactotransferrin, transferrin, polymeric immunoglobulin receptor, Ig A L, Ig J chain, mucin 5 AC, and lipocalin 1 isoform X1. These findings are consistent with previous studies by our lab, and others, and point to dysregulations in the immune system, lipid metabolism and/or transport, and gastrointestinal disturbances, which are common and reoccurring topics in ASD research.

Morphologically intact airways in lung fibrosis have an abnormal proteome

Honeycombing is a histological pattern consistent with Usual Interstitial Pneumonia (UIP). Honeycombing refers to cystic airways located at sites of dense fibrosis with marked mucus accumulation. Utilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the fibrotic honeycomb airway cells and fibrotic uninvolved airway cells (distant from honeycomb airways and morphologically intact) in specimens from 10 patients with UIP. Non-fibrotic airway cell specimens from 6 patients served as controls. Furthermore, we performed LCM-MS on the mucus plugs found in 6 patients with UIP and 6 patients with mucinous adenocarcinoma. The mass spectrometry data were subject to both qualitative and quantitative analysis and validated by immunohistochemistry. Surprisingly, fibrotic uninvolved airway cells share a similar protein profile to honeycomb airway cells, showing deregulation of the slit and roundabout receptor (Slit and Robo) pathway as the strongest category. We find that (BPI) fold-containing family B member 1 (BPIFB1) is the most significantly increased secretome-associated protein in UIP, whereas Mucin-5AC (MUC5AC) is the most significantly increased in mucinous adenocarcinoma. We conclude that fibrotic uninvolved airway cells share pathological features with fibrotic honeycomb airway cells. In addition, fibrotic honeycomb airway cells are enriched in mucin biogenesis proteins with a marked derangement in proteins essential for ciliogenesis. This unbiased spatial proteomic approach generates novel and testable hypotheses to decipher fibrosis progression.

Spatiotemporally deciphering the mysterious mechanism of persistent HPV-induced malignant transition and immune remodelling from HPV-infected normal cervix, precancer to cervical cancer: Integrating single-cell RNA-sequencing and spatial transcriptome

BACKGROUND

The mechanism underlying cervical carcinogenesis that is mediated by persistent human papillomavirus (HPV) infection remains elusive.

AIMS

Here, for the first time, we deciphered both the temporal transition and spatial distribution of cellular subsets during disease progression from normal cervix tissues to precursor lesions to cervical cancer.

MATERIALS & METHODS

We generated scRNA-seq profiles and spatial transcriptomics data from nine patient samples, including two HPV-negative normal, two HPV-positive normal, two HPV-positive HSIL and three HPV-positive cancer samples.

RESULTS

We not only identified three 'HPV-related epithelial clusters' that are unique to normal, high-grade squamous intraepithelial lesions (HSIL) and cervical cancer tissues but also discovered node genes that potentially regulate disease progression. Moreover, we observed the gradual transition of multiple immune cells that exhibited positive immune responses, followed by dysregulation and exhaustion, and ultimately established an immune-suppressive microenvironment during the malignant program. In addition, analysis of cellular interactions further verified that a 'homeostasis-balance-malignancy' change occurred within the cervical microenvironment during disease progression.

DISCUSSION

We for the first time presented a spatiotemporal atlas that systematically described the cellular heterogeneity and spatial map along the four developmental steps of HPV-related cervical oncogenesis, including normal, HPV-positive normal, HSIL and cancer. We identified three unique HPV-related clusters, discovered critical node genes that determined the cell fate and uncovered the immune remodeling during disease escalation.

CONCLUSION

Together, these findings provided novel possibilities for accurate diagnosis, precise treatment and prognosis evaluation of patients with precancer and cervical cancer.

Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals

Bactericidal/permeability-increasing protein, a primary factor of the innate immune system of mammals, participates in natural immune protection against invading bacteria. BPIFA1 actively contributes to host defense via multiple mechanisms, such as antibacterial, surfactant, airway surface liquid control, and immunomodulatory activities. However, the evolutionary history and selection forces on the BPIFA1 gene in mammals during adaptive evolution are poorly understood. This study examined the BPIFA1 gene of humans compared with that of other mammalian species to estimate the selective pressure derived by adaptive evolution. To assess whether or not positive selection occurred, we employed several different possibility tests (M1 vs. M2 and M7 vs. M8). The proportions of positively selected sites were significant, with a likelihood log value of 93.63 for the BPIFA1 protein. The Selecton server was used on the same dataset to reconfirm positive selection for specific sites by employing the Mechanistic-Empirical Combination model, thus providing additional evidence supporting the findings of positive selection. There was convincing evidence for positive selection signals in the BPIFA1 genes of mammalian species, which was more significant for selection signs and creating signals. We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. BPIFA1 activates the upper airway's innate immune system in response to numerous genetic signals in the mammalian genome. These findings highlight evolutionary advancements in immunoregulatory effects that play a significant role in the antibacterial and antiviral defenses of mammalian species.

Simulated Microgravity Influences Immunity-Related Biomarkers in Lung Cancer

Microgravity is a novel strategy that may serve as a complementary tool to develop future cancer therapies. In lung cancer, the influence of microgravity on cellular processes and the migratory capacity of cells is well addressed. However, its effect on the mechanisms that drive lung cancer progression remains in their infancy. In this study, 13 differentially expressed genes were shown to be associated with the prognosis of lung cancer under simulated microgravity (SMG). Using gene set enrichment analysis, these genes are enriched in humoral immunity pathways. In lieu, alveolar basal-epithelial (A549) cells were exposed to SMG via a 2D clinostat system in vitro. In addition to morphology change and decrease in proliferation rate, SMG reverted the epithelial-to-mesenchymal transition (EMT) phenotype of A549, a key mechanism in cancer progression. This was evidenced by increased epithelial E-cadherin expression and decreased mesenchymal N-cadherin expression, hence exhibiting a less metastatic state. Interestingly, we observed increased expression of FCGBP, BPIFB, F5, CST1, and CFB and their correlation to EMT under SMG, rendering them potential tumor suppressor biomarkers. Together, these findings reveal new opportunities to establish novel therapeutic strategies for lung cancer treatment.

Smoking-associated Downregulation of FILIP1L Enhances Lung Adenocarcinoma Progression Through Mucin Production, Inflammation, and Fibrosis

Lung adenocarcinoma (LUAD) is the major subtype in lung cancer, and cigarette smoking is essentially linked to its pathogenesis. We show that downregulation of Filamin A interacting protein 1-like (FILIP1L) is a driver of LUAD progression. Cigarette smoking causes its downregulation by promoter methylation in LUAD. Loss of FILIP1L increases xenograft growth, and, in lung-specific knockout mice, induces lung adenoma formation and mucin secretion. In syngeneic allograft tumors, reduction of FILIP1L and subsequent increase in its binding partner, prefoldin 1 (PFDN1) increases mucin secretion, proliferation, inflammation, and fibrosis. Importantly, from the RNA-sequencing analysis of these tumors, reduction of FILIP1L is associated with upregulated Wnt/β-catenin signaling, which has been implicated in proliferation of cancer cells as well as inflammation and fibrosis within the tumor microenvironment. Overall, these findings suggest that down-regulation of FILIP1L is clinically relevant in LUAD, and warrant further efforts to evaluate pharmacologic regimens that either directly or indirectly restore FILIP1L-mediated gene regulation for the treatment of these neoplasms.

Significance

This study identifies FILIP1L as a tumor suppressor in LUADs and demonstrates that downregulation of FILIP1L is a clinically relevant event in the pathogenesis and clinical course of these neoplasms.

Comparative Proteome Profiling of Saliva Between Estrus and Non-Estrus Stages by Employing Label-Free Quantitation (LFQ) and Tandem Mass Tag (TMT)-LC-MS/MS Analysis: An Approach for Estrus Biomarker Identification in Bubalus bubalis

Accurate determination of estrus is essentially required for efficient reproduction management of farm animals. Buffalo is a shy breeder and does not manifest overt signs of estrus that make estrus detection difficult resulting in a poor conception rate. Therefore, identifying estrus biomarkers in easily accessible biofluid such as saliva is of utmost interest. In the current study, we generated saliva proteome profiles during proestrus (PE), estrus (E), metestrus (ME), and diestrus (DE) stages of the buffalo estrous cycle using both label-free quantitation (LFQ) and labeled (TMT) quantitation and mass spectrometry analysis. A total of 520 proteins were identified as DEPs in LFQ; among these, 59 and four proteins were upregulated (FC ≥ 1.5) and downregulated (FC ≤ 0.5) during E vs. PE, ME, and DE comparisons, respectively. Similarly, TMT-LC-MS/MS analysis identified 369 DEPs; among these, 74 and 73 proteins were upregulated and downregulated during E vs. PE, ME, and DE stages, respectively. Functional annotations of GO terms showed enrichment of glycolysis, pyruvate metabolism, endopeptidase inhibitor activity, salivary secretion, innate immune response, calcium ion binding, oocyte meiosis, and estrogen signaling. Over-expression of SERPINB1, HSPA1A, VMO1, SDF4, LCN1, OBP, and ENO3 proteins during estrus was further confirmed by Western blotting. This is the first comprehensive report on differential proteome analysis of buffalo saliva between estrus and non-estrus stages. This study generated an important panel of candidate proteins that may be considered buffalo estrus biomarkers which can be applied in the development of a diagnostic kit for estrus detection in buffalo.

Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer

Upper gastrointestinal cancer (UGIC) is an aggressive carcinoma with increasing incidence and poor outcomes worldwide. Here, we collected 39,057 cells, and they were annotated into nine cell types. By clustering cancer stem cells (CSCs), we discovered the ubiquitous existence of sub-cluster CSCs in all UGICs, which is named upper gastrointestinal cancer stem cells (UGCSCs). The identification of UGCSC function is coincident with the carcinogen of UGICs. We compared the UGCSC expression profile with 215,291 single cells from six other cancers and discovered that UGCSCs are specific tumor stem cells in UGIC. Exploration of the expression network indicated that inflammatory genes (CXCL8, CXCL3, PIGR, and RNASE1) and Wnt pathway genes (GAST, REG1A, TFF3, and ZG16B) are upregulated in tumor stem cells of UGICs. These results suggest a new mechanism for carcinogenesis in UGIC: mucosa damage and repair caused by poor eating habits lead to chronic inflammation, and the persistent chronic inflammation triggers the Wnt pathway; ultimately, this process induces UGICs. These findings establish the core signal pathway that connects poor eating habits and UGIC. Our system provides deeper insights into UGIC carcinogens and a platform to promote gastrointestinal cancer diagnosis and therapy.

Downregulation of Three Novel miRNAs in the Lymph Nodes of Sheep Immunized With the Brucella suis Strain 2 Vaccine

Ovine and caprine brucellosis, both caused by Brucella melitensis, lead to substantial economic losses in the animal industry and health problems in human populations. Brucella suis strain 2 (B.suis S2), as a live attenuated vaccine, is used extensively in China to prevent brucellosis. It has been proven that microRNA (miRNAs) are involved in the immunopathogenesis of brucellosis; however, the miRNA-driven mechanism of immune response to B.suis S2 in vivo remains unknown. To determine which new miRNAs are involved in the host immune response to B.suis S2 and elucidate the function of these miRNAs, we performed a comprehensive analysis of miRNA expression profiles in sheep immunized with B.suis S2 using the high-throughput sequencing approach. The submandibular lymphatic nodes from sheep seropositive for Brucella were collected at 7, 14, 21, 30, 60 and 90 days post-immunization. MiRNA sequencing analysis revealed that 282 differentially expressed miRNAs (|log₂ fold-change |>0.5 and p < 0.05) were significantly enriched in the immune pathways, including the NF-kappa B signaling pathway, B cell receptor signaling pathway, p53 signaling pathway and complement and coagulation cascades. Increasing the threshold to |log₂ fold change|>1 and p < 0.01 revealed 48 differentially expressed miRNAs, 31 of which were novel miRNAs. Thirteen of these novel miRNAs, which were differentially expressed for at least two time points, were detected via RT-qPCR assays. The novel_229, novel_609, novel_973 and oar-miR-181a assessed by RT-qPCR were detectable and consistent with the expression patterns obtained by miRNA sequencing. Functional analyses of these miRNAs demonstrated that their target genes participated in the immune response pathways, including the innate and adaptive immunity pathways. The immune-related target genes of novel_229 included ENSOARG00000000649 and TMED1, as well as LCN2, PDPK1 and LPO were novel_609 target genes. The immune-related target genes of novel_973 included C6orf58, SPPL3, BPIFB1, ENSOARG00000021083, MPTX1, CCL28, FGB, IDO1, OLR1 and ENSOARG00000020393. The immune-related target genes of oar-miR-181a included ENSOARG00000002722, ARHGEF2, MFAP4 and DOK2. These results will deepen our understanding of the host miRNA-driven defense mechanism in sheep immunized with B.suis S2 vaccine, and provide the valuable information for optimizing vaccines and developing molecular diagnostic targets.

Clinical and prognostic implications of an immune-related risk model based on TP53 status in lung adenocarcinoma

TP53 mutation is the most widespread mutation in lung adenocarcinoma (LUAD). Meanwhile, p53 (encoded by TP53) has recently been implicated in immune responses. However, it is still unknown whether TP53 mutation remodels the tumour microenvironment to influence tumour progression and prognosis in LUAD. In this study, we developed a 6‐gene immune‐related risk model (IRM) to predict the survival of patients with LUAD in The Cancer Genome Atlas (TCGA) cohort based on TP53 status, and the predictive ability was confirmed in 2 independent cohorts. TP53 mutation led to a decreased immune response in LUAD. Further analysis revealed that patients in the high‐index group had observably lower relative infiltration of memory B cells and regulatory T cells and significantly higher relative infiltration of neutrophils and resting memory CD4⁺ T cells. Additionally, the IRM index positively correlated with the expression of critical immune checkpoint genes, including PDCD1 (encoding PD‐1) and CD274 (encoding PD‐L1), which was validated in the Nanjing cohort. Furthermore, as an independent prognostic factor, the IRM index was used to establish a nomogram for clinical application. In conclusion, this IRM may serve as a powerful prognostic tool to further optimize LUAD immunotherapy.

Proteomic profiling of saliva reveals association of complement system with primary Sjögren's syndrome

INTRODUCTION

To compare the saliva proteomes of experimental Sjögren's syndrome (ESS) model mice and healthy controls to identify potential diagnostic biomarkers for primary Sjögren's syndrome (pSS).

METHODS

Proteins were extracted from the saliva of three ESS and three normal control mice using the data-independent acquisition technique. R language was used to identify the differentially expressed proteins (DEPs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to functionally annotate the DEPs. The protein-protein interaction (PPI) network was constructed and the core proteins were identified with the STRING website and Cytoscape software. The concentrations of Serpin family G member 1 (SERPING1), C3, complement factor H (CFH), fibrinogen alpha (FGA), and fibrinogen gamma (FGG) in saliva were determined by ELISA.

RESULTS

A total of 1722 DEPs were identified in the saliva of the ESS mice relative to the controls, of which 50 showed significantly different expression levels between the two groups. SERPING1, C3, CFH, FGA, and FGG were significantly downregulated, and keratin 4 (Krt4) and transglutaminase 3 (TGM3) were upregulated in the saliva of ESS mice. The PPI network showed that SERPING1, C3, FGG, FGA, TGM3, and hemopexin (HPX) were the core proteins. ELISA results showed that the expression of C3, CFH, FGA, and SERPING1 were significantly downregulated in the saliva of ESS mice. However, the expression of FGG was a little downregulated but with no significant difference. SERPING1, FGG, and FGA may downregulate the complement C3 by inhibiting immune complement system, thereby promoting pSS progression.

CONCLUSIONS

The salivary proteome of ESS mice was markedly different from that of healthy controls, suggesting that salivary proteomics is a promising noninvasive diagnostic tool for pSS. SERPING1, C3, CFH, FGA, and FGG are potential biomarkers of pSS.

Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic Carcinoma

Adenoid cystic carcinoma (ACC) belongs to salivary gland malignancies commonly occurring in an oral cavity with a poor long-term prognosis. The potential biomarkers and cellular functions acting on local recurrences and distant metastases remain to be illustrated. Proteomics is the core content of precision medicine research, which provides accurate information for early detection of cancer, benign and malignant diagnosis, classification and personalized medication, efficacy monitoring, and prognosis judgment. To obtain a comprehensive regulation network and supply clues for the treatment of oral ACC (OACC), we utilized mass spectrometry-based quantitative proteomics to analyze the protein expression profile in paired tumor and adjacent normal tissues. We identified a total of 40,547 specific peptides and 4454 differentially expressed proteins (DEPs), in which HAPLN1 was the most upregulated protein and BPIFB1 was the most downregulated. Then, we annotated the functions and characteristics of DEPs in detail from the aspects of gene ontology, subcellular structural localization, KEGG, and protein domain to thoroughly understand the identified and quantified proteins. Glycosphingolipid biosynthesis and glycosaminoglycan degradation pathways showed the biggest difference according to KEGG analysis. Moreover, we confirmed 20 proteins from the ECM-receptor signaling pathway by a parallel reaction monitoring quantitative detection and 19 proteins were quantified. This study provides useful insights to analyze DEPs in OACC and guide in-depth thinking of the pathogenesis from a proteomics view for anticancer mechanisms and potential biomarkers.