Oxidation-reduction process of Arabidopsis thaliana roots induced by bisphenol compounds based on RNA-seq analysis.

Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves were collected for internal BPs exposure concentration detection, RNA-seq (only roots), and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of reactive oxygen species, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicated that BPs tended to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicated that the shared 211 differently expressed genes (DEGs) of these 5 exposure groups were enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation-reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored.

Identification of deregulated lncRNAs in Alzheimer's disease: an integrated gene co-expression network analysis of hippocampus and fusiform gyrus RNA-seq datasets.

Introduction: The deregulation of lncRNAs expression has been associated with neuronal damage in Alzheimer's disease (AD), but how or whether they can influence its onset is still unknown. We investigated 2 RNA-seq datasets consisting, respectively, of the hippocampal and fusiform gyrus transcriptomic profile of AD patients, matched with non-demented controls. Methods: We performed a differential expression analysis, a gene correlation network analysis (WGCNA) and a pathway enrichment analysis of two RNA-seq datasets. Results: We found deregulated lncRNAs in common between hippocampus and fusiform gyrus and deregulated gene groups associated to functional pathways related to neurotransmission and memory consolidation. lncRNAs, co-expressed with known AD-related coding genes, were identified from the prioritized modules of both brain regions. Discussion: We found common deregulated lncRNAs in the AD hippocampus and fusiform gyrus, that could be considered common signatures of AD pathogenesis, providing an important source of information for understanding the molecular changes of AD.

Isolation, expansion, and adoptive transfer of human ILC2s for the treatment of mice bearing liquid and solid tumors.

Type 2 innate lymphoid cells (ILC2s) are crucial in regulating immune responses and various physiological processes, including tissue repair, metabolic homeostasis, inflammation, and cancer surveillance. Here, we present a protocol that outlines the isolation, expansion, and adoptive transfer of human ILC2s from peripheral blood mononuclear cells for an in vivo lineage tracking experiment in a mouse model. Additionally, we detail the steps involved in the adoptive transfer of human ILC2s to recipient mice bearing human liquid or solid tumors. For complete details on the use and execution of this protocol, please refer to Li et al.1.

Disease heterogeneity and molecular classification of inflammatory palmoplantar diseases.

BACKGROUND: Palmoplantar pustulosis (PPP) is an inflammatory disease characterized by relapsing eruptions of neutrophil-filled, sterile pustules on the palms and soles that can be clinically difficult to differentiate from non-pustular palmoplantar psoriasis (palmPP) and dyshidrotic palmoplantar eczema (DPE). OBJECTIVE: To identify overlapping and unique PPP, palmPP, and DPE drivers to provide molecular insight into their pathogenesis. METHODS: We performed bulk RNA sequencing of lesional PPP (n=33), palmPP (n=5), and DPE (n=28) samples, as well as 5 healthy non-acral and 10 healthy acral skin samples. RESULTS: Acral skin shows a unique immune environment, likely contributing to a unique niche for palmoplantar inflammatory diseases. Compared with healthy acral skin, PPP, palmPP, and DPE displayed a broad overlapping transcriptomic signature characterized by shared upregulation of pro-inflammatory cytokines (TNF, IL36), chemokines, and T cell-associated genes, along with unique disease features of each disease state, including enriched neutrophil processes in PPP and to a lesser extent in palmPP, and lipid antigen processing in DPE. Strikingly, unsupervised clustering and trajectory analyses demonstrated divergent inflammatory profiles within the three disease states. These identified putative key upstream immunological switches, including eicosanoids, interferon responses, and neutrophil degranulation, contributing to disease heterogeneity. CONCLUSION: We demonstrate the molecular overlap between different inflammatory palmoplantar diseases that supersedes clinical and histologic assessment, yet highlighting the heterogeneity within each condition, suggesting limitations of current disease classification and the need to move toward a molecular classification of inflammatory acral diseases.

The PAH1-encoded phosphatidate phosphatase of Yarrowia lipolytica differentially affects gene expression and lipid biosynthesis.

Yarrowia lipolytica is a model oleaginous yeast with a strong capacity for lipid accumulation, yet its lipid metabolic pathways and regulatory mechanisms remain largely unexplored. The PAH1-encoded phosphatidate (PA) phosphatase governs lipid biosynthesis by its enzymatic activity and regulating the transcription of genes involved in phospholipid biosynthesis. In this work, we examined the effect of the loss of Pah1 (i.e., pah1Δ) on cell metabolism in cells growing in low- and high-glucose media. Multi-omics analyses revealed the global effect of the pah1Δ mutation on lipid and central carbon metabolism. Lipidomics analyses showed that the pah1Δ mutation caused a massive decrease in the masses of triacylglycerol (TAG) and diacylglycerol (DAG), and these effects were independent of glucose concentration in the media. Conversely, phospholipid levels declined in low-glucose media but increased in high-glucose media. The loss of Pah1 affected the expression of genes involved in key pathways of glucose metabolism, such as glycolysis, citric acid cycle, oxidative phosphorylation, and the pentose phosphate pathway, and these effects were more pronounced in high-glucose media. In lipid biosynthesis, the genes catalyzing phosphatidylcholine (PC) synthesis from phosphatidylethanolamine (PE) were upregulated within the CDP-DAG pathway. In contrast, PC synthesis through the Kennedy pathway was downregulated. The ethanolamine branch of the Kennedy pathway that synthesizes PE was also upregulated in pah1Δ. Interestingly, we noted a massive increase in the levels of lysophospholipids, consistent with the upregulation of genes involved in lipid turnover. Overall, this work identified novel regulatory roles of Pah1 in lipid biosynthesis and gene expression.

Machine learning-driven diagnosis of multiple sclerosis from whole blood transcriptomics.

Multiple sclerosis (MS) is a neurological disorder characterized by immune dysregulation. It begins with a first clinical manifestation, a clinically isolated syndrome (CIS), which evolves to definite MS in case of further clinical and/or neuroradiological episodes. Here we evaluated the diagnostic value of transcriptional alterations in MS and CIS blood by machine learning (ML). Deep sequencing of more than 200 blood RNA samples comprising CIS, MS and healthy subjects, generated transcriptomes that were analyzed by the binary classification workflow to distinguish MS from healthy subjects and the Time-To-Event pipeline to predict CIS conversion to MS along time. To identify optimal classifiers, we performed algorithm benchmarking by nested cross-validation with the train set in both pipelines and then tested models generated with the train set on an independent dataset for final validation. The binary classification model identified a blood transcriptional signature classifying definite MS from healthy subjects with 97% accuracy, indicating that MS is associated with a clear predictive transcriptional signature in blood cells. When analyzing CIS data with ML survival models, prediction power of CIS conversion to MS was about 72% when using paraclinical data and 74.3% when using blood transcriptomes, indicating that blood-based classifiers obtained at the first clinical event can efficiently predict risk of developing MS. Coupling blood transcriptomics with ML approaches enables retrieval of predictive signatures of CIS conversion and MS state, thus introducing early non-invasive approaches to MS diagnosis.

Physiological and transcriptional changes associated with obligate aestivation in the cabbage stem flea beetle (Psylliodes chrysocephala).

Aestivation is a form of seasonal dormancy observed in various insect species, usually coinciding with the summer season. The cabbage stem flea beetle, Psylliodes chrysocephala (Coleoptera: Chrysomelidae), is a key pest of oilseed rape that obligatorily aestivates as adult in late summer. Since the physiological and transcriptional processes linked to aestivation in P. chrysocephala are still little understood, we analyzed relevant physiological parameters and performed RNA-seq analyses on laboratory-reared beetles in their pre-aestivation, aestivation, and post-aestivation stages. We found that the beetles reached aestivation at 15 days post-eclosion, showing strongly reduced metabolic activity, with less than 50% CO2 production, compared to pre-aestivating individuals. Under constant laboratory conditions, the beetles aestivated for about 25 days. Female beetles reached reproductive maturity at a median of 52 days post-eclosion. Furthermore, aestivating beetles had significantly reduced carbohydrate reserves and increased lipid reserves compared with pre-aestivating beetles, indicating that aestivation is associated with drastic changes in energy metabolism. Aestivating beetles contained 30% less water and their survival rates under high-temperature conditions (30 °C) were 40% higher compared to pre-aestivating beetles. RNA-seq studies showed that, in particular, gene ontology terms related to carbohydrate and lipid metabolism, digestion, and mitochondrial activity were enriched, with clear differences in transcript abundance between beetles in aestivation compared to pre- or post-aestivation. Specifically, mitochondrial transcripts, such as respiratory chain I subunits, and digestion-related transcripts, such as trypsin, were less abundant during aestivation, which supports the idea that aestivation is associated with decreased metabolic activity. This study represents the first exploration of the transcriptomic and physiological processes linked to aestivation in P. chrysocephala.

Screening of reliable reference genes for the normalization of RT-qPCR in chicken liver tissues and LMH cells.

The liver plays a vital role in lipid synthesis and metabolism in poultry. To study the functional genes more effectively, it is essential to screen of reliable reference genes in the chicken liver, including females, males, embryos, as well as the Leghorn Male Hepatoma (LMH) cell line. Traditional reference gene screening involves selecting commonly used housekeeping genes (HKGs) for RT-qPCR experiments and using different algorithms to identify the most stable ones. However, this approach is limited in selecting the best reference gene from a small pool of HKGs. High-throughput sequencing technology may offer a solution to this limitation. This study aimed to identify the most consistently expressed genes by utilizing multiple published RNA-seq data of chicken liver and LMH cells. Subsequently, the stability of the newly identified reference genes was assessed in comparison to previously validated stable poultry liver expressed reference genes and the commonly employed HKGs using RT-qPCR. The findings indicated that there is a higher degree of similarity in stable expression genes between female and male liver (such as LSM14A and CDC40). In embryonic liver, the optimal new reference genes were SUDS3, TRIM33, and ERAL1. For LMH cells, the optimal new reference genes were ALDH9A1, UGGT1, and C21H1orf174. However, it is noteworthy that most HKGs did not exhibit stable expression across multiple samples, indicating potential instability under diverse conditions. Furthermore, RT-qPCR experiments proved that the stable expression genes identified from RNA-seq data outperformed commonly used HKGs and certain validated reference genes specific to poultry liver. Over all, this study successfully identified new stable reference genes in chicken liver and LMH cells using RNA-seq data, offering researchers a wider range of reference gene options for RT-qPCR in diverse situations.

Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.

To thrive on melting alpine and polar snow, some Chlorophytes produce an abundance of astaxanthin, causing red blooms, often dominated by genus Sanguina. The red cells have not been cultured, but we recently grew a green biciliate conspecific with Sanguina aurantia from a sample of watermelon snow. This culture provided source material for Oxford Nanopore Technology and Illumina sequencing. Our assembly pipeline exemplifies the value of a hybrid long- and short-read approach for the complexities of working with a culture grown from a field sample. Using bioinformatic tools we separated assembled contigs into two genomic pools based on a difference in GC content (57.5% and 55.1%). We present the data as two assemblies of S. aurantia variants but explore other possibilities. High-throughput chromatin conformation capture analysis (Hi-C sequencing) was used to scaffold the assemblies into a 96 MB genome designated 'A' and a 102 MB genome designated 'B'. Both assemblies are highly contiguous: genome A consists of 38 scaffolds with an N50 of 5.4 Mb while genome B has 50 scaffolds with an N50 of 6.4 Mb. RNA-sequencing was used to improve gene annotation.

Regeneration of tunic cuticle is suppressed in edible ascidian Halocynthia roretzi contracting soft tunic syndrome.

Soft tunic syndrome is an infectious disease caused by the flagellate Azumiobodo hoyamushi, which severely damages the aquaculture of the edible ascidian Halocynthia roretzi. Tunic is a cellulosic extracellular matrix entirely covering the body in ascidians and other tunicates, and its dense cuticle layer covers the tunic surface as a physical barrier against microorganisms. When the tunic of intact H. roretzi individuals was cut into strips, electron-dense fibers (DFs) appeared on the cut surface of the tunic matrix and aggregated to regenerate a new cuticular layer in seawater within a few days. DF formation was partially or completely inhibited in individuals with soft tunic syndrome, and DF formation was also inhibited by the presence of some proteases, indicating the involvement of proteolysis in the process of tunic softening as well as cuticle regeneration. Using pure cultures of the causative flagellate A. hoyamushi, the expression of protease genes and secretion of some proteases were confirmed by RNA-seq analysis and a 4-methylcoumaryl-7-amide substrate assay. Some of these proteases may degrade proteins in the tunic matrix. These findings suggest that the proteases of A. hoyamushi is the key to understanding the mechanisms of cuticular regeneration inhibition and tunic softening.

Protocol to identify and isolate rare murine tumor-resident dendritic cell populations for low-input transcriptomic profiling.

Conventional type 1 dendritic cells (cDC1s) are critical for innate sensing of cancer, yet they are scarce in the tumor microenvironment (TME). Here, we present a protocol to identify and isolate cDC1 subsets from murine implantable tumors for subsequent transcriptomic profiling using a flow sorting-based strategy. We describe steps for cell culture of mouse tumors, tumoral growth, dissociation and isolation of tumoral cells, extracellular staining, and cell sorting. We then detail procedures for RNA isolation, mRNA library preparation, and sequencing. For complete details on the use and execution of this protocol, please refer to Papadas et al.1.

Protocol to achieve high-resolution single-cell transcriptomics of cardiomyocytes in multiple species.

Single-cell RNA sequencing (scRNA-seq) remains state-of-the-art for transcriptomic cell-mapping. Here, we provide a protocol to generate high-resolution scRNA-seq of rare cardiomyocyte populations (e.g., regenerating/dividing, etc.) from mouse and zebrafish hearts as well as induced pluripotent stem cells, collected in time to achieve detailed transcriptomic insight. We describe the serial steps of viability staining, methanol fixation, storage, and cell sorting to preserve RNA integrity suited for scRNA-seq as well as the quality assessment of the data as shown by examples. For complete details on the use and execution of this protocol, please refer to Bak et al.1.

Comparative transcriptome reveals EphA2 and c-Fos as key factors driving enhanced replication in high-passage porcine deltacoronavirus strain.

Porcine deltacoronavirus (PDCoV), a cross-species transmissible enterovirus, frequently induces severe diarrhea and vomiting symptoms in piglets, which not only pose a significant menace to the global pig industry but also a potential public safety risk. In a previous study, we isolated a vaccine candidate, PDCoV CZ2020-P100, by passaging a parental PDCoV strain in vitro, exhibiting attenuated virulence and enhanced replication. However, the factors underlying these differences between primary and passaged strains remain unknown. In this study, we present the transcriptional landscapes of porcine kidney epithelial cells (LLC-PK1) cells infected with PDCoV CZ2020-P1 strain and P100 strain using the RNA-sequencing. We identified 105 differentially expressed genes (DEGs) in P1-infected cells and 295 DEGs in P100-infected cells. Enrichment analyses indicated that many DEGs showed enrichment in immune and inflammatory responses, with a more and higher upregulation of DEGs enriched in the P100-infected group. Notably, the DEGs were concentrated in the MAPK pathway within the P100-infected group, with significant upregulation in EphA2 and c-Fos. Knockdown of EphA2 and c-Fos reduced PDCoV infection and significantly impaired P100 replication compared to P1, suggesting a novel mechanism in which EphA2 and c-Fos are highly involved in passaged virus replication. Our findings illuminate the resemblances and distinctions in the gene expression patterns of host cells infected with P1 and P100, confirming that EphA2 and c-Fos play key roles in high-passage PDCoV replication. These results enhance our understanding of the changes in virulence and replication capacity during the process of passaging.

Combined salt and low nitrate stress conditions lead to morphophysiological changes and tissue-specific transcriptome reprogramming in tomato.

Despite intense research towards the understanding of abiotic stress adaptation in tomato, the physiological adjustments and transcriptome modulation induced by combined salt and low nitrate (low N) conditions remain largely unknown. Here, three traditional tomato genotypes were grown under long-term single and combined stresses throughout a complete growth cycle. Physiological, molecular, and growth measurements showed extensive morphophysiological modifications under combined stress compared to the control, and single stress conditions, resulting in the highest penalty in yield and fruit size. The mRNA sequencing performed on both roots and leaves of genotype TRPO0040 indicated that the transcriptomic signature in leaves under combined stress conditions largely overlapped that of the low N treatment, whereas root transcriptomes were highly sensitive to salt stress. Differentially expressed genes were functionally interpreted using GO and KEGG enrichment analysis, which confirmed the stress and the tissue-specific changes. We also disclosed a set of genes underlying the specific response to combined conditions, including ribosome components and nitrate transporters, in leaves, and several genes involved in transport and response to stress in roots. Altogether, our results provide a comprehensive understanding of above- and below-ground physiological and molecular responses of tomato to salt stress and low N treatment, alone or in combination.

Candesartan restores blood-brain barrier dysfunction, mitigates aberrant gene expression, and extends lifespan in a knockin mouse model of epileptogenesis.

Blockade of Angiotensin type 1 receptor (AT1R) has potential therapeutic utility in the treatment of numerous detrimental consequences of epileptogenesis, including oxidative stress, neuroinflammation, blood-brain barrier (BBB) dysfunction. We have recently shown that many of these pathological processes played a critical role in seizure onset and propagation in the Scn8a-N1768D mouse model. Here we investigate the efficacy and potential mechanism(s) of action of candesartan (CND), an FDA-approved angiotensin receptor blocker (ARB) indicated for hypertension, in improving outcomes in this model of pediatric epilepsy. We compared length of lifespan, seizure frequency, and BBB permeability in juvenile (D/D) and adult (D/+) mice treated with CND at times after seizure onset. We performed RNAseq on hippocampal tissue to quantify differences in genome-wide patterns of transcript abundance and inferred beneficial and detrimental effects of canonical pathways identified by enrichment methods in untreated and treated mice. Our results demonstrate that treatment with CND gives rise to increased survival, longer periods of seizure freedom, and diminished BBB permeability, as well as partially reversed or "normalized" disease-induced genome-wide gene expression profiles associated with inhibition of NF-κB, TNFα, IL-6, and TGF-ß signaling in juvenile and adult mice. Pathway analyses reveal that efficacy of CND is due to its known dual mechanism of action as both an AT1R antagonist and a PPARγ agonist. The robust efficacy of CND across ages, sexes and mouse strains is a positive indication for its translation to humans and its suitability of use for clinical trials in children with SCN8A epilepsy.

The cytoglobin-dependent transcriptome in melanoma indicates a protective function associated with oxidative stress, inflammation and cancer-associated pathways.

Cytoglobin (CYGB) is a member of the oxygen-binding globin superfamily. In this study we generated stable CYGB overexpressing A375 melanoma cells and performed RNA-sequencing to comprehensively explore the CYGB-dependent transcriptome. Our findings reveal that ectopic expression of CYGB dysregulated multiple cancer-associated genes, including the mTORC1 and AKT/mTOR signaling pathways, which are frequently overactivated in tumors. Moreover, several cancer-associated pathways, such as epithelial-mesenchymal transition (EMT) mediated by CSPG4, were downregulated upon CYGB overexpression. Intriguingly, ectopic expression suggested anti-inflammatory potential of CYGB, as exemplified by downregulation of key inflammasome-associated genes, including NLRP1, CASP1 and CD74, which play pivotal roles in cytokine regulation and inflammasome activation. Consistent with established globin functions, CYGB appears to be involved in redox homeostasis. Furthermore, our study indicates CYGB's association to DNA repair mechanisms and its regulation of NOX4, reinforcing its functional versatility. Additionally, multiple significantly enriched pathways in CYGB overexpressing cells were consistently dysregulated in opposite direction in CYGB depleted cells. Collectively, our RNA-sequencing based investigations illustrate the diverse functions of CYGB in melanoma cells, pointing to its putative roles in cellular protection against oxidative stress, inflammation, and cancer-associated pathways. These findings pave the way for further research into the physiological role of CYGB and its potential as a candidate therapeutic target in melanoma.

Integrating Multi-omics to Identify Age-Related Macular Degeneration Subtypes and Biomarkers.

Age-related macular degeneration (AMD) is one of the most common causes of irreversible vision loss in the elderly. Its pathogenesis is likely multifactorial, involving a complex interaction of metabolic and environmental factors, and remains poorly understood. Previous studies have shown that mitochondrial dysfunction and oxidative stress play a crucial role in the development of AMD. Oxidative damage to the retinal pigment epithelium (RPE) has been identified as one of the major mediators in the pathogenesis of age-related macular degeneration (AMD). Therefore, this article combines transcriptome sequencing (RNA-seq) and single-cell sequencing (scRNA-seq) data to explore the role of mitochondria-related genes (MRGs) in AMD. Firstly, differential expression analysis was performed on the raw RNA-seq data. The intersection of differentially expressed genes (DEGs) and MRGs was performed. This paper proposes a deep subspace nonnegative matrix factorization (DS-NMF) algorithm to perform a multi-layer nonlinear transformation on the intersection of gene expression profiles corresponding to AMD samples. The age of AMD patients is used as prior information at the network's top level to change the data distribution. The classification is based on reconstructed data with altered distribution. The types obtained significantly differ in scores of multiple immune-related pathways and immune cell infiltration abundance. Secondly, an optimal AMD diagnosis model was constructed using multiple machine learning algorithms for external and qRT-PCR verification. Finally, ten potential therapeutic drugs for AMD were identified based on cMAP analysis. The AMD subtypes identified in this article and the diagnostic model constructed can provide a reference for treating AMD and discovering new drug targets.

Abnormal amino acid synthesis and glutathione metabolism may affect PCOS blastocyst development: an examination of in vitro mouse blastocysts model utilizing RNA-sequencing.

BACKGROUND: Extensive research has been conducted on embryonic developmental disorders linked to Polycystic Ovary Syndrome (PCOS), a pathological condition that affects 5-10% of women and is characterized by irregularities in the menstrual cycle and infertility. By employing RNA sequencing (RNA-seq), we performed an in-depth investigation of PCOS-related changes in gene expression patterns at the mouse blastocyst stage. METHODS: The zygotes of female B6D2 mice were obtained and then differentiated into blastocysts in K + Simplex Optimised Medium (KSOM) cultures containing exo-NC (negative control for exosomes) or exo-LIPE-AS1 (a novel exosomal marker of PCOS). Subsequently, blastocysts were collected for RNA-seq. The bioinformatics was performed to analyze and compare the differences of gene expression profile between blastocysts of control and PCOS group. RESULTS: There were 1150 differentially expressed genes (DEGs) between the two groups of mouse blastocysts; 243 genes were upregulated and 907 downregulated in the blastocysts of the exo-LIPE-AS1 group compared to those of the exo-NC group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the genes involved in amino acid synthesis and glutathione metabolic pathways were down-regulated in exo-LIPE-AS1 group. CONCLUSION: This study has revealed that blastocyst developmental retardation may be associated with the downregulation of amino acid synthesis and glutathione metabolism, which may affect energy metabolism, biosynthesis, cellular osmotic pressure, antioxidant synthesis, ROS clearance or mitochondrial function, and ultimately cause blastocyst cell development abnormalities. Our research offers encouraging data on the mechanisms underlying aberrant embryonic development in patients with PCOS as well as potential treatment strategies.

Identification of Biomarkers for Lung Adenocarcinoma With Qi Deficiency and Phlegm Dampness.

BACKGROUND: Qi deficiency and phlegm dampness (QPD) is one of the most common traditional Chinese medicine (TCM) syndromes in lung adenocarcinoma (LUAD). This study aimed to identify syndrome-specific biomarkers for LUAD with QPD syndrome. METHODS: Peripheral blood mononuclear cells (PBMCs) from LUAD patients with QPD, LUAD patients with non-QPD (N-QPD), and healthy control (H) were collected and analyzed with RNA-seq to identify differentially expressed genes (DEGs). The area under the receiver operator characteristic curve (AUC) of each DEG was calculated, and the top 10 highest AUC DEGs were validated by qRT-PCR. Logistic regression analysis was used to develop a diagnostic model evaluated with AUC. RESULTS: A total of 135 individuals were enrolled in this study (training set: 15 QPD, 15 N-QPD, 15 H; validation set: 30 QPD, 30 N-QPD, 30 H). A total of 1480 DEGs were identified between QPD and N-QPD. The qRT-PCR results showed that the expression of DDR2 was downregulated, and PPARG was upregulated, which was in line with the finding of the training set. We developed a diagnostic model with these two genes. The AUC of the diagnostic model in the training cohort and validation cohort was 0.891 and 0.777, respectively. CONCLUSIONS: We identified the two genes (DDR2 and PPARG) as syndrome-specific biomarkers for LUAD with QPD syndrome and developed a novel diagnostic model, which may help to improve the accuracy and sensibility of clinical diagnosis and provide a new target for natural drug treatment of LUAD.