Peptide Recognition Research Articles

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen.

T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility complex protein is a major event in triggering the adaptive immune response to pathogens or cancer. The prediction of TCR-peptide interactions has great importance for therapy of cancer as well as infectious and autoimmune diseases but remains a major challenge, particularly for novel (unseen) peptide epitopes. Here we present TCRen, a structure-based method for ranking candidate unseen epitopes for a given TCR. The first stage of the TCRen pipeline is modeling of the TCR-peptide-major histocompatibility complex structure. Then a TCR-peptide residue contact map is extracted from this structure and used to rank all candidate epitopes on the basis of an interaction score with the target TCR. Scoring is performed using an energy potential derived from the statistics of TCR-peptide contact preferences in existing crystal structures. We show that TCRen has high performance in discriminating cognate versus unrelated peptides and can facilitate the identification of cancer neoepitopes recognized by tumor-infiltrating lymphocytes.

Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103

Pyroglutamylated RF-amide peptide (QRFP) is a peptide hormone with a C-terminal RF-amide motif. QRFP selectively activates a class A G-protein-coupled receptor (GPCR) GPR103 to exert various physiological functions such as energy metabolism and appetite regulation. Here, we report the cryo-electron microscopy structure of the QRFP26-GPR103-Gq complex at 3.19 Å resolution. QRFP26 adopts an extended structure bearing no secondary structure, with its N-terminal and C-terminal sides recognized by extracellular and transmembrane domains of GPR103 respectively. This movement, reminiscent of class B1 GPCRs except for orientation and structure of the ligand, is critical for the high-affinity binding and receptor specificity of QRFP26. Mutagenesis experiments validate the functional importance of the binding mode of QRFP26 by GPR103. Structural comparisons with closely related receptors, including RY-amide peptide-recognizing GPCRs, revealed conserved and diversified peptide recognition mechanisms, providing profound insights into the biological significance of RF-amide peptides. Collectively, this study not only advances our understanding of GPCR-ligand interactions, but also paves the way for the development of novel therapeutics targeting metabolic and appetite disorders and emergency medical care.

Structural basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor

The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the extracellular region of the receptor and the N-terminus of the peptide, and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa by the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptide recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide peptide receptors.

Antigen Delivery Controlled by an On-Demand Photorelease.

To eliminate infected and cancerous cells, antigen processing and presentation play a pivotal role through the recognition of antigenic peptides displayed on Major Histocompatibility Complex class I (MHC I) molecules. Here, we developed a photostimulated antigen release system that enables the temporal inception of antigen flux. Simple and effective photocaging of the human immunodeficiency virus (HIV)-Nef73-derived epitope, a representative high-affinity MHC I ligand, was provided by steric hindrance to block the recognition by the transporter associated with antigen processing (TAP) in the peptide loading complex (PLC). In response to light, a heteronomous release of antigens and subsequent translocation in various scenarios is demonstrated, including a TAP-related ATP-binding cassette (ABC) transporter reconstituted in liposomes and the native PLC in the endoplasmic reticulum (ER) membrane of human cells. The photochemically induced 'burst' of antigens opens new opportunities for a mechanistic analysis of the antigen translocation machinery and will help to provide insights into antigen processing pathways via an on-demand, subcellular pulse-chase release of antigens.

Management of immune-mediated necrotizing myopathy.

The immune-mediated necrotizing myopathies (IMNM) are autoimmune myositides clinically characterized by proximal predominant weakness and elevated creatine kinase (CK). They may be associated with autoantibodies (anti-HMGCR, anti-SRP), triggered by statin use (e.g., anti-HMGCR myopathy), associated with cancer, or may be idiopathic. Immunotherapy is required to improve strength and decrease the CK level, but no therapies are currently approved by the U.S. Food and Drug Administration for the treatment of IMNM. The optimal treatment strategy for IMNM is currently unknown and wide practice variation exists in the management of this condition. However, observational studies and expert opinion suggest that certain therapies may be more effective for the different serological subtypes of IMNM. HMGCR IMNM often responds favorably to intravenous immunoglobulin (IVIG) even as monotherapy. Signal recognition peptide and seronegative IMNM typically require combination immunotherapy, most often consisting of an oral immunosuppressant, corticosteroids, and IVIG or rituximab. Patients often remain on immunotherapy for years and relapse is common during tapering of immunotherapy. Further studies are needed to guide the optimal management of these patients.

A Super-Antifouling Electrochemical Biosensor for Protein Detection in Complex Biofluids Based on PEGylated Multifunctional Peptide.

Overcoming the influence of interfering substances in the environment and achieving superior sensing performance are significant challenges in biomarker detection within complex matrices. Herein, an integrated electrochemical sensing platform for sensitive detection of biomarkers in complex biofluids was developed based on a newly designed PEGylated multifunctional peptide (PEG-MPEP). The designed PEG-MPEP contains a poly(serine) sequence (-ssssss-) as the antifouling part and recognition peptide sequence (-avwgrwh) specific for the target human immunoglobulin G (IgG). To improve the peptide stability to protease hydrolysis, d-amino acids were adopted to synthesize the whole peptide. Additionally, the PEGylation can further enhance the stability of the peptide, and the PEG itself was also antifouling, ensuring superstrong antifouling capability of the PEG-MPEP. The designed PEG-MPEP-based biosensor possessed a high sensitivity for the detection of IgG in the range of 1.0 pg mL-1 to 1.0 μg mL-1, with a low limit of detection (0.41 pg mL-1), and it was capable of assaying targets accurately in real serum samples. Compared with conventional peptide-modified biosensors, the PEG-MPEP-modified biosensor exhibited superior antifouling and antihydrolysis properties in complex biofluid, showcasing promising potential for practical assay applications.

Potential of Nettle Infusion to Protect Common Bean from Halo Blight Disease

The use of plant-based preparations to replace chemical pesticides is a challenge for sustainable agriculture. Preparations from nettle (Urtica dioica L.) are good candidates, as the treatment of common bean plants (Phaseolus vulgaris L.) with aqueous suspensions of nettle reduced symptoms of halo blight disease caused by Pseudomonas syringae pv. phaseolicola (Pph). The aim of the present work was to test if nettle infusions (Ui) have similar effects and find out what activity is behind this: antimicrobial, promotion of the natural defenses of plants, and/or antioxidant. To achieve this, Pph growth was tested in the presence of infusions of nettle leaves collected in two different years (Ui18 and Ui22), and we found that it was only weakly inhibited at high concentrations of Ui18. Interestingly, Ui22 promoted bacteria growth at all concentrations. Second, we estimated the production of reactive oxygen species (ROS) in response to flagellin22 (flg22) in common bean leaf discs, since recognition of this bacterial peptide usually leads to ROS accumulation in tissues as a plant immune response. However, leaf discs that were preincubated in Ui showed no accumulation of ROS after flg22 treatment, suggesting that Ui can neutralize ROS production. Finally, in a Pph inoculation experiment of common bean plants grown in vitro, we observed that pretreatment of plants with Ui drastically reduced foliar oxidative damage and disease symptoms 6 h after inoculation. This effect was more noticeable for Ui22, which was related to the higher antioxidant activity found in this extract in comparison with Ui18. These results suggest that the protective properties of Ui are mainly due to the content of antioxidant bioactive compounds.

The involvement of VEGF and VEGFR in bacterial recognition and regulation of antimicrobial peptides in Eriocheir sinensis

Vascular endothelial growth factor (VEGF) and VEGF reporter (VEGFR) are essential molecules in VEGF signalling pathway. Although the functions of VEGF and VEGFR have been well reported in vertebrates, their functions are still poorly understood in invertebrates. In this study, the open reading frame sequences of EsVEGF1 and EsVEGFR4 were cloned from Eriocheir sinensis, and their corresponding proteins shared typical structure characteristics with their counterparts in other species. EsVEGF1 were predominantly expressed in hepatopancreas and muscle while EsVEGFR4 mainly expressed in hemocytes and intestine. The expression levels of EsVEGF1 in hemocytes were rapidly induced by Staphylococcus aureus and Vibrio parahaemolyticus, and it also increased rapidly in hepatopancreas after being challenged with V. parahaemolyticus. The expression levels of EsVEGFR4 only increased in hepatopancreas of crabs injected with S. aureus. The extracellular immunoglobulin domain of EsVEGFR4 could bind with Gram-negative and Gram-positive bacteria as well as lipopolysaccharide and peptidoglycan. EsVEGF1 could act as the ligand for EsVEGFR4 and Toll-like receptor and regulate the expression of crustins and lysozyme with a tissue-specific manner, while have no regulatory function on that of anti-lipopolysaccharide factors. This study will provide new insights into the immune defense mechanisms mediated by VEGF and VEGFR in crustaceans.

A sandwich FRET biosensor for lysozyme detection based on peptide-functionalized gold nanoparticles and FAM-labeled aptamer

Lysozyme (LYZ) plays a crucial role in the body's immune defense system. Monitoring LYZ levels can provide valuable insights into the diagnosis and severity assessment of various diseases. Traditionally, antibody-based sandwich assays are employed for LYZ detection, but they are often time-consuming and operationally complicated. In this research, a novel sandwich FRET biosensor was developed, which enables rapid detection of LYZ based on peptide-functionalized gold nanoparticles (pAuNPs) and FAM-labeled aptamer (Apt-FAM). Initially, a mixture of Apt-FAM and pAuNPs resulted in partial quenching of the Apt-FAM fluorescence emission through an inner filter effect (IFE), with negligible energy transfer because of the electrostatic repulsion between the negatively charged pAuNPs and Apt-FAM. The introduction of LYZ into the mixture drove the specific binding of Apt-FAM and pAuNPs to LYZ, facilitating the formation of a pAuNPs-LYZ-aptamer sandwich structure. The formation of this complex drew the pAuNPs and Apt-FAM into close enough proximity to enable FRET to occur, which in turn effectively quenched the fluorescence emission of FAM. The decrease in FAM fluorescence intensity was correlated with the increasing concentration of LYZ. Thus, a sandwich FRET biosensor was successfully developed for LYZ detection with a linear detection range of 0–1.75 μM and a detection limit of 85 nM. Additionally, the biosensor allowed visual detection of LYZ in a 96-well microplate, with a rapid response time of just 15 s. This study introduces a innovative sandwich FRET biosensor that combines aptamer and peptide recognition elements, offering a fast and antibody-free method for protein detection.

RuSe2/CuO nanohybrids coupled with ALP-assisted for MMP-9 photoelectrochemical assay

A photoelectrochemical (PEC) assay strategy for the detection of matrix metalloproteinase-9 (MMP-9) was fabricated. RuSe2/CuO nanohybrids were first prepared by hydrothermal method. As a transition metal element semiconductor, RuSe2 has excellent optical and electrical properties. By combining the excellent conductivity and adjustable bandgap of CuO, a binary heterojunction nanoflower with high photoelectric response was obtained. The combination of RuSe2 and CuO reduces the electron hole recombination rate; the RuSe2/CuO nanohybrids exhibits a higher photocurrent response. In the MMP-9 PEC strategy determination, the magnetic beads (MB)-peptide-alkaline phosphatase (ALP) recognition probe was formed by modifying C-terminal of the peptide chain with biotin and binding to ALP, and the N-terminal was connected to carboxylated MB. When the target MMP-9 exists, the recognition probe, MB-Peptide-ALP, was recognized by MMP-9 to cut the substrate area and coding area and release ALP, catalyzing the hydrolysis of O-phosphonoxyphenol (OPP) to produce benzene-1,2-diol in situ, the photocurrent response was generated. This strategy provides lower background PEC noise for detecting MMP-9, with the advantage of simplicity and the sensitivity than conventional ELISA. The results showed that the recognition peptide probe PEC method achieved ultra-high sensitivity detection of target MMP-9, with a linear detection range of 1 pg/mL–100 ng/mL and a detection limit of 0.3 pg/mL (S/N = 3). The results of PEC assay strategy in human serum sample give the recoveries rate of 94.3 % to 108.1 % and relative standard deviation of 0.45–5.87 %.

Antigenic Peptide-Thioredoxin Fusion Chimeras for In Vitro Stimulus of CD4+ TCR+ Jurkat T Cells.

Study of CD4+ T cell response and T cell receptor (TCR) specificity is crucial for understanding etiology of immune-mediated diseases and developing targeted therapies. However, solubility, accessibility, and stability of synthetic antigenic peptides used in T cell assays may be a critical point in such studies. Here we present a T cell activation reporter system using recombinant proteins containing antigenic epitopes fused with bacterial thioredoxin (trx-peptides) and obtained by bacterial expression. We report that co-incubation of CD4+ HA1.7 TCR+ reporter Jurkat 76 TRP cells with CD80+ HLA-DRB1*01:01+ HeLa cells or CD4+ Ob.1A12 TCR+ Jurkat 76 TRP with CD80+ HLA-DRB1*15:01+ HeLa cells resulted in activation of reporter Jurkat 76 TPR after addition of recombinant trx-peptide fusion proteins, containing TCR-specific epitopes. Trx-peptides were comparable with corresponding synthetic peptides in their capacity to activate Jurkat 76 TPR. These data demonstrate that thioredoxin as a carrier protein (trx) for antigenic peptides exhibits minimal interference with recognition of MHC-specific peptides by TCRs and consequent T cell activation. Our findings highlight potential feasibility of trx-peptides as a reagent for assessing the immunogenicity of antigenic fragments.

Ultrasensitive dual-mode detection of amyloid β oligomer via Au NRs modulated photoelectrochemical/electrochemiluminescent response from HOFs/g-C3N4

In this work, a heterojunction composite of HOFs/g-C3N4 was synthesized using solution-plasticized self-assembly of g-C3N4 nanosheet on hydrogen-bonded organic frameworks (HOFs). HOFs/g-C3N4 was then used as a substrate material to construct a novel photoelectrochemical/electrochemiluminescent (PEC/ECL) biosensor for the detection of amyloid β oligomer (Aβo). HOFs/g-C3N4 composites were first drop-coated on the electrode surface. Subsequently, the Aβ aptamer was modified on the electrode surface via amide bonding. The target Aβo and the gold nanorods (Au NRs)-labeled Aβ recognition peptide (Au NRs-KLVFF) were simultaneously dropped onto the electrode surface, thus a “sandwich” dual-mode biosensor was constructed. In the PEC detection of the Aβo, the surface plasmon resonance effect of Au NRs enhanced the visible absorption of HOF/g-C3N4, and the sensor exhibited a "signal-on" photocurrent signal. Meanwhile, the ECL emission spectrum of HOF/g-C3N4 in ECL mode overlaps with the ultraviolet-visible (UV) absorption of Au NRs, and the sensor signal showed a “signal-off” ECL response. Under the optimal conditions experiments, the constructed dual-mode biosensor showed a wide detection range and low detection limit for Aβo. The proposed dual-mode detection method has a detection range of 10 fM to 10 nM with a detection limit of 5.97 fM for PEC detection and a detection range of 0.1 pM to 1.0 μM with a detection limit of 0.051 pM for ECL detection respectively. Additionally, the detection method achieved satisfactory results in the analysis of real samples. Dual-mode sensing platform provides a new strategy for HOFs application in PEC/ECL assay and sensitive detection of AβO.

Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs

Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the “Asn-Ala-Leu” motif and an N-terminus “Arg-Leu” as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, “Asn-Ala-Leu” and “Arg-Leu” under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.

VitTCR: A deep learning method for peptide recognition prediction

This study introduces VitTCR, a predictive model based on the vision transformer (ViT) architecture, aimed at identifying interactions between Tcell receptors (TCRs) and peptides, crucial for developing cancer immunotherapies and vaccines. VitTCR converts TCR-peptide interactions into numerical AtchleyMaps using Atchley factors for prediction, achieving AUROC (0.6485) and AUPR (0.6295) values. Benchmark analysis indicates VitTCR's performance is comparable to other models, with further comparative studies suggested to understand its effectiveness in varied contexts. Additionally, integrating a positional bias weight matrix (PBWM), derived from amino acid contact probabilities in structurally resolved pMHC-TCR complexes, slightly improves VitTCR's accuracy. The model's predictions show weak yet statistically significant correlations with immunological factors like Tcell clonal expansion and activation percentages, underscoring the biological relevance of VitTCR's predictive capabilities. VitTCR emerges as a valuable computational tool for predicting TCR-peptide interactions, offering insights for immunotherapy and vaccine development.

UsIL-6: An unbalanced learning strategy for identifying IL-6 inducing peptides by undersampling technique

Background and objectiveInterleukin-6 (IL-6) is the critical factor of early warning, monitoring, and prognosis in the inflammatory storm of COVID-19 cases. IL-6 inducing peptides, which can induce cytokine IL-6 production, are very important for the development of diagnosis and immunotherapy. Although the existing methods have some success in predicting IL-6 inducing peptides, there is still room for improvement in the performance of these models in practical application. MethodsIn this study, we proposed UsIL-6, a high-performance bioinformatics tool for identifying IL-6 inducing peptides. First, we extracted five groups of physicochemical properties and sequence structural information from IL-6 inducing peptide sequences, and obtained a 636-dimensional feature vector, we also employed NearMiss3 undersampling method and normalization method StandardScaler to process the data. Then, a 40-dimensional optimal feature vector was obtained by Boruta feature selection method. Finally, we combined this feature vector with extreme randomization tree classifier to build the final model UsIL-6. ResultsThe AUC value of UsIL-6 on the independent test dataset was 0.87, and the BACC value was 0.808, which indicated that UsIL-6 had better performance than the existing methods in IL-6 inducing peptide recognition. ConclusionsThe performance comparison on independent test dataset confirmed that UsIL-6 could achieve the highest performance, best robustness, and most excellent generalization ability. We hope that UsIL-6 will become a valuable method to identify, annotate and characterize new IL-6 inducing peptides.

ACP-DRL: an anticancer peptides recognition method based on deep representation learning.

Cancer, a significant global public health issue, resulted in about 10 million deaths in 2022. Anticancer peptides (ACPs), as a category of bioactive peptides, have emerged as a focal point in clinical cancer research due to their potential to inhibit tumor cell proliferation with minimal side effects. However, the recognition of ACPs through wet-lab experiments still faces challenges of low efficiency and high cost. Our work proposes a recognition method for ACPs named ACP-DRL based on deep representation learning, to address the challenges associated with the recognition of ACPs in wet-lab experiments. ACP-DRL marks initial exploration of integrating protein language models into ACPs recognition, employing in-domain further pre-training to enhance the development of deep representation learning. Simultaneously, it employs bidirectional long short-term memory networks to extract amino acid features from sequences. Consequently, ACP-DRL eliminates constraints on sequence length and the dependence on manual features, showcasing remarkable competitiveness in comparison with existing methods.

Impact of different spacers on the conjugation between Anderson-Evans polyoxometalates and peptides

The Anderson-Evans polyoxometalates (POM) display a promising anticancer activity. The conjugation with the GRP-receptor antagonist peptide Demobesin (fQWAVGHL-NHEt) was exploited to impart cell targeting capabilities and improve the selectivity of such polyanions. However, the POM interacts with the grafted peptides, inducing chains folding and self-assembly of the resulting hybrids, thus decreasing their recognition ability. Within this context, a tailored spacer, including two domains, i.e., a hydrophilic one (1,13-diamino-4,7,10-trioxatridecan-succinamic acid, Ttds) and a tetra-anionic one (Glu-Glu-Glu-Glu-βAla, EEEE-βA) was previously utilized to mitigate such interaction. In this work, hybrid POMs containing only Ttds or EEEE-βA were prepared and the contribution of the two spacers was separately studied by using 2D NMR, fluorimetry and circular dichroism (CD). Transmission electron microscopy (TEM) was also used to observe the impact of the different spacers on self-assembly. Owing to the relevant effects observed for EEEE-βA, MD calculations were finally performed to elucidate its behavior when incorporated in the hybrid POM. Our results show that, despite the stronger impact of EEEE-βA spacer, only when both spacer are present together it is possible to observe a significant effect on the retention of peptide's secondary structure and recognition capability.

Abstract 1838: Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si

Abstract Protein sequencing has the potential of playing a crucial role in advancing cancer research by providing insights into the specific proteins involved in cancer pathways. New discoveries from protein sequencing advance our understanding of cancer and potential targeted therapies. Here, we demonstrate the power of next-generation protein sequencing™ using the insight-generating Platinum™ platform. Individual peptides are digested from proteins and immobilized on a semiconductor chip and probed by dye-labeled N-terminal amino acid (NAA) recognizers, followed by subsequent aminopeptidase cleavage to expose each NAA in the peptide for recognition. By recording and analyzing fluorescent intensity, lifetime, and binding kinetics of each NAA binding event, we can decipher single amino acid substitutions and modifications. To demonstrate the versatility of this methodology across proteins associated with cellular biology, we sequenced a series of interleukins: IL4, IL6, IL7, IL13, IL20, and IL34. Interleukins, a group of cytokines that play a vital role in cancer by modulating immune responses, promoting inflammation, and influencing tumor microenvironment, impacting tumor growth and the efficacy of treatments. We have successfully sequenced all the mentioned interleukins individually or within protein mixtures. Furthermore, we were able to sequence IL6 that was enriched through immunoprecipitation from human serum. Finally, we demonstrated the unique potential of Platinum in detecting post-translational modifications (PTMs) relevant to cancer, as exemplified by the successful identification of arginine citrullination in vimentin, an onco-protein that promotes cancer cell mobility and invasion into surround tissues. These results demonstrate the transformative potential of next-generation protein sequencing using Platinum™ in enabling the identification of proteins in complex mixtures and biofluids, as well as the detection of critical PTMs implicated in human pathophysiology, offering valuable insights into cancer research. Citation Format: Khanh Dinh Nguyen. Advancing cancer research with Next-Generation Protein Sequencing™ on Platinum™ by Quantum-Si [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1838.

Abstract 860: Pan-tissue master regulator inference reveals mechanisms of MHC alterations in cancers

Abstract Introduction: Major histocompatibility complex (MHC) genes are an integral part of the adaptive immune system. The T-cells can detect and kill cancer cells through the recognition of mutant peptides on the cell surface via the MHC. As a result, many cancers evade the immune system by altering their MHC regulation which can also lead to resistance to immune checkpoint blockade (ICB). Therefore, understanding MHC regulation in both baseline (normal state) and cancer is critical for uncovering mechanisms behind MHC alterations. Here, we have undertaken a pan-tissue evaluation to comprehensively decode MHC transcriptional regulation in healthy tissues and various cancers using a large compendium of single-cell RNA-seq (scRNA-seq) datasets. Methods: To study MHC class I (MHC-I) and MHC class II (MHC-II) transcriptional regulation at baseline we leveraged a large-scale scRNA-seq dataset encompassing 18 tissues and 124 epithelial cell types. Upon re-clustering and annotation, we investigated MHC expression across cell types and tissues and quantified its heterogeneity using the Gini coefficient. Next, we sought to identify transcription factors (TF) predictive of MHC-I and MHC-II expression, for that, we employed a master regulator inference that utilizes uni- and multi- regression models. Further, to investigate MHC and nominated TFs dysregulation in cancer, we curated a compendium of scRNA-seq datasets comprising 43 datasets, 20 cancer types, across 538 patients. Results: In normal epithelial cell types, we observed a large range (~8 fold) in MHC-I expression. We also detected MHC-II expression in unexpected cell types such as club cells in the prostate. We found that lung epithelial cells showed elevated MHC-II expression. Immunohistochemistry was performed to validate these findings. Using master regulator inference, we nominated 104 and 107 TFs which predict MHC-I and MHC-II expression, respectively. The nominated TFs showed significant enrichment (p < 0.001) for known TFs, alongside putative novel transcriptional regulators such as YBX1 (MHC-I p < 2e-16, MHC-II p = 8e-07) and XBP1 (MHC-I p < 2e-16, MHC-II p = 7e-04). Using our single-cell compendium of 20 cancer types we also observed a pan-cancer repression in MHC genes (p < 0.001). Next, we utilized an ICB cohort to identify specific TFs that could predict therapeutic benefits. Interestingly, XBP1 (p < 1e-16) and SP100 (p < 2.2e-08) were strong predictors of patients' survival. We also observed a large heterogeneity in MHC-II expression among colon cancer patients. Upon investigation, we found that patients with high MHC-II expression were mismatch repair deficient, this implicates MHC-II upregulation as an immune evasion mechanism. Conclusion: In conclusion, we have comprehensively evaluated MHC expression in 124 epithelial cell types and across 20 cancers identifying TFs predictive of MHC-I and MHC-II expression and their effects on patient outcomes. Citation Format: Mahnoor N. Gondal, Rahul Mannan, Yi Bao, Jing Hu, Marcin Cieslik, Arul M. Chinnaiyan. Pan-tissue master regulator inference reveals mechanisms of MHC alterations in cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 860.

Role of co‑inhibitory molecules in the treatment of psoriasis (Review).

Psoriasis is a common chronic inflammatory skin disease characterized by abnormal activation and infiltration of T-cells and excessive proliferation of keratinocytes (KCs). Its pathogenesis is complex and frequently accompanied by the imbalance of T-cell subpopulations, contributing to its development and further exacerbation. Therefore, the immune system, especially T-cells, is mainly involved in the pathogenesis of psoriasis. While T-cell activation not only requires the first recognition of T-cell receptor and major histocompatibility complex peptide, co-stimulatory and co-inhibitory pathways are reported to promote or dampen T-cell responses through a variety of mechanisms. In recent years, immuno-related agents have been applied in the treatment of numerous clinical diseases, including psoriasis, and are starting to show promising and potential therapy prospects in autoimmune skin diseases. The present review outlined the role of co-inhibitory molecules in the pathogenesis of psoriasis and their application in the treatment of psoriasis.