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1.
J Pain Res ; 17: 1547-1553, 2024.
Article in English | MEDLINE | ID: mdl-38699069

ABSTRACT

Purpose: Postoperative pain relief after laparoscopic appendicectomy is a key determinant of early rehabilitation in children. Recent guidelines recommend performing either a transversus abdominis plane (TAP) block or local anesthesia (LA) wound infiltration as part of multimodal postoperative analgesia after appendectomy. To date, the clinical effectiveness of TAP block versus LA wound infiltration has never been compared. The hypothesis of this study is that the TAP block may provide a greater opioid-sparing effect after laparoscopic appendicectomy in children than LA wound infiltration. Study Design and Methods: We designed a multicenter double-blind randomized controlled phase III trial and aim to include 110 children who undergo laparoscopic appendicectomy. Children are randomized to receive either TAP block (TAP group) or LA wound infiltration (infiltration group). Multimodal analgesia is standardized in the two groups using the same protocol, which includes the stepwise prescription of paracetamol, phloroglucinol, ketoprofene, and nalbuphine according to the hetero-evaluation of pain performed by the nurses who were blinded to the treatment allocated using the validated FLACC scale. The primary outcome is the total dose of nalbuphine administered within 24 hours after surgery. Discussion: No study has specifically compared the clinical effectiveness of TAP block versus LA wound infiltration for postoperative pain relief after laparoscopic appendectomy in children. This paper describes the protocol for a randomized trial that addresses this issue. The results of this trial will be useful for editing guidelines with a higher level of evidence on this topic.

2.
Mol Cell Proteomics ; 23(5): 100767, 2024 May.
Article in English | MEDLINE | ID: mdl-38615877

ABSTRACT

DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.


Subject(s)
DNA Replication , Hydroxyurea , Proteomics , Hydroxyurea/pharmacology , Proteomics/methods , Humans , DNA Damage , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Proteome/metabolism
3.
Biomedicines ; 12(2)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38397935

ABSTRACT

Inflammatory bowel disease (IBD) flare-ups exhibit symptoms that are similar to other diseases and conditions, making diagnosis and treatment complicated. Currently, the gold standard for diagnosing and monitoring IBD is colonoscopy and biopsy, which are invasive and uncomfortable procedures, and the fecal calprotectin test, which is not sufficiently accurate. Therefore, it is necessary to develop an alternative method. In this study, our aim was to provide proof of concept for the application of Sequential Window Acquisition of All Theoretical Mass Spectra-Mass spectrometry (SWATH-MS) and machine learning to develop a non-invasive and accurate predictive model using the stool proteome to distinguish between active IBD patients and symptomatic non-IBD patients. Proteome profiles of 123 samples were obtained and data processing procedures were optimized to select an appropriate pipeline. The differentially abundant analysis identified 48 proteins. Utilizing correlation-based feature selection (Cfs), 7 proteins were selected for proceeding steps. To identify the most appropriate predictive machine learning model, five of the most popular methods, including support vector machines (SVMs), random forests, logistic regression, naive Bayes, and k-nearest neighbors (KNN), were assessed. The generated model was validated by implementing the algorithm on 45 prospective unseen datasets; the results showed a sensitivity of 96% and a specificity of 76%, indicating its performance. In conclusion, this study illustrates the effectiveness of utilizing the stool proteome obtained through SWATH-MS in accurately diagnosing active IBD via a machine learning model.

4.
Cancers (Basel) ; 16(2)2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38254783

ABSTRACT

SOCS1 is a tumor suppressor in hepatocellular carcinoma (HCC). Recently, we showed that a loss of SOCS1 in hepatocytes promotes NRF2 activation. Here, we investigated how SOCS1 expression in HCC cells affected oxidative stress response and modulated the cellular proteome. Murine Hepa1-6 cells expressing SOCS1 (Hepa-SOCS1) or control vector (Hepa-Vector) were treated with cisplatin or tert-butyl hydroperoxide (t-BHP). The induction of NRF2 and its target genes, oxidative stress, lipid peroxidation, cell survival and cellular proteome profiles were evaluated. NRF2 induction was significantly reduced in Hepa-SOCS1 cells. The gene and protein expression of NRF2 targets were differentially induced in Hepa-Vector cells but markedly suppressed in Hepa-SOCS1 cells. Hepa-SOCS1 cells displayed an increased induction of reactive oxygen species but reduced lipid peroxidation. Nonetheless, Hepa-SOCS1 cells treated with cisplatin or t-BHP showed reduced survival. GCLC, poorly induced in Hepa-SOCS1 cells, showed a strong positive correlation with NFE2L2 and an inverse correlation with SOCS1 in the TCGA-LIHC transcriptomic data. A proteomic analysis of Hepa-Vector and Hepa-SOCS1 cells revealed that SOCS1 differentially modulated many proteins involved in diverse molecular pathways, including mitochondrial ROS generation and ROS detoxification, through peroxiredoxin and thioredoxin systems. Our findings indicate that maintaining sensitivity to oxidative stress is an important tumor suppression mechanism of SOCS1 in HCC.

5.
Nucleic Acids Res ; 52(D1): D522-D528, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37956315

ABSTRACT

The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.


Subject(s)
Databases, Protein , Peptides , Proteomics , Amino Acid Sequence , Genomics , Internet , Peptides/genetics , Proteome/genetics , Proteomics/methods , Humans
6.
Biochem Cell Biol ; 102(2): 135-144, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38113480

ABSTRACT

Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.


Subject(s)
DNA Replication , Proteome , Proteome/metabolism , Proteomics/methods , Mass Spectrometry , Protein Processing, Post-Translational
7.
BMJ Glob Health ; 8(12)2023 12 16.
Article in English | MEDLINE | ID: mdl-38103896

ABSTRACT

INTRODUCTION: Social determinants of health, such as living and working conditions, economical and environmental context and access to care, combine to impact the health of individuals and communities. In French Guiana (FG), the persons working in informal artisanal and small-scale gold mining in the rainforest are a particularly vulnerable population which lives in precarious conditions and far from the health system. Previous studies have demonstrated their high morbidity due to infectious diseases. This study aims to describe the social determinants of health in this specific population. METHODS: This international multicentre cross-sectional survey included people working on the informal FG gold mines at the crossing points located at both borders with Suriname and Brazil. After collecting written informed consent, a structured questionnaire was administered. RESULTS: From September to December 2022, 539 gold miners were included. These poorly educated migrants, mainly from Brazil (99.1%) did not have access to drinkable water (95.4%), lived in close contact with wild fauna by hunting, eating bushmeat or being bitten and were exposed to mercury by inhalation (58.8%) or ingestion (80.5%). They report frequent accidents (13.5%) and chronic treatment interruptions (26.6% of the 11.9% reporting chronic treatment). Half of them considered themselves in good health (56.4%). CONCLUSION: This study shows a singular combination of adverse exposures of gold miners working in FG such as zoonoses, heavy metal poisoning, aggression of wild fauna. For ethical as well as public health reasons, actions towards health equity must be considered at different levels: individual, community, environmental, systemic and global level. As end users of minerals, we must assume our responsibilities for the well-being of the extractors by including health in political decisions to engage together in global health. TRIAL REGISTRATION NUMBER: NCT05540470.


Subject(s)
Gold , Social Determinants of Health , Humans , Cross-Sectional Studies , French Guiana/epidemiology , Mining
9.
Nucleic Acids Res ; 51(20): 11056-11079, 2023 11 10.
Article in English | MEDLINE | ID: mdl-37823600

ABSTRACT

Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.


Subject(s)
Poly ADP Ribosylation , Poly Adenosine Diphosphate Ribose , Humans , DNA/genetics , DNA/metabolism , DNA Damage , DNA Repair , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly Adenosine Diphosphate Ribose/metabolism
10.
Cell ; 186(22): 4898-4919.e25, 2023 10 26.
Article in English | MEDLINE | ID: mdl-37827155

ABSTRACT

Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes.


Subject(s)
Replication Protein A , Trinucleotide Repeat Expansion , Animals , Humans , Mice , DNA/genetics , DNA Mismatch Repair , Huntington Disease/genetics , Proteins/genetics , Spinocerebellar Ataxias/genetics , Replication Protein A/metabolism
11.
Biol Open ; 12(9)2023 09 15.
Article in English | MEDLINE | ID: mdl-37670689

ABSTRACT

Ubiquitination is a post-translational modification responsible for one of the most complex multilayered communication and regulation systems in the cell. Over the past decades, new ubiquitin variants and ubiquitin-like proteins arose to further enrich this mechanism. Recently discovered ubiquitin variant UbKEKS can specifically target several proteins and yet, functional consequences of this new modification remain unknown. Depletion of UbKEKS induces accumulation of lamin A in the nucleoli, highlighting the need for deeper investigations about protein composition and functions regulation of this highly dynamic and membrane-less compartment. Using data-independent acquisition mass spectrometry and microscopy, we show that despite not impacting protein stability, UbKEKS is required to maintain a normal nucleolar organization. The absence of UbKEKS increases nucleoli's size and accentuate their circularity while disrupting dense fibrillar component and fibrillar centre structures. Moreover, depletion of UbKEKS leads to distinct changes in nucleolar composition. Lack of UbKEKS favours nucleolar sequestration of known apoptotic regulators such as IFI16 or p14ARF, resulting in an increase of apoptosis observed by flow cytometry and real-time monitoring. Overall, these results identify the first cellular functions of the UbKEKS variant and lay the foundation stone to establish UbKEKS as a new universal layer of regulation in the ubiquitination system.


Subject(s)
CRISPR-Cas Systems , Ubiquitin , Ubiquitin/genetics , Ubiquitins , Ubiquitination , Apoptosis
12.
Mol Cell Proteomics ; 22(10): 100644, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37689310

ABSTRACT

Cullin-RING finger ligases represent the largest family of ubiquitin ligases. They are responsible for the ubiquitination of ∼20% of cellular proteins degraded through the proteasome, by catalyzing the transfer of E2-loaded ubiquitin to a substrate. Seven cullins are described in vertebrates. Among them, cullin 4 (CUL4) associates with DNA damage-binding protein 1 (DDB1) to form the CUL4-DDB1 ubiquitin ligase complex, which is involved in protein ubiquitination and in the regulation of many cellular processes. Substrate recognition adaptors named DDB1/CUL4-associated factors (DCAFs) mediate the specificity of CUL4-DDB1 and have a short structural motif of approximately forty amino acids terminating in tryptophan (W)-aspartic acid (D) dipeptide, called the WD40 domain. Using different approaches (bioinformatics/structural analyses), independent studies suggested that at least sixty WD40-containing proteins could act as adaptors for the DDB1/CUL4 complex. To better define this association and classification, the interaction of each DCAFs with DDB1 was determined, and new partners and potential substrates were identified. Using BioID and affinity purification-mass spectrometry approaches, we demonstrated that seven WD40 proteins can be considered DCAFs with a high confidence level. Identifying protein interactions does not always lead to identifying protein substrates for E3-ubiquitin ligases, so we measured changes in protein stability or degradation by pulse-stable isotope labeling with amino acids in cell culture to identify changes in protein degradation, following the expression of each DCAF. In conclusion, these results provide new insights into the roles of DCAFs in regulating the activity of the DDB1-CUL4 complex, in protein targeting, and characterized the cellular processes involved.

13.
Kidney Int ; 104(4): 787-802, 2023 10.
Article in English | MEDLINE | ID: mdl-37507049

ABSTRACT

Both clinical and experimental data suggest that podocyte injury is involved in the onset and progression of diabetic kidney disease (DKD). Although the mechanisms underlying the development of podocyte loss are not completely understood, critical structural proteins such as podocin play a major role in podocyte survival and function. We have reported that the protein tyrosine phosphatase SHP-1 expression increased in podocytes of diabetic mice and glomeruli of patients with diabetes. However, the in vivo contribution of SHP-1 in podocytes is unknown. Conditional podocyte-specific SHP-1-deficient mice (Podo-SHP-1-/-) were generated to evaluate the impact of SHP-1 deletion at four weeks of age (early) prior to the onset of diabetes and after 20 weeks (late) of diabetes (DM; Ins2+/C96Y) on kidney function (albuminuria and glomerular filtration rate) and kidney pathology. Ablation of the SHP-1 gene specifically in podocytes prevented and even reversed the elevated albumin/creatinine ratio, glomerular filtration rate progression, mesangial cell expansion, glomerular hypertrophy, glomerular basement membrane thickening and podocyte foot process effacement induced by diabetes. Moreover, podocyte-specific deletion of SHP-1 at an early and late stage prevented diabetes-induced expression of collagen IV, fibronectin, transforming growth factor-ß, transforming protein RhoA, and serine/threonine kinase ROCK1, whereas it restored nephrin, podocin and cation channel TRPC6 expression. Mass spectrometry analysis revealed that SHP-1 reduced SUMO2 post-translational modification of podocin while podocyte-specific deletion of SHP-1 preserved slit diaphragm protein complexes in the diabetic context. Thus, our data uncovered a new role of SHP-1 in the regulation of cytoskeleton dynamics and slit diaphragm protein expression/stability, and its inhibition preserved podocyte function preventing DKD progression.


Subject(s)
Diabetes Mellitus, Experimental , Diabetic Nephropathies , Podocytes , Animals , Mice , Diabetes Mellitus, Experimental/chemically induced , Diabetic Nephropathies/genetics , Diabetic Nephropathies/prevention & control , Diabetic Nephropathies/metabolism , Podocytes/pathology , Protein Tyrosine Phosphatase, Non-Receptor Type 6/genetics , Protein Tyrosine Phosphatase, Non-Receptor Type 6/metabolism , rho-Associated Kinases/metabolism , Sumoylation
14.
Immunity ; 56(9): 2021-2035.e8, 2023 09 12.
Article in English | MEDLINE | ID: mdl-37516105

ABSTRACT

Environmental nutrient availability influences T cell metabolism, impacting T cell function and shaping immune outcomes. Here, we identified ketone bodies (KBs)-including ß-hydroxybutyrate (ßOHB) and acetoacetate (AcAc)-as essential fuels supporting CD8+ T cell metabolism and effector function. ßOHB directly increased CD8+ T effector (Teff) cell cytokine production and cytolytic activity, and KB oxidation (ketolysis) was required for Teff cell responses to bacterial infection and tumor challenge. CD8+ Teff cells preferentially used KBs over glucose to fuel the tricarboxylic acid (TCA) cycle in vitro and in vivo. KBs directly boosted the respiratory capacity and TCA cycle-dependent metabolic pathways that fuel CD8+ T cell function. Mechanistically, ßOHB was a major substrate for acetyl-CoA production in CD8+ T cells and regulated effector responses through effects on histone acetylation. Together, our results identify cell-intrinsic ketolysis as a metabolic and epigenetic driver of optimal CD8+ T cell effector responses.


Subject(s)
CD8-Positive T-Lymphocytes , Histones , 3-Hydroxybutyric Acid/metabolism , 3-Hydroxybutyric Acid/pharmacology , Acetylation , Histones/metabolism , Ketone Bodies , Animals , Mice
15.
Acta Crystallogr B Struct Sci Cryst Eng Mater ; 79(Pt 4): 263-270, 2023 Aug 01.
Article in English | MEDLINE | ID: mdl-37347140

ABSTRACT

The discovery of a new FeII oxalate framework of composition K2Fe[(C2O4)2(H2O)2]·0.18H2O is reported. Its crystal structure was solved by means of single crystal and powder X-ray diffraction. The new organic-inorganic hybrid compound crystallizes in the orthorhombic space group Pca21 with unit-cell parameters: a = 12.0351 (4) Å, b = 15.1265 (5) Å, c = 10.5562 (4) Å. This crystal structure, containing eight chemical formula, consists of a succession of FeO4(H2O)2 octahedra and K+ cations growing along b direction. Magnetization measurements indicate that the title compound is paramagnetic over the investigated temperature range (2-300 K). Both magnetization and 57Fe Mössbauer data indicate that Fe2+ is in a high-spin state.

16.
Proteomics ; 23(13-14): e2200372, 2023 07.
Article in English | MEDLINE | ID: mdl-37232233

ABSTRACT

Hepatocyte nuclear factor 4-alpha (HNF4α) is a master regulator gene belonging to the nuclear receptor superfamily and is involved in regulating a wide range of critical biological processes in different organs. Structurally, the HNF4A locus is organized into two independent promoters and is subjected to alternative splicing to produce twelve distinct isoforms. However, little is known about the biological impact of each isoform and the mechanisms by which they regulate transcription. Proteomic analyses have led to the identification of proteins that interact with specific HNF4α isoforms. The identification and validation of these interactions and their roles in the co-regulation of targeted gene expression are essential to better understand the role of this transcription factor in different biological processes and pathologies. This review addresses the discoveries of different HNF4α isoforms and the main functions of the P1 and P2 isoform subgroups. It also provides information on the most recent focus areas in research on the nature and function of proteins associated with each of the isoforms in some biological contexts.


Subject(s)
Hepatocyte Nuclear Factor 4 , Proteomics , Protein Isoforms/genetics , Hepatocyte Nuclear Factor 4/genetics , Hepatocyte Nuclear Factor 4/metabolism , Gene Expression Regulation , Promoter Regions, Genetic
17.
Int J Mol Sci ; 24(8)2023 Apr 13.
Article in English | MEDLINE | ID: mdl-37108368

ABSTRACT

Aggressive tumors evade cytotoxic T lymphocytes by suppressing MHC class-I (MHC-I) expression that also compromises tumor responsiveness to immunotherapy. MHC-I defects strongly correlate to defective expression of NLRC5, the transcriptional activator of MHC-I and antigen processing genes. In poorly immunogenic B16 melanoma cells, restoring NLRC5 expression induces MHC-I and elicits antitumor immunity, raising the possibility of using NLRC5 for tumor immunotherapy. As the clinical application of NLRC5 is constrained by its large size, we examined whether a smaller NLRC5-CIITA fusion protein, dubbed NLRC5-superactivator (NLRC5-SA) as it retains the ability to induce MHC-I, could be used for tumor growth control. We show that stable NLRC5-SA expression in mouse and human cancer cells upregulates MHC-I expression. B16 melanoma and EL4 lymphoma tumors expressing NLRC5-SA are controlled as efficiently as those expressing full-length NLRC5 (NLRC5-FL). Comparison of MHC-I-associated peptides (MAPs) eluted from EL4 cells expressing NLRC5-FL or NLRC5-SA and analyzed by mass spectrometry revealed that both NLRC5 constructs expanded the MAP repertoire, which showed considerable overlap but also included a substantial proportion of distinct peptides. Thus, we propose that NLRC5-SA, with its ability to increase tumor immunogenicity and promote tumor growth control, could overcome the limitations of NLRC5-FL for translational immunotherapy applications.


Subject(s)
Gene Expression Regulation , Melanoma, Experimental , Humans , Animals , Mice , Melanoma, Experimental/genetics , Melanoma, Experimental/therapy , Genes, MHC Class I , Histocompatibility Antigens Class I , Antigen Presentation , Intracellular Signaling Peptides and Proteins/genetics
18.
Cells ; 12(4)2023 02 14.
Article in English | MEDLINE | ID: mdl-36831282

ABSTRACT

During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.


Subject(s)
Brain , Proteomics , Mice , Animals , RNA, Messenger/genetics , Brain/metabolism , Aging/metabolism , Proteome/metabolism
19.
J Proteomics ; 271: 104755, 2023 01 16.
Article in English | MEDLINE | ID: mdl-36272709

ABSTRACT

Recent studies have identified FoxL1+-telocytes (TCFoxL1+) as key players in gut epithelial-mesenchymal interactions which can determine the colonic microenvironment. Bone morphogenetic protein signaling disruption in TCFoxL1+ alters the physical and cellular microenvironment and leads to colon pathophysiology. This suggests a role for TCFoxL1+ in stromagenesis, but it is hard to identify the specific contribution of TCFoxL1+ when analyzing whole tissue profiling studies. We performed ex vivo deconstruction of control and BmpR1a△FoxL1+ colon samples, isolated the mesenchyme-enriched fractions, and determined the protein composition of the in vivo extracellular matrix (ECM) to analyze microenvironment variation. Matrisomic analysis of mesenchyme fractions revealed modulations in ECM proteins with functions associated with innate immunity, epithelial wound healing, and the collagen network. These results show that TCFoxL1+ is critical in orchestrating the biodynamics of the colon ECM. TCFoxL1+ disfunction reprograms the gut's microenvironment and drives the intestinal epithelium toward colonic pathologies. SIGNIFICANCE: In this study, the method that was elected to isolate ECM proteins might not encompass the full extent of ECM proteins in a tissue, due to the protocol chosen, as this protocol by Naba et al., targets more the insoluble part of the matrisome and eliminates the more soluble components in the first steps. However, this ECM-enrichment strategy represents an improvement and interesting avenue to study ECM proteins in the colon compared to total tissue analysis with a background of abundant cellular protein. Thus, the matrisomic approach presented in this study, and its target validation delivered a broader evaluation of the matrix remodeling occurring in the colonic sub-epithelial mesenchyme of the BmpR1a△FoxL1+ mouse model.


Subject(s)
Extracellular Matrix , Telocytes , Mice , Animals , Extracellular Matrix/metabolism , Extracellular Matrix Proteins/metabolism , Telocytes/metabolism , Colon , Wound Healing , Forkhead Transcription Factors/metabolism
20.
Cancer Immunol Immunother ; 72(5): 1089-1102, 2023 May.
Article in English | MEDLINE | ID: mdl-36326893

ABSTRACT

BACKGROUND:  Radioresistance of HNSCCs remains a major challenge for effective tumor control. Combined radiotherapy (RT) and immunotherapy (IT) treatment improved survival for a subset of patients with inflamed tumors or tumors susceptible to RT-induced inflammation. To overcome radioresistance and improve treatment outcomes, an understanding of factors that suppress anti-tumor immunity is necessary. In this regard, regulatory T cells (Tregs) are critical mediators of immune suppression in HNSCCs. In this study, we investigated how radiation modulates Treg infiltration in tumors through the chemokine CCL20. We hypothesized that radiation induces CCL20 secretion resulting in Treg infiltration and suppression of anti-tumor immunity. METHODS:  Human and mouse HNSCC cell lines with different immune phenotypes were irradiated at doses of 2 or 10 Gy. Conditioned media, RNA and protein were collected for assessment of CCL20. qPCR was used to determine CCL20 gene expression. In vivo, MOC2 cells were implanted into the buccal cavity of mice and the effect of neutralizing CCL20 antibody was determined alone and in combination with RT. Blood samples were collected before and after RT for analysis of CCL20. Tumor samples were analyzed by flow cytometry to determine immune infiltrates, including CD8 T cells and Tregs. Mass-spectrometry was performed to analyze proteomic changes in the tumor microenvironment after anti-CCL20 treatment. RESULTS:  Cal27 and MOC2 HNSCCs had a gene signature associated with Treg infiltration, whereas SCC9 and MOC1 tumors displayed a gene signature associated with an inflamed TME. In vitro, tumor irradiation at 10 Gy significantly induced CCL20 in Cal27 and MOC2 cells relative to control. The increase in CCL20 was associated with increased Treg migration. Neutralization of CCL20 reversed radiation-induced migration of Treg cells in vitro and decreased intratumoral Tregs in vivo. Furthermore, inhibition of CCL20 resulted in a significant decrease in tumor growth compared to control in MOC2 tumors. This effect was further enhanced after combination with RT compared to either treatment alone. CONCLUSION:  Our results suggest that radiation promotes CCL20 secretion by tumor cells which is responsible for the attraction of Tregs. Inhibition of the CCR6-CCL20 axis prevents infiltration of Tregs in tumors and suppresses tumor growth resulting in improved response to radiation.


Subject(s)
Head and Neck Neoplasms , T-Lymphocytes, Regulatory , Humans , Squamous Cell Carcinoma of Head and Neck/radiotherapy , Squamous Cell Carcinoma of Head and Neck/metabolism , Chemokine CCL20/genetics , Chemokine CCL20/metabolism , Proteomics , Head and Neck Neoplasms/radiotherapy , Head and Neck Neoplasms/metabolism , Tumor Microenvironment , Receptors, CCR6/genetics , Receptors, CCR6/metabolism
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