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1.
Mol Cell ; 84(18): 3371-3373, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39303676

ABSTRACT

In this issue of Molecular Cell, Engeholm et al.1 present cryo-EM structures of the chromatin remodeler Chd1 bound to a hexasome-nucleosome complex, an intermediate state during transcription either with or without FACT to restore the missing H2A-H2B dimer. These two binding modes reveal how Chd1 and FACT cooperate in nucleosome re-establishment during transcription.


Subject(s)
Cryoelectron Microscopy , DNA-Binding Proteins , Nucleosomes , Nucleosomes/metabolism , Nucleosomes/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Chromatin Assembly and Disassembly , Histones/metabolism , Histones/genetics , Humans , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , DNA Helicases/metabolism , DNA Helicases/genetics , Protein Binding , Transcription, Genetic , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , Transcriptional Elongation Factors/metabolism , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/chemistry
2.
Mol Cell ; 84(18): 3423-3437.e8, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39270644

ABSTRACT

To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII.


Subject(s)
Chromatin Assembly and Disassembly , Cryoelectron Microscopy , DNA-Binding Proteins , High Mobility Group Proteins , Histones , Nucleosomes , RNA Polymerase II , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Transcription, Genetic , Transcriptional Elongation Factors , Nucleosomes/metabolism , Nucleosomes/genetics , Nucleosomes/ultrastructure , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transcriptional Elongation Factors/metabolism , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/chemistry , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , RNA Polymerase II/metabolism , RNA Polymerase II/genetics , Histones/metabolism , Histones/genetics , Protein Binding , Models, Molecular , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics
3.
Redox Rep ; 29(1): 2395779, 2024 Dec.
Article in English | MEDLINE | ID: mdl-39221774

ABSTRACT

OBJECTIVES: Alcohol and its metabolites, such as acetaldehyde, induced hepatic mitochondrial dysfunction play a pathological role in the development of alcohol-related liver disease (ALD). METHODS: In this study, we investigated the potential of nobiletin (NOB), a polymethoxylated flavone, to counter alcohol-induced mitochondrial dysfunction and liver injury. RESULTS: Our findings demonstrate that NOB administration markedly attenuated alcohol-induced hepatic steatosis, endoplasmic reticulum stress, inflammation, and tissue damage in mice. NOB reversed hepatic mitochondrial dysfunction and oxidative stress in both alcohol-fed mice and acetaldehyde-treated hepatocytes. Mechanistically, NOB restored the reduction of hepatic mitochondrial transcription factor A (TFAM) at both mRNA and protein levels. Notably, the protective effects of NOB against acetaldehyde-induced mitochondrial dysfunction and cell death were abolished in hepatocytes lacking Tfam. Furthermore, NOB administration reinstated the levels of hepatocellular NRF1, a key transcriptional regulator of TFAM, which were decreased by alcohol and acetaldehyde exposure. Consistent with these findings, hepatocyte-specific overexpression of Nrf1 protected against alcohol-induced hepatic Tfam reduction, mitochondrial dysfunction, oxidative stress, and liver injury. CONCLUSIONS: Our study elucidates the involvement of the NRF1-TFAM signaling pathway in the protective mechanism of NOB against chronic-plus-binge alcohol consumption-induced mitochondrial dysfunction and liver injury, suggesting NOB supplementation as a potential therapeutic strategy for ALD.


Subject(s)
Flavones , Signal Transduction , Animals , Mice , Flavones/pharmacology , Signal Transduction/drug effects , Male , Transcription Factors/metabolism , Transcription Factors/genetics , Oxidative Stress/drug effects , Mice, Inbred C57BL , Liver/drug effects , Liver/metabolism , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Ethanol/toxicity , Ethanol/adverse effects , Mitochondria/drug effects , Mitochondria/metabolism , Liver Diseases, Alcoholic/metabolism , Liver Diseases, Alcoholic/drug therapy , Liver Diseases, Alcoholic/prevention & control , Liver Diseases, Alcoholic/pathology , Hepatocytes/drug effects , Hepatocytes/metabolism , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Nuclear Respiratory Factor 1/metabolism , Nuclear Respiratory Factor 1/genetics , Protective Agents/pharmacology , NF-E2-Related Factor 1/metabolism , NF-E2-Related Factor 1/genetics , High Mobility Group Proteins
4.
JCI Insight ; 9(18)2024 Aug 01.
Article in English | MEDLINE | ID: mdl-39088272

ABSTRACT

Energy metabolism, through pathways such as oxidative phosphorylation (OxPhos) and glycolysis, plays a pivotal role in cellular differentiation and function. Our study investigates the impact of OxPhos disruption in cortical bone development by deleting mitochondrial transcription factor A (TFAM). TFAM controls OxPhos by regulating the transcription of mitochondrial genes. The cortical bone, constituting the long bones' rigid shell, is sheathed by the periosteum, a connective tissue layer populated with skeletal progenitors that spawn osteoblasts, the bone-forming cells. TFAM-deficient mice presented with thinner cortical bone, spontaneous midshaft fractures, and compromised periosteal cell bioenergetics, characterized by reduced ATP levels. Additionally, they exhibited an enlarged periosteal progenitor cell pool with impaired osteoblast differentiation. Increasing hypoxia-inducible factor 1a (HIF1) activity within periosteal cells substantially mitigated the detrimental effects induced by TFAM deletion. HIF1 is known to promote glycolysis in all cell types. Our findings underscore the indispensability of OxPhos for the proper accrual of cortical bone mass and indicate a compensatory mechanism between OxPhos and glycolysis in periosteal cells. The study opens new avenues for understanding the relationship between energy metabolism and skeletal health and suggests that modulating bioenergetic pathways may provide a therapeutic avenue for conditions characterized by bone fragility.


Subject(s)
Cortical Bone , DNA-Binding Proteins , Hypoxia-Inducible Factor 1, alpha Subunit , Osteogenesis , Oxidative Phosphorylation , Animals , Mice , Cortical Bone/metabolism , Cortical Bone/pathology , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Osteoblasts/metabolism , Glycolysis , Transcription Factors/metabolism , Transcription Factors/genetics , Mice, Knockout , Periosteum/metabolism , Periosteum/pathology , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Energy Metabolism , Male , Cell Differentiation , Female , Mitochondria/metabolism , High Mobility Group Proteins
5.
Cell ; 187(18): 5010-5028.e24, 2024 Sep 05.
Article in English | MEDLINE | ID: mdl-39094570

ABSTRACT

Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.


Subject(s)
DNA Replication , Epigenesis, Genetic , Heterochromatin , Histones , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Histones/metabolism , Heterochromatin/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , Transcriptional Elongation Factors/metabolism , Transcriptional Elongation Factors/genetics , Histone Chaperones/metabolism , Molecular Chaperones/metabolism , DNA Polymerase I/metabolism , DNA Polymerase I/genetics
6.
Cell ; 187(16): 4336-4354.e19, 2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39121847

ABSTRACT

Exhausted CD8 T (Tex) cells in chronic viral infection and cancer have sustained co-expression of inhibitory receptors (IRs). Tex cells can be reinvigorated by blocking IRs, such as PD-1, but synergistic reinvigoration and enhanced disease control can be achieved by co-targeting multiple IRs including PD-1 and LAG-3. To dissect the molecular changes intrinsic when these IR pathways are disrupted, we investigated the impact of loss of PD-1 and/or LAG-3 on Tex cells during chronic infection. These analyses revealed distinct roles of PD-1 and LAG-3 in regulating Tex cell proliferation and effector functions, respectively. Moreover, these studies identified an essential role for LAG-3 in sustaining TOX and Tex cell durability as well as a LAG-3-dependent circuit that generated a CD94/NKG2+ subset of Tex cells with enhanced cytotoxicity mediated by recognition of the stress ligand Qa-1b, with similar observations in humans. These analyses disentangle the non-redundant mechanisms of PD-1 and LAG-3 and their synergy in regulating Tex cells.


Subject(s)
Antigens, CD , CD8-Positive T-Lymphocytes , Histocompatibility Antigens Class I , Lymphocyte Activation Gene 3 Protein , NK Cell Lectin-Like Receptor Subfamily D , Programmed Cell Death 1 Receptor , Animals , Antigens, CD/metabolism , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Mice , Programmed Cell Death 1 Receptor/metabolism , NK Cell Lectin-Like Receptor Subfamily D/metabolism , Histocompatibility Antigens Class I/metabolism , Humans , NK Cell Lectin-Like Receptor Subfamily C/metabolism , Mice, Inbred C57BL , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , Cytotoxicity, Immunologic , Cell Proliferation , Killer Cells, Natural/metabolism , Killer Cells, Natural/immunology
7.
Cell Death Dis ; 15(8): 630, 2024 Aug 27.
Article in English | MEDLINE | ID: mdl-39191749

ABSTRACT

Lymph node metastasis (LNM) is a common invasive feature of hepatocellular carcinoma (HCC) associated with poor clinical outcomes. Through microarray profiling and bioinformatic analyses, we identified the circ-0044539-miR-29a-3p-VEGFA axis as a potential key factor in the progression of HCC LNM. In HCC cells and nude mice, circ-0044539 downregulation or miR-29a-3p upregulation was associated with small tumor size, PI3K-AKT-mTOR pathway inactivation, and downregulation of the key LNM factors (HIF-1α and CXCR4). Furthermore, circ-0044539 was also responsible for exosomal miR-29a-3p secretion. Exosomal miR-29a-3p was then observed to migrate to the LNs and downregulate High-mobility group box transcription factor 1 (Hbp1) in Polymorphonuclear Myeloid-derived suppressor cells (PMN-MDSCs), inducing the formation of a microenvironment suitable for tumor colonization. Overall, circ-0044539 promotes HCC cell LNM abilities and induces an immune-suppressive environment in LNs through exosomes, highlighting its potential as a target for HCC LNM and HCC immunotherapy.


Subject(s)
Carcinoma, Hepatocellular , Exosomes , Liver Neoplasms , Lymphatic Metastasis , Mice, Nude , MicroRNAs , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/metabolism , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Liver Neoplasms/metabolism , Humans , MicroRNAs/metabolism , MicroRNAs/genetics , Animals , Exosomes/metabolism , Mice , Cell Line, Tumor , RNA, Circular/genetics , RNA, Circular/metabolism , Gene Expression Regulation, Neoplastic , Mice, Inbred BALB C , Male , Tumor Microenvironment , Signal Transduction , High Mobility Group Proteins , Repressor Proteins
8.
Mol Cell ; 84(16): 3011-3025.e7, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39116874

ABSTRACT

The histone variant macroH2A is generally linked to transcriptionally inactive chromatin, but how macroH2A regulates chromatin structure and functions in the transcriptional process remains elusive. This study reveals that while the integration of human macroH2A1.2 into nucleosomes does not affect their stability or folding dynamics, it notably hinders the maintenance of facilitates chromatin transcription's (FACT's) function. We show that FACT effectively diminishes the stability of macroH2A1.2-nucleosomes and expedites their depletion subsequent to the initial unfolding process. Furthermore, we identify the residue S139 in macroH2A1.2 as a critical switch to modulate FACT's function in nucleosome maintenance. Genome-wide analyses demonstrate that FACT-mediated depletion of macroH2A-nucleosomes allows the correct localization of macroH2A, while the S139 mutation reshapes macroH2A distribution and influences stimulation-induced transcription and cellular response in macrophages. Our findings provide mechanistic insights into the intricate interplay between macroH2A and FACT at the nucleosome level and elucidate their collective role in transcriptional regulation and immune response of macrophages.


Subject(s)
Histones , Nucleosomes , Transcription, Genetic , Transcriptional Elongation Factors , Humans , Nucleosomes/metabolism , Nucleosomes/genetics , Histones/metabolism , Histones/genetics , Transcriptional Elongation Factors/genetics , Transcriptional Elongation Factors/metabolism , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , Animals , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Macrophages/metabolism , Mutation , Chromatin Assembly and Disassembly , Mice , Chromatin/metabolism , Chromatin/genetics , Gene Expression Regulation , RAW 264.7 Cells , Protein Binding , HEK293 Cells
9.
Cell ; 187(16): 4373-4388.e15, 2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39121849

ABSTRACT

Relatlimab (rela; anti-LAG-3) plus nivolumab (nivo; anti-PD-1) is safe and effective for treatment of advanced melanoma. We designed a trial (NCT03743766) where advanced melanoma patients received rela, nivo, or rela+nivo to interrogate the immunologic mechanisms of rela+nivo. Analysis of biospecimens from this ongoing trial demonstrated that rela+nivo led to enhanced capacity for CD8+ T cell receptor signaling and altered CD8+ T cell differentiation, leading to heightened cytotoxicity despite the retention of an exhaustion profile. Co-expression of cytotoxic and exhaustion signatures was driven by PRDM1, BATF, ETV7, and TOX. Effector function was upregulated in clonally expanded CD8+ T cells that emerged after rela+nivo. A rela+nivo intratumoral CD8+ T cell signature was associated with a favorable prognosis. This intratumoral rela+nivo signature was validated in peripheral blood as an elevated frequency of CD38+TIM3+CD8+ T cells. Overall, we demonstrated that cytotoxicity can be enhanced despite the retention of exhaustion signatures, which will inform future therapeutic strategies.


Subject(s)
CD8-Positive T-Lymphocytes , Lymphocyte Activation Gene 3 Protein , Melanoma , Programmed Cell Death 1 Receptor , Humans , Antigens, CD/metabolism , Antigens, CD/genetics , Basic-Leucine Zipper Transcription Factors/metabolism , Basic-Leucine Zipper Transcription Factors/genetics , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cell Differentiation , Cytotoxicity, Immunologic , High Mobility Group Proteins , Immune Checkpoint Inhibitors/therapeutic use , Immune Checkpoint Inhibitors/pharmacology , Lymphocyte Activation Gene 3 Protein/antagonists & inhibitors , Melanoma/immunology , Melanoma/drug therapy , Melanoma/genetics , Nivolumab/therapeutic use , Nivolumab/pharmacology , Positive Regulatory Domain I-Binding Factor 1/metabolism , Positive Regulatory Domain I-Binding Factor 1/genetics , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Signal Transduction
10.
Zhejiang Da Xue Xue Bao Yi Xue Ban ; 53(3): 358-367, 2024 Mar 29.
Article in English, Chinese | MEDLINE | ID: mdl-39188182

ABSTRACT

OBJECTIVES: To investigate the effect of Chinese medicine He's Yangchao recipe on premature ovarian insufficiency (POI) and its relationship with mitochondrial function of ovarian granulose cells in an animal model. METHODS: Thirty-six female C57BL/6J mice were randomly divided into blank control group, model group, low-, medium- and high-dose He's Yangchao recipe treatment group and coenzyme Q10 (Q10) treatment group (positive control). The POI model was induced by a single intraperitoneal injection of cyclophosphamide (90 mg/kg). The animals were sacrificed after 21 days. Primary granulose cells were obtained from POI mice and treated with He's Yangchao recipe, ERß inhibitor PHTPP, and He's Yangchao recipe+PHTPP in vitro for 24 h, respectively. Ovarian histopathological changes were observed by hematoxylin-eosin (HE) staining, ATP levels were detected by luciferase assay, mtDNA copy numbers were detected by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), mitochondrial structure changes were observed by transmission electron microscopy, protein and mRNA expression levels of estrogen receptor ß (ERß), peroxisome proliferator-activated receptor γ coactivator 1α (PGC1α), mitochondrial transcription factor A (TFAM), and superoxide dismutase 2 (SOD2) were detected by Western blotting and qRT-PCR. RESULTS: The ovarian tissue in model group exhibited few secondary and tertiary follicles, whereas the He's Yangchao recipe groups and Q10 group had abundant secondary and tertiary follicles. Compared with the blank control group, ATP and mtDNA levels in model group decreased (P<0.01), mitochondrial crista disappeared or abnormal vacuolated structure increased; the protein and mRNA levels of ERß, PGC1α, TFAM, and SOD2 decreased (all P<0.01). ATP production increased in granulose cells of high-dose He's Yangchao recipe group and Q10 group; mtDNA copy numbers increased (P<0.05 or P<0.01); abnormal mitochondrial structure was reduced; the protein and mRNA expressions of ERß, PGC1α, TFAM, and SOD2 increased (P<0.05 or P<0.01). Compared with the PHTPP intervention group, the proportion of normal mitochondrial structure in the granulose cells of He's Yangchao recipe + PHTPP group was higher; ATP content increased (P<0.05 or P<0.01); mtDNA copy numbers increased (P<0.05 or P<0.01); the protein and mRNA expression of ERß, PGC1α, TFAM and SOD2 increased (P<0.05 or P<0.01). CONCLUSIONS: He's Yangchao recipe can regulate mitochondrial biogenesis through ERß/PGC1α/TFAM pathway to improve ovarian function in POI mice.


Subject(s)
DNA-Binding Proteins , Estrogen Receptor beta , Mice, Inbred C57BL , Mitochondria , Organelle Biogenesis , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha , Primary Ovarian Insufficiency , Transcription Factors , Female , Animals , Estrogen Receptor beta/metabolism , Estrogen Receptor beta/genetics , Mice , Primary Ovarian Insufficiency/metabolism , Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism , Mitochondria/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Drugs, Chinese Herbal/pharmacology , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Superoxide Dismutase/metabolism , High Mobility Group Proteins
11.
Proc Natl Acad Sci U S A ; 121(26): e2319322121, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38900789

ABSTRACT

Thymocyte selection-associated high-mobility group box (TOX) is a transcription factor that is crucial for T cell exhaustion during chronic antigenic stimulation, but its role in inflammation is poorly understood. Here, we report that TOX extracellularly mediates drastic inflammation upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by binding to the cell surface receptor for advanced glycation end-products (RAGE). In various diseases, including COVID-19, TOX release was highly detectable in association with disease severity, contributing to lung fibroproliferative acute respiratory distress syndrome (ARDS). Recombinant TOX-induced blood vessel rupture, similar to a clinical signature in patients experiencing a cytokine storm, further exacerbating respiratory function impairment. In contrast, disruption of TOX function by a neutralizing antibody and genetic removal of RAGE diminished TOX-mediated deleterious effects. Altogether, our results suggest an insight into TOX function as an inflammatory mediator and propose the TOX-RAGE axis as a potential target for treating severe patients with pulmonary infection and mitigating lung fibroproliferative ARDS.


Subject(s)
COVID-19 , Receptor for Advanced Glycation End Products , SARS-CoV-2 , Humans , Receptor for Advanced Glycation End Products/metabolism , COVID-19/immunology , COVID-19/metabolism , COVID-19/pathology , COVID-19/complications , COVID-19/virology , Animals , Mice , Inflammation/metabolism , Inflammation/pathology , Respiratory Distress Syndrome/immunology , Respiratory Distress Syndrome/metabolism , Respiratory Distress Syndrome/pathology , Respiratory Distress Syndrome/virology , Lung Injury/immunology , Lung Injury/metabolism , Lung Injury/pathology , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , Male , Lung/pathology , Lung/metabolism , Lung/immunology , Female
12.
Genes Cells ; 29(7): 567-583, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38837646

ABSTRACT

Chromatin condensation state is the key for retrieving genetic information. High-mobility group protein (HMG) proteins exhibit DNA-binding and bending activities, playing an important role in the regulation of chromatin structure. We have shown that nucleosomes tightly packaged into heterochromatin undergo considerable dynamic histone H2A-H2B maintenance via the direct interaction between HP1/Swi6 and facilitate chromatin transcription (FACT), which is composed of the Spt16/Pob3 heterodimer and Nhp6. In this study, we analyzed the role of Nhp6, an HMG box protein, in the FACT at heterochromatin. Pob3 mutant strains showed derepressed heterochromatin-dependent gene silencing, whereas Nhp6 mutant strains did not show significant defects in chromatin regulation or gene expression, suggesting that these two modules play different roles in chromatin regulation. We expressed a protein fusing Nhp6 to the C-terminus of Pob3, which mimics the multicellular FACT component Ssrp1. The chromatin-binding activity of FACT increased with the number of Nhp6 fused to Pob3, and the heterochromatin formation rate was promoted more strongly. Furthermore, we demonstrated that this promotion of heterochromatinization inhibited the heterochromatic variegation caused by epe1+ disruption. Heterochromatic variegation can be observed in a variety of regulatory steps; however, when it is caused by fluctuations in chromatin arrangement, it can be eliminated through the strong recruitment of the FACT complex.


Subject(s)
Heterochromatin , Schizosaccharomyces pombe Proteins , Schizosaccharomyces , Heterochromatin/metabolism , Heterochromatin/genetics , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces pombe Proteins/genetics , Gene Expression Regulation, Fungal , Epigenesis, Genetic , Gene Silencing , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics
13.
Cell Rep ; 43(7): 114401, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-38943641

ABSTRACT

Human CD8 tumor-infiltrating lymphocytes (TILs) with impaired effector functions and PD-1 expression are categorized as exhausted. However, the exhaustion-like features reported in TILs might stem from their activation rather than the consequence of T cell exhaustion itself. Using CRISPR-Cas9 and lentiviral overexpression in CD8 T cells from non-cancerous donors, we show that the T cell receptor (TCR)-induced transcription factor interferon regulatory factor 4 (IRF4) promotes cell proliferation and PD-1 expression and hampers effector functions and expression of nuclear factor κB (NF-κB)-regulated genes. While CD8 TILs with impaired interferon γ (IFNγ) production exhibit activation markers IRF4 and CD137 and exhaustion markers thymocyte selection associated high mobility group box (TOX) and PD-1, activated T cells in patients with COVID-19 do not demonstrate elevated levels of TOX and PD-1. These results confirm that IRF4+ TILs are exhausted rather than solely activated. Our study indicates, however, that PD-1 expression, low IFNγ production, and active cycling in TILs are all influenced by IRF4 upregulation after T cell activation.


Subject(s)
CD8-Positive T-Lymphocytes , Cell Proliferation , Interferon Regulatory Factors , Interferon-gamma , Lymphocyte Activation , Programmed Cell Death 1 Receptor , Humans , Programmed Cell Death 1 Receptor/metabolism , Programmed Cell Death 1 Receptor/genetics , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Interferon Regulatory Factors/metabolism , Interferon Regulatory Factors/genetics , Interferon-gamma/metabolism , Lymphocyte Activation/immunology , COVID-19/immunology , COVID-19/virology , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , SARS-CoV-2/immunology , NF-kappa B/metabolism , High Mobility Group Proteins
14.
Mol Cell ; 84(11): 2053-2069.e9, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38810649

ABSTRACT

Facilitates chromatin transcription (FACT) is a histone chaperone that supports transcription through chromatin in vitro, but its functional roles in vivo remain unclear. Here, we analyze the in vivo functions of FACT with the use of multi-omics analysis after rapid FACT depletion from human cells. We show that FACT depletion destabilizes chromatin and leads to transcriptional defects, including defective promoter-proximal pausing and elongation, and increased premature termination of RNA polymerase II. Unexpectedly, our analysis revealed that promoter-proximal pausing depends not only on the negative elongation factor (NELF) but also on the +1 nucleosome, which is maintained by FACT.


Subject(s)
Chromatin , High Mobility Group Proteins , Nucleosomes , Promoter Regions, Genetic , RNA Polymerase II , Transcription, Genetic , Transcriptional Elongation Factors , RNA Polymerase II/metabolism , RNA Polymerase II/genetics , Humans , Transcriptional Elongation Factors/metabolism , Transcriptional Elongation Factors/genetics , Chromatin/metabolism , Chromatin/genetics , Nucleosomes/metabolism , Nucleosomes/genetics , High Mobility Group Proteins/metabolism , High Mobility Group Proteins/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , HeLa Cells , Chromatin Assembly and Disassembly , HEK293 Cells , Transcription Elongation, Genetic , Transcription Termination, Genetic
15.
Nat Cell Biol ; 26(6): 878-891, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38783142

ABSTRACT

When cells are stressed, DNA from energy-producing mitochondria can leak out and drive inflammatory immune responses if not cleared. Cells employ a quality control system called autophagy to specifically degrade damaged components. We discovered that mitochondrial transcription factor A (TFAM)-a protein that binds mitochondrial DNA (mtDNA)-helps to eliminate leaked mtDNA by interacting with the autophagy protein LC3 through an autolysosomal pathway (we term this nucleoid-phagy). TFAM contains a molecular zip code called the LC3 interacting region (LIR) motif that enables this binding. Although mutating TFAM's LIR motif did not affect its normal mitochondrial functions, more mtDNA accumulated in the cell cytoplasm, activating inflammatory signalling pathways. Thus, TFAM mediates autophagic removal of leaked mtDNA to restrict inflammation. Identifying this mechanism advances understanding of how cells exploit autophagy machinery to selectively target and degrade inflammatory mtDNA. These findings could inform research on diseases involving mitochondrial damage and inflammation.


Subject(s)
Autophagy , DNA, Mitochondrial , DNA-Binding Proteins , Inflammation , Mitochondria , Mitochondrial Proteins , Transcription Factors , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Inflammation/metabolism , Inflammation/pathology , Inflammation/genetics , Animals , Humans , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Mitochondria/metabolism , Mitochondria/genetics , Mice , Transcription Factors/metabolism , Transcription Factors/genetics , Microtubule-Associated Proteins/metabolism , Microtubule-Associated Proteins/genetics , Protein Binding , Cytoplasm/metabolism , Lysosomes/metabolism , Signal Transduction , HEK293 Cells , Mice, Inbred C57BL , High Mobility Group Proteins
16.
Free Radic Biol Med ; 222: 106-121, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38797339

ABSTRACT

PURPOSE: Severe dry eye disease causes ocular surface damage, which is highly associated with mitochondrial dysfunction. Mitochondrial transcription factor A (TFAM) is essential for packaging mitochondrial DNA (mtDNA) and is crucial for maintaining mitochondrial function. Herein, we aimed to explore the effect of a decreased TFAM expression on ocular surface damage. METHODS: Female C57BL/6 mice were induced ocular surface injury by topical administrating benzalkonium chloride (BAC). Immortalized human corneal epithelial cells (HCECs) were stimulated by tert-butyl hydroperoxide (t-BHP) to create oxidative stress damage. HCECs with TFAM knockdown were established. RNA sequencing was employed to analyze the whole-genome expression. Mitochondrial changes were measured by transmission electron microscopy, Seahorse metabolic flux analysis, mitochondrial membrane potential, and mtDNA copy number. TFAM expression and inflammatory cytokines were determined using RT-qPCR, immunohistochemistry, immunofluorescence, and immunoblotting. RESULTS: In both the corneas of BAC-treated mice and t-BHP-induced HCECs, we observed impaired TFAM expression, accompanied by mitochondrial structure and function defects. TFAM downregulation in HCECs suppressed mitochondrial respiratory capacity, reduced mtDNA content, induced mtDNA leakage into the cytoplasm, and led to inflammation. RNA sequencing revealed the absent in melanoma 2 (AIM2) inflammasome was activated in the corneas of BAC-treated mice. The AIM2 inflammasome activation was confirmed in TFAM knockdown HCECs. TFAM knockdown in t-BHP-stimulated HCECs aggravated mitochondrial dysfunction and the AIM2 inflammasome activation, thereby further triggering the secretion of inflammatory factors such as interleukin (IL) -1ß and IL-18. CONCLUSIONS: TFAM reduction impaired mitochondrial function, activated AIM2 inflammasome and promoted ocular surface inflammation, revealing an underlying molecular mechanism for ocular surface disorders.


Subject(s)
DNA, Mitochondrial , DNA-Binding Proteins , Inflammasomes , Mitochondria , Mitochondrial Proteins , Transcription Factors , Animals , Inflammasomes/metabolism , Inflammasomes/genetics , Mice , Humans , Mitochondria/metabolism , Mitochondria/pathology , Mitochondria/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Female , Transcription Factors/genetics , Transcription Factors/metabolism , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , Inflammation/pathology , Inflammation/metabolism , Inflammation/genetics , Mice, Inbred C57BL , Oxidative Stress , Gene Expression Regulation , Epithelium, Corneal/metabolism , Epithelium, Corneal/pathology , Disease Models, Animal , High Mobility Group Proteins
17.
Oncoimmunology ; 13(1): 2346359, 2024.
Article in English | MEDLINE | ID: mdl-38737794

ABSTRACT

Immune exhaustion is a hallmark of ovarian cancer. Using multiparametric flow cytometry, the study aimed to analyze protein expression of novel immunological targets on CD3+ T cells isolated from the peripheral blood (n = 20), malignant ascites (n = 16), and tumor tissue (n = 6) of patients with ovarian cancer (OVCA). The study revealed an increased proportion of effector memory CD8+ T cells in OVCA tissue and malignant ascites. An OVCA-characteristic PD-1high CD8+ T cell population was detected, which differed from PD-1lowCD8+ T cells by increased co-expression of TIGIT, CD39, and HLA-DR. In addition, these OVCA-characteristic CD8+ T cells showed reduced expression of the transcription factor TCF-1, which may also indicate reduced effector function and memory formation. On the contrary, the transcription factor TOX, which significantly regulates terminal T cell-exhaustion, was found more frequently in these cells. Further protein and gene analysis showed that CD39 and CD73 were also expressed on OVCA tumor cells isolated from solid tumors (n = 14) and malignant ascites (n = 9). In the latter compartment, CD39 and CD73 were also associated with the expression of the "don't eat me" molecule CD24 on tumor cells. Additionally, ascites-derived CD24+EpCAM+ tumor cells showed a higher frequency of CD39+ or CD73+ cells. Furthermore, CD39 expression was associated with unfavorable clinical parameters. Expression of CD39 on T cells was upregulated through CD3/CD28 stimulation and its blockade by a newly developed nanobody construct resulted in increased proliferation (eFluor), activation (CD25 and CD134), and production of cytotoxic cytokines (IFN-γ, TNF-α, and granzyme-B) of CD8+ T cells.


Subject(s)
Apyrase , CD8-Positive T-Lymphocytes , Ovarian Neoplasms , Humans , Female , Ovarian Neoplasms/immunology , Ovarian Neoplasms/pathology , Ovarian Neoplasms/metabolism , Apyrase/metabolism , Apyrase/genetics , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Middle Aged , Ascites/immunology , Ascites/pathology , Ascites/metabolism , Antigens, CD/metabolism , Antigens, CD/genetics , Aged , Programmed Cell Death 1 Receptor/metabolism , Receptors, Immunologic/metabolism , Receptors, Immunologic/genetics , Receptors, Immunologic/antagonists & inhibitors , T Cell Transcription Factor 1/metabolism , T Cell Transcription Factor 1/genetics , HLA-DR Antigens/metabolism , Adult , T-Cell Exhaustion , High Mobility Group Proteins
18.
Cancer Sci ; 115(7): 2184-2195, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38590234

ABSTRACT

Recent studies have highlighted the pivotal roles of T cell transcription factors TCF-1 and TOX in modulating the immune response in cancer, with TCF-1 maintaining CD8+ T cell stemness and TOX promoting T cell exhaustion. The prognostic significance of these factors in lung adenocarcinoma (LUAD) remains a critical area of investigation. The retrospective study included 191 patients with LUAD who underwent surgery, of whom 83% were in stages II and III. These patients were divided into exploratory (n = 135) and validation (n = 56) groups based on the time of diagnosis. Multiplex fluorescence immunohistochemistry was used to examine the infiltration levels of CD8+ T cells, TCF1+ CD8+ T cells, and TOX+ CD8+ T cells. The percentage of CD8+ T cells in tumor was markedly lower than that in stroma (p < 0.05). In tumor-draining lymph nodes (TDLNs) invaded by tumor, the proportion of stem-like TCF1+ CD8+ T cells was significantly decreased (p < 0.01). Importantly, higher infiltration levels of CD8+ T cells and TCF1+ CD8+ T cells were associated with improved disease-free survival (DFS) (p = 0.009 and p = 0.006, respectively) and overall survival (OS) (p = 0.018 and p = 0.010, respectively). This study underscores the potential of TCF1+ CD8+ T cells as prognostic biomarkers in LUAD, providing insights into the tumor immune microenvironment and guiding future therapeutic strategies.


Subject(s)
Adenocarcinoma of Lung , CD8-Positive T-Lymphocytes , Hepatocyte Nuclear Factor 1-alpha , Lung Neoplasms , Lymphocytes, Tumor-Infiltrating , Humans , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Adenocarcinoma of Lung/immunology , Adenocarcinoma of Lung/pathology , Adenocarcinoma of Lung/mortality , Female , Lung Neoplasms/immunology , Lung Neoplasms/pathology , Lung Neoplasms/mortality , Prognosis , Male , Middle Aged , Hepatocyte Nuclear Factor 1-alpha/metabolism , Hepatocyte Nuclear Factor 1-alpha/genetics , Aged , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Retrospective Studies , Tumor Microenvironment/immunology , Disease-Free Survival , High Mobility Group Proteins/metabolism , Trans-Activators
19.
Life Sci Alliance ; 7(7)2024 Jul.
Article in English | MEDLINE | ID: mdl-38664021

ABSTRACT

Mitochondrial transcription factor A, TFAM, is essential for mitochondrial function. We examined the effects of overexpressing the TFAM gene in mice. Two types of transgenic mice were created: TFAM heterozygous (TFAM Tg) and homozygous (TFAM Tg/Tg) mice. TFAM Tg/Tg mice were smaller and leaner notably with longer lifespans. In skeletal muscle, TFAM overexpression changed gene and protein expression in mitochondrial respiratory chain complexes, with down-regulation in complexes 1, 3, and 4 and up-regulation in complexes 2 and 5. The iMPAQT analysis combined with metabolomics was able to clearly separate the metabolomic features of the three types of mice, with increased degradation of fatty acids and branched-chain amino acids and decreased glycolysis in homozygotes. Consistent with these observations, comprehensive gene expression analysis revealed signs of mitochondrial stress, with elevation of genes associated with the integrated and mitochondrial stress responses, including Atf4, Fgf21, and Gdf15. These found that mitohormesis develops and metabolic shifts in skeletal muscle occur as an adaptive strategy.


Subject(s)
DNA-Binding Proteins , High Mobility Group Proteins , Longevity , Mice, Transgenic , Mitochondrial Proteins , Muscle, Skeletal , Transcription Factors , Animals , Mice , Muscle, Skeletal/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Longevity/genetics , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Mitochondria/metabolism , Mitochondria/genetics , Male , Metabolomics/methods , Growth Differentiation Factor 15/genetics , Growth Differentiation Factor 15/metabolism , Gene Expression Regulation
20.
Physiol Rep ; 12(8): e16014, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38644513

ABSTRACT

HMG (high mobility group) proteins are a diverse family of nonhistone chromosomal proteins that interact with DNA and a wide range of transcriptional regulators to regulate the structural architecture of DNA. HMGXB4 (also known as HMG2L1) is an HMG protein family member that contains a single HMG box domain. Our previous studies have demonstrated that HMGXB4 suppresses smooth muscle differentiation and exacerbates endotoxemia by promoting a systemic inflammatory response in mice. However, the expression of Hmgxb4 in vivo has not fully examined. Herein, we generated a mouse model that harbors a gene trap in the form of a lacZ gene insertion into the Hmgxb4 gene. This mouse enables the visualization of endogenous HMGXB4 expression in different tissues via staining for the ß-galactosidase activity of LacZ which is under the control of the endogenous Hmgxb4 gene promoter. We found that HMGXB4 is widely expressed in mouse tissues and is a nuclear protein. Furthermore, the Hmgxb4 gene trap mice exhibit normal cardiac function and blood pressure. Measurement of ß-galactosidase activity in the Hmgxb4 gene trap mice demonstrated that the arterial injury significantly induces Hmgxb4 expression. In summary, the Hmgxb4 gene trap reporter mouse described here provides a valuable tool to examine the expression level of endogenous Hmgxb4 in both physiological and pathological settings in vivo.


Subject(s)
High Mobility Group Proteins , Mice, Inbred C57BL , Animals , Male , Mice , beta-Galactosidase/metabolism , beta-Galactosidase/genetics , High Mobility Group Proteins/genetics , High Mobility Group Proteins/metabolism , Lac Operon/genetics , Mice, Transgenic , Transcription Factors/genetics , Transcription Factors/metabolism
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