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Jing H, Song Y, Duan E, Liu J, Ke W, Tao R, Lv Y, Zhao P, Dong W, Li X, Guo Y, Li H. NLRP12 inhibits PRRSV-2 replication by promoting GP2a degradation via MARCH8. Vet Microbiol 2024; 298:110271. [PMID: 39362085 DOI: 10.1016/j.vetmic.2024.110271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/25/2024] [Accepted: 09/28/2024] [Indexed: 10/05/2024]
Abstract
NLRP12, a member of the NLR family, has been shown to exert a vital function in orchestrating immune responses. Here, using the immunosuppressive porcine reproductive and respiratory syndrome virus (PRRSV) as a model, the role of NLRP12 in virus infection was deciphered. We demonstrated that overexpression of NLRP12 significantly restrained PRRSV replication, while NLRP12 silencing resulted in increased viral titer. Mechanistically, NLRP12 interacts with glycoprotein 2a (GP2a) through its LRR domain and recruits the membrane-associated RING-CH E3 ubiquitin ligase 8 (MARCH8) via the PYD domain. NLRP12 facilitates the lysine-48 (K48)-linked polyubiquitination of GP2a at K128 and induces its lysosome degradation via the MARCH8-NDP52 (nuclear dot protein 52 kDa) pathway. To counteract this, PRRSV Nsp2 effectively prevented the polyubiquitination of GP2a induced by NLRP12 by its deubiquitinating activity. Meanwhile, the overexpression of Nsp4 decreased the mRNA of endogenous NLRP12 and cleaved NLRP12 in a 3C-like protease activity-dependent manner, which collaboratively counteracts the antiviral function of NLRP12. Collectively, this study revealed the mechanisms of the NLRP12-MARCH8-NDP52 axis in the host defense against PRRSV, which might be harnessed for the development of anti-PRRSV therapies.
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Affiliation(s)
- Huiyuan Jing
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China.
| | - Yuzhen Song
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Erzhen Duan
- College of Biological Engineering, Henan university of technology, Zhengzhou, China
| | - Jie Liu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Wenting Ke
- College of Animal Science and Technology, Yangtze University, Jingzhou, China
| | - Ran Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yujin Lv
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Pandeng Zhao
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Wang Dong
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Xianghui Li
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Yongbin Guo
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Huawei Li
- Key Laboratory of Veterinary Biological Products, College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, China.
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Han M, Lu Q, Wang D, Zhou K, Jia C, Teng L, Hamuti A, Peng X, Hu Y, Li W, Yue M, Li Y. Oral co-administration of Lactiplantibacillus plantarum 16 and Lacticaseibacillus rhamnosus P118 improves host defense against influenza A virus infection. J Virol 2024:e0095024. [PMID: 39258911 DOI: 10.1128/jvi.00950-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 08/25/2024] [Indexed: 09/12/2024] Open
Abstract
Influenza is an important zoonotic disease that persistently threatens global public health. While it is widely acknowledged that probiotics can modulate the host response to protect the host against infectious disease, the prophylactic efficacy on respiratory viral infection and the detailed mechanism remains elusive. Lactobacillus, the most commonly used probiotic widely applied in food production, has garnered significant attention. In our study utilizing both C57BL/6 and BALB/c mouse models, we explored the protective effect against two strains of influenza virus, A/Mink/China/01/2014(H9N2) and A/California/04/2009(H1N1), through the administration of Lactiplantibacillus plantarum strain 16 (L. plantarum 16) and Lacticaseibacillus rhamnosus strain P118 (L. rhamnosus P118), aiming to identify robust probiotic strains with antiviral properties. Our findings indicate that administering L. plantarum 16 or L. rhamnosus P118 alone does not provide sufficient protection against influenza. However, the co-administration of L. plantarum 16 and L. rhamnosus P118 dramatically reduces viral titers in the respiratory tract and lung, thereby markedly alleviating the clinical symptoms, improving prognosis, and reducing mortality. The mechanisms underlying this effect involve the modulation of host gut microbiota and metabolism through the co-administration of L. plantarum 16 and L. rhamnosus P118, resulting in enrichment of Firmicutes and enhancement of phenylalanine-related metabolism, ultimately leading to an augmentation of the antiviral immune response. Notably, we identified that the circulating metabolic molecule 2-Hydroxycinnamic acid plays a significant role in combating influenza. Our data suggest the potential utility of L. plantarum 16 and L. rhamnosus P118 two-bacterium or 2-Hydroxycinnamic acid in preventing influenza.IMPORTANCEVaccination represents the most optimal strategy to control influenza. Nevertheless, influenza viruses constantly evolve due to antigenic drift and shift, leading to the need for regular updates on influenza vaccines. Additionally, vaccination failure poses significant challenges to influenza prevention. Therefore, it is essential and beneficial to identify novel or universal antiviral measures to protect against influenza. While cumulative data suggest that probiotics offer protection against infectious diseases, the specific mechanisms, such as the effective metabolites or components, remain largely unknown. Our research discovered the capacity of combinational two-bacterium Lactiplantibacillus plantarum 16 and Lacticaseibacillus rhamnosus P118 to fight against influenza infection in a mouse model. The protection may occur through modulating the host's gut microbiota and metabolism, further influencing the host's antiviral immune response. Notably, we have identified a novel metabolic molecule, 2-Hydroxycinnamic acid, capable of enhancing antiviral response and restricting viral replication in vivo.
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Affiliation(s)
- Meiqing Han
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Qi Lu
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Di Wang
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Kun Zhou
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Chenghao Jia
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Lin Teng
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Azeguli Hamuti
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Xianqi Peng
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Yixiang Hu
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Weifen Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Institute of Feed Science, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
| | - Min Yue
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Li
- Department of Veterinary Medicine and Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, Hainan, China
- MOA Key Laboratory of Animal Virology, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
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Kori M, Kasavi C, Arga KY. Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine. J Microbiol 2024; 62:785-798. [PMID: 38980578 PMCID: PMC11436439 DOI: 10.1007/s12275-024-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024]
Abstract
Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples. Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.
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Affiliation(s)
- Medi Kori
- Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, 34752, Istanbul, Turkey.
- Faculty of Health Sciences, Acibadem Mehmet Ali Aydinlar University, 34752, Istanbul, Turkey.
| | - Ceyda Kasavi
- Department of Bioengineering, Marmara University, 34722, Istanbul, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, 34722, Istanbul, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34722, Istanbul, Turkey
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4
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Egbewale SO, Kumar A, Olasehinde TA, Mokoena MP, Olaniran AO. Anthracene detoxification by Laccases from indigenous fungal strains Trichoderma lixii FLU1 and Talaromyces pinophilus FLU12. Biodegradation 2024; 35:769-787. [PMID: 38822999 PMCID: PMC11246312 DOI: 10.1007/s10532-024-10084-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/13/2024] [Indexed: 06/03/2024]
Abstract
The persistence and ubiquity of polycyclic aromatic hydrocarbons (PAHs) in the environment necessitate effective remediation strategies. Hence, this study investigated the potential of purified Laccases, TlFLU1L and TpFLU12L, from two indigenous fungi Trichoderma lixii FLU1 (TlFLU1) and Talaromyces pinophilus FLU12 (TpFLU12), respectively for the oxidation and detoxification of anthracene. Anthracene was degraded with vmax values of 3.51 ± 0.06 mg/L/h and 3.44 ± 0.06 mg/L/h, and Km values of 173.2 ± 0.06 mg/L and 73.3 ± 0.07 mg/L by TlFLU1L and TpFLU12L, respectively. The addition of a mediator compound 2,2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) to the reaction system significantly increased the degradation of anthracene, with up to a 2.9-fold increase in vmax value and up to threefold decrease in Km values of TlFLU1L and TpFLU12L. The GC-MS analysis of the metabolites suggests that anthracene degradation follows one new pathway unique to the ABTS system-hydroxylation and carboxylation of C-1 and C-2 position of anthracene to form 3-hydroxy-2-naphthoic acid, before undergoing dioxygenation and side chain removal to form chromone which was later converted into benzoic acid and CO2. This pathway contrasts with the common dioxygenation route observed in the free Laccase system, which is observed in the second degradation pathways. Furthermore, toxicity tests using V. parahaemolyticus and HT-22 cells, respectively, demonstrated the non-toxic nature of Laccase-ABTS-mediated metabolites. Intriguingly, analysis of the expression level of Alzheimer's related genes in HT-22 cells exposed to degradation products revealed no induction of neurotoxicity unlike untreated cells. These findings propose a paradigm shift for bioremediation by highlighting the Laccase-ABTS system as a promising green technology due to its efficiency with the discovery of a potentially less harmful degradation pathway, and the production of non-toxic metabolites.
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Affiliation(s)
- Samson O Egbewale
- Discipline of Microbiology, University of KwaZulu-Natal (Westville Campus), Durban, 4000, South Africa
| | - Ajit Kumar
- Discipline of Microbiology, University of KwaZulu-Natal (Westville Campus), Durban, 4000, South Africa
| | - Tosin A Olasehinde
- Discipline of Microbiology, University of KwaZulu-Natal (Westville Campus), Durban, 4000, South Africa
| | - Mduduzi P Mokoena
- Department of Pathology, School of Medicine, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, University of KwaZulu-Natal (Westville Campus), Durban, 4000, South Africa.
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5
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Su G, Chen Y, Li X, Shao JW. Virus versus host: influenza A virus circumvents the immune responses. Front Microbiol 2024; 15:1394510. [PMID: 38817972 PMCID: PMC11137263 DOI: 10.3389/fmicb.2024.1394510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Influenza A virus (IAV) is a highly contagious pathogen causing dreadful losses to humans and animals around the globe. As is known, immune escape is a strategy that benefits the proliferation of IAVs by antagonizing, blocking, and suppressing immune surveillance. The HA protein binds to the sialic acid (SA) receptor to enter the cytoplasm and initiate viral infection. The conserved components of the viral genome produced during replication, known as the pathogen-associated molecular patterns (PAMPs), are thought to be critical factors for the activation of effective innate immunity by triggering dependent signaling pathways after recognition by pattern recognition receptors (PRRs), followed by a cascade of adaptive immunity. Viral infection-induced immune responses establish an antiviral state in the host to effectively inhibit virus replication and enhance viral clearance. However, IAV has evolved multiple mechanisms that allow it to synthesize and transport viral components by "playing games" with the host. At its heart, this review will describe how host and viral factors interact to facilitate the viral evasion of host immune responses.
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Affiliation(s)
- Guanming Su
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, China
| | - Yiqun Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan, China
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Ren P, Niu D, Chang S, Yu L, Ren J, Ma Y, Lan K. RUNX3 inhibits KSHV lytic replication by binding to the viral genome and repressing transcription. J Virol 2024; 98:e0156723. [PMID: 38197631 PMCID: PMC10878072 DOI: 10.1128/jvi.01567-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the gamma herpesvirus family, which can cause human malignancies including Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman's diseases. KSHV typically maintains a persistent latent infection within the host. However, after exposure to intracellular or extracellular stimuli, KSHV lytic replication can be reactivated. The reactivation process of KSHV triggers the innate immune response to limit viral replication. Here, we found that the transcriptional regulator RUNX3 is transcriptionally upregulated by the NF-κB signaling pathway in KSHV-infected SLK cells and B cells during KSHV reactivation. Notably, knockdown of RUNX3 significantly promotes viral lytic replication as well as the gene transcription of KSHV. Consistent with this finding, overexpression of RUNX3 impairs viral lytic replication. Mechanistically, RUNX3 binds to the KSHV genome and limits viral replication through transcriptional repression, which is related to its DNA- and ATP-binding ability. However, KSHV has also evolved corresponding strategies to antagonize this inhibition by using the viral protein RTA to target RUNX3 for ubiquitination and proteasomal degradation. Altogether, our study suggests that RUNX3, a novel host-restriction factor of KSHV that represses the transcription of viral genes, may serve as a potential target to restrict KSHV transmission and disease development.IMPORTANCEThe reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) from latent infection to lytic replication is important for persistent viral infection and tumorigenicity. However, reactivation is a complex event, and the regulatory mechanisms of this process are not fully elucidated. Our study revealed that the host RUNX3 is upregulated by the NF-κB signaling pathway during KSHV reactivation, which can repress the transcription of KSHV genes. At the late stage of lytic replication, KSHV utilizes a mechanism involving RTA to degrade RUNX3, thus evading host inhibition. This finding helps elucidate the regulatory mechanism of the KSHV life cycle and may provide new clues for the development of therapeutic strategies for KSHV-associated diseases.
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Affiliation(s)
- Pengyu Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Danping Niu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Sijia Chang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junrui Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuanming Ma
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
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7
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Ji L, Li T, Chen H, Yang Y, Lu E, Liu J, Qiao W, Chen H. The crucial regulatory role of type I interferon in inflammatory diseases. Cell Biosci 2023; 13:230. [PMID: 38124132 PMCID: PMC10734085 DOI: 10.1186/s13578-023-01188-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Type I interferon (IFN-I) plays crucial roles in the regulation of inflammation and it is associated with various inflammatory diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and periodontitis, impacting people's health and quality of life. It is well-established that IFN-Is affect immune responses and inflammatory factors by regulating some signaling. However, currently, there is no comprehensive overview of the crucial regulatory role of IFN-I in distinctive pathways as well as associated inflammatory diseases. This review aims to provide a narrative of the involvement of IFN-I in different signaling pathways, mainly mediating the related key factors with specific targets in the pathways and signaling cascades to influence the progression of inflammatory diseases. As such, we suggested that IFN-Is induce inflammatory regulation through the stimulation of certain factors in signaling pathways, which displays possible efficient treatment methods and provides a reference for the precise control of inflammatory diseases.
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Affiliation(s)
- Ling Ji
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Tianle Li
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Huimin Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Yanqi Yang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
- Division of Pediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, China
| | - Jieying Liu
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Qiao
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
| | - Hui Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
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8
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Crain CR, Traunbauer AK, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Dorazio D, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Sieg S, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and host mediators of non-suppressible HIV-1 viremia. Nat Med 2023; 29:3212-3223. [PMID: 37957382 PMCID: PMC10719098 DOI: 10.1038/s41591-023-02611-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) is defined as persistent low-level viremia on antiretroviral therapy (ART) without evidence of ART non-adherence or significant drug resistance. Unraveling the mechanisms behind NSV would broaden our understanding of HIV-1 persistence. Here we analyzed plasma virus sequences in eight ART-treated individuals with NSV (88% male) and show that they are composed of large clones without evidence of viral evolution over time in those with longitudinal samples. We defined proviruses that match plasma HIV-1 RNA sequences as 'producer proviruses', and those that did not as 'non-producer proviruses'. Non-suppressible viremia arose from expanded clones of producer proviruses that were significantly larger than the genome-intact proviral reservoir of ART-suppressed individuals. Integration sites of producer proviruses were enriched in proximity to the activating H3K36me3 epigenetic mark. CD4+ T cells from participants with NSV demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, participants with NSV showed significantly lower HIV-specific CD8+ T cell responses compared with untreated viremic controllers with similar viral loads. We identified potential critical host and viral mediators of NSV that may represent targets to disrupt HIV-1 persistence.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Valley Health System, Las Vegas, NV, USA
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Beijing Friendship Hospital Pinggu Campus, Capital Medical University, Beijing, China
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory J Bedwell
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Anna K Traunbauer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Francoise Giguel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dominic Dorazio
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Peter L Anderson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M Lederman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D Lichterfeld
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Scott Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Athe Tsibris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jose R Castillo-Mancilla
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan N Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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9
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Wang Y, Li Y, Wang C, Lio CWJ, Ma Q, Liu B. CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq. Brief Bioinform 2023; 25:bbad505. [PMID: 38189539 PMCID: PMC10772951 DOI: 10.1093/bib/bbad505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/21/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
Sequence motif discovery algorithms enhance the identification of novel deoxyribonucleic acid sequences with pivotal biological significance, especially transcription factor (TF)-binding motifs. The advent of assay for transposase-accessible chromatin using sequencing (ATAC-seq) has broadened the toolkit for motif characterization. Nonetheless, prevailing computational approaches have focused on delineating TF-binding footprints, with motif discovery receiving less attention. Herein, we present Cis rEgulatory Motif Influence using de Bruijn Graph (CEMIG), an algorithm leveraging de Bruijn and Hamming distance graph paradigms to predict and map motif sites. Assessment on 129 ATAC-seq datasets from the Cistrome Data Browser demonstrates CEMIG's exceptional performance, surpassing three established methodologies on four evaluative metrics. CEMIG accurately identifies both cell-type-specific and common TF motifs within GM12878 and K562 cell lines, demonstrating its comparative genomic capabilities in the identification of evolutionary conservation and cell-type specificity. In-depth transcriptional and functional genomic studies have validated the functional relevance of CEMIG-identified motifs across various cell types. CEMIG is available at https://github.com/OSU-BMBL/CEMIG, developed in C++ to ensure cross-platform compatibility with Linux, macOS and Windows operating systems.
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Affiliation(s)
- Yizhong Wang
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Yang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Chan-Wang Jerry Lio
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, 250100, China
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10
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Ji N, Huang W, Dang H, Xiao H, Shi Y, Guo J, Chen K, Wang J, Zou J. CBFβ is induced by spring viremia of carp virus and promotes virus replication in zebrafish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104751. [PMID: 37268261 DOI: 10.1016/j.dci.2023.104751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
The core binding factor subunit beta (CBFβ) is a transcription factor that forms a complex with virial proteins to promote viral infection. In this study, we identified a CBFβ homolog from zebrafish (zfCBFβ) and characterized the biological activity. The deduced zfCBFβ protein was highly similar to orthologs from other species. The zfcbfβ gene was constitutively expressed in tissues and was induced in immune tissues after infection with spring viremia carp virus (SVCV) and stimulation with poly(I:C). Interestingly, zfcbfβ is not induced by type I interferons. Overexpression of zfcbfβ induced tnfα expression but inhibited isg15 expression. Also, overexpression of zfcbfβ significantly increased SVCV titer in the EPC cells. Co-immunoprecipitation assay revealed that zfCBFβ interacts with SVCV phosphoprotein (SVCVP) and host p53, resulting in the increased stability of zfCBFβ. Our results provide evidence that CBFβ is targeted by virus to suppress host antiviral response.
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Affiliation(s)
- Ning Ji
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Huifeng Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hehe Xiao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahong Guo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kangyong Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.
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11
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Rozen EJ, Ozeroff CD, Allen MA. RUN(X) out of blood: emerging RUNX1 functions beyond hematopoiesis and links to Down syndrome. Hum Genomics 2023; 17:83. [PMID: 37670378 PMCID: PMC10481493 DOI: 10.1186/s40246-023-00531-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND RUNX1 is a transcription factor and a master regulator for the specification of the hematopoietic lineage during embryogenesis and postnatal megakaryopoiesis. Mutations and rearrangements on RUNX1 are key drivers of hematological malignancies. In humans, this gene is localized to the 'Down syndrome critical region' of chromosome 21, triplication of which is necessary and sufficient for most phenotypes that characterize Trisomy 21. MAIN BODY Individuals with Down syndrome show a higher predisposition to leukemias. Hence, RUNX1 overexpression was initially proposed as a critical player on Down syndrome-associated leukemogenesis. Less is known about the functions of RUNX1 in other tissues and organs, although growing reports show important implications in development or homeostasis of neural tissues, muscle, heart, bone, ovary, or the endothelium, among others. Even less is understood about the consequences on these tissues of RUNX1 gene dosage alterations in the context of Down syndrome. In this review, we summarize the current knowledge on RUNX1 activities outside blood/leukemia, while suggesting for the first time their potential relation to specific Trisomy 21 co-occurring conditions. CONCLUSION Our concise review on the emerging RUNX1 roles in different tissues outside the hematopoietic context provides a number of well-funded hypotheses that will open new research avenues toward a better understanding of RUNX1-mediated transcription in health and disease, contributing to novel potential diagnostic and therapeutic strategies for Down syndrome-associated conditions.
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Affiliation(s)
- Esteban J Rozen
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., Boulder, CO, 80303, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, 12700 East 19th Avenue, Aurora, CO, 80045, USA.
| | - Christopher D Ozeroff
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., Boulder, CO, 80303, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, 12700 East 19th Avenue, Aurora, CO, 80045, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Ave., Boulder, CO, 80309, USA
| | - Mary Ann Allen
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., Boulder, CO, 80303, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, 12700 East 19th Avenue, Aurora, CO, 80045, USA.
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12
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Zezulin AU, Yen D, Ye D, Howell ED, Bresciani E, Diemer J, Ren JG, Ahmad MH, Castilla LH, Touw IP, Minn AJ, Tong W, Liu PP, Tan K, Yu W, Speck NA. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. Genes Dev 2023; 37:605-620. [PMID: 37536952 PMCID: PMC10499021 DOI: 10.1101/gad.350418.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
The transcription factor RUNX1 is mutated in familial platelet disorder with associated myeloid malignancy (FPDMM) and in sporadic myelodysplastic syndrome and leukemia. RUNX1 was shown to regulate inflammation in multiple cell types. Here we show that RUNX1 is required in granulocyte-monocyte progenitors (GMPs) to epigenetically repress two inflammatory signaling pathways in neutrophils: Toll-like receptor 4 (TLR4) and type I interferon (IFN) signaling. RUNX1 loss in GMPs augments neutrophils' inflammatory response to the TLR4 ligand lipopolysaccharide through increased expression of the TLR4 coreceptor CD14. RUNX1 binds Cd14 and other genes encoding proteins in the TLR4 and type I IFN signaling pathways whose chromatin accessibility increases when RUNX1 is deleted. Transcription factor footprints for the effectors of type I IFN signaling-the signal transducer and activator of transcription (STAT1::STAT2) and interferon regulatory factors (IRFs)-were enriched in chromatin that gained accessibility in both GMPs and neutrophils when RUNX1 was lost. STAT1::STAT2 and IRF motifs were also enriched in the chromatin of retrotransposons that were derepressed in RUNX1-deficient GMPs and neutrophils. We conclude that a major direct effect of RUNX1 loss in GMPs is the derepression of type I IFN and TLR4 signaling, resulting in a state of fixed maladaptive innate immunity.
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Affiliation(s)
- Alexandra U Zezulin
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel Yen
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Darwin Ye
- Department of Radiation Oncology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth D Howell
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jamie Diemer
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jian-Gang Ren
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mohd Hafiz Ahmad
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Lucio H Castilla
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ivo P Touw
- Department of Hematology, Erasmus Medical College, Rotterdam 3015CN, the Netherlands
| | - Andy J Minn
- Department of Radiation Oncology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wei Tong
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Oncology and Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Wenbao Yu
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Division of Oncology and Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Nancy A Speck
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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13
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287124. [PMID: 37034605 PMCID: PMC10081408 DOI: 10.1101/2023.03.30.23287124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) can occur in persons with HIV despite adherence to combination antiretroviral therapy (ART) and in the absence of significant drug resistance. Here, we show that plasma NSV sequences are comprised primarily of large clones without evidence of viral evolution over time. We defined proviruses that contribute to plasma viremia as "producer", and those that did not as "non-producer". Compared to ART-suppressed individuals, NSV participants had a significantly larger producer reservoir. Producer proviruses were enriched in chromosome 19 and in proximity to the activating H3K36me3 epigenetic mark. CD4+ cells from NSV participants demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, NSV participants showed no elevation in HIV-specific CD8+ cell responses and producer proviruses were enriched for HLA escape mutations. We identified critical host and viral mediators of NSV that represent potential targets to disrupt HIV persistence and promote viral silencing.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rinki Deo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter L. Anderson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M. Lederman
- Center for AIDS Research, Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D. Lichterfeld
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jose R. Castillo-Mancilla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alan N. Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D. Gaiha
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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14
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Ernst MPT, Pronk E, van Dijk C, van Strien PMH, van Tienhoven TVD, Wevers MJW, Sanders MA, Bindels EMJ, Speck NA, Raaijmakers MHGP. Hematopoietic Cell Autonomous Disruption of Hematopoiesis in a Germline Loss-of-function Mouse Model of RUNX1-FPD. Hemasphere 2023; 7:e824. [PMID: 36741355 PMCID: PMC9891454 DOI: 10.1097/hs9.0000000000000824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/29/2022] [Indexed: 02/01/2023] Open
Abstract
RUNX1 familial platelet disorder (RUNX1-FPD) is a hematopoietic disorder caused by germline loss-of-function mutations in the RUNX1 gene and characterized by thrombocytopathy, thrombocytopenia, and an increased risk of developing hematologic malignancies, mostly of myeloid origin. Disease pathophysiology has remained incompletely understood, in part because of a shortage of in vivo models recapitulating the germline RUNX1 loss of function found in humans, precluding the study of potential contributions of non-hematopoietic cells to disease pathogenesis. Here, we studied mice harboring a germline hypomorphic mutation of one Runx1 allele with a loss-of-function mutation in the other Runx1 allele (Runx1 L148A/- mice), which display many hematologic characteristics found in human RUNX1-FPD patients. Runx1 L148A/- mice displayed robust and pronounced thrombocytopenia and myeloid-biased hematopoiesis, associated with an HSC intrinsic reconstitution defect in lymphopoiesis and expansion of myeloid progenitor cell pools. We demonstrate that specific deletion of Runx1 from bone marrow stromal cells in Prrx1-cre;Runx1 fl/fl mice did not recapitulate these abnormalities, indicating that the hematopoietic abnormalities are intrinsic to the hematopoietic lineage, and arguing against a driving role of the bone marrow microenvironment. In conclusion, we report a RUNX1-FPD mouse model faithfully recapitulating key characteristics of human disease. Findings do not support a driving role of ancillary, non-hematopoietic cells in the disruption of hematopoiesis under homeostatic conditions.
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Affiliation(s)
- Martijn P. T. Ernst
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eline Pronk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Claire van Dijk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Michiel J. W. Wevers
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mathijs A. Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eric M. J. Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Nancy A. Speck
- Abramson Family Cancer Research Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
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15
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Zezulin AU, Ye D, Howell E, Yen D, Bresciani E, Diemer J, Ren JG, Ahmad MH, Castilla LH, Touw IP, Minn AJ, Tong W, Liu PP, Tan K, Yu W, Speck NA. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525911. [PMID: 36747636 PMCID: PMC9900925 DOI: 10.1101/2023.01.27.525911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The transcription factor RUNX1 is mutated in familial platelet disorder with associated myeloid malignancies (FPDMM) and in sporadic myelodysplastic syndrome and leukemia. RUNX1 regulates inflammation in multiple cell types. Here we show that RUNX1 is required in granulocyte-monocyte progenitors (GMPs) to restrict the inflammatory response of neutrophils to toll-like receptor 4 (TLR4) signaling. Loss of RUNX1 in GMPs increased the TLR4 coreceptor CD14 on neutrophils, which contributed to neutrophils’ increased inflammatory cytokine production in response to the TLR4 ligand lipopolysaccharide. RUNX1 loss increased the chromatin accessibility of retrotransposons in GMPs and neutrophils and induced a type I interferon signature characterized by enriched footprints for signal transducer and activator of transcription (STAT1::STAT2) and interferon regulatory factors (IRF) in opened chromatin, and increased expression of interferon-stimulated genes. The overproduction of inflammatory cytokines by neutrophils was reversed by inhibitors of type I IFN signaling. We conclude that RUNX1 restrains the chromatin accessibility of retrotransposons in GMPs and neutrophils, and that loss of RUNX1 increases proinflammatory cytokine production by elevating tonic type I interferon signaling.
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16
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Dutta B, Osato M. The RUNX Family, a Novel Multifaceted Guardian of the Genome. Cells 2023; 12:255. [PMID: 36672189 PMCID: PMC9856552 DOI: 10.3390/cells12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/24/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
The DNA repair machinery exists to protect cells from daily genetic insults by orchestrating multiple intrinsic and extrinsic factors. One such factor recently identified is the Runt-related transcription factor (RUNX) family, a group of proteins that act as a master transcriptional regulator for multiple biological functions such as embryonic development, stem cell behaviors, and oncogenesis. A significant number of studies in the past decades have delineated the involvement of RUNX proteins in DNA repair. Alterations in RUNX genes cause organ failure and predisposition to cancers, as seen in patients carrying mutations in the other well-established DNA repair genes. Herein, we review the currently existing findings and provide new insights into transcriptional and non-transcriptional multifaceted regulation of DNA repair by RUNX family proteins.
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Affiliation(s)
- Bibek Dutta
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Motomi Osato
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
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Hao Q, Kundu S, Shetty S, Tucker TA, Idell S, Tang H. Inducible general knockout of Runx3 profoundly reduces pulmonary cytotoxic CD8+ T cells with minimal effect on outcomes in mice following influenza infection. Front Immunol 2022; 13:1011922. [PMID: 36275778 PMCID: PMC9586250 DOI: 10.3389/fimmu.2022.1011922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Respiratory viruses pose a continuing and substantive threat to human health globally. Host innate and adaptive immune responses are the critical antiviral defense mechanisms to control viral replication and spread. The present study is designed to determine the role of transcription factor Runx3 in the host immune response to influenza A virus (IAV) infection. As Runx3 is required for embryonic development, we generated an inducible Runx3 global knockout (KO) mouse model and found that Runx3 KO in adult C57BL/6 mice minimally affected thymic function under normal conditions and survival was at least 250 days post Runx3 deletion. We applied the mouse model to IAV infection and found that Runx3 KO resulted in a huge reduction (>85%) in numbers of total and antigen-specific pulmonary CD8+ cytotoxic T cells during IAV infection, while it had a minor effect on pulmonary generation of CD4+ T cells. To our surprise, this general KO of Runx3 did not significantly alter viral clearance and animal survival following IAV infection. Interestingly, we found that Runx3 KO significantly increased the numbers of pulmonary innate immune cells such as macrophages and neutrophils and the production of pro-inflammatory cytokines during IAV infection. We further found that Runx3 was strongly detected in CCR2+ immune cells in IAV-infected mouse lungs and was induced in activated macrophages and dendritic cells (DCs). As pulmonary CD8+ cytotoxic T cells play a central role in the clearance of IAV, our findings suggest that Runx3 KO may enhance host innate immunity to compensate for the loss of pulmonary CD8+ cytotoxic T cells during IAV infection.
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Sakleshpur S, Steed AL. Influenza: Toward understanding the immune response in the young. Front Pediatr 2022; 10:953150. [PMID: 36061377 PMCID: PMC9437304 DOI: 10.3389/fped.2022.953150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/28/2022] [Indexed: 12/12/2022] Open
Abstract
Annually influenza causes a global epidemic resulting in 290,000 to 650,000 deaths and extracts a massive toll on healthcare and the economy. Infants and children are more susceptible to infection and have more severe symptoms than adults likely mitigated by differences in their innate and adaptive immune responses. While it is unclear the exact mechanisms with which the young combat influenza, it is increasingly understood that their immune responses differ from adults. Specifically, underproduction of IFN-γ and IL-12 by the innate immune system likely hampers viral clearance while upregulation of IL-6 may create excessive damaging inflammation. The infant's adaptive immune system preferentially utilizes the Th-2 response that has been tied to γδ T cells and their production of IL-17, which may be less advantageous than the adult Th-1 response for antiviral immunity. This differential immune response of the young is considered to serve as a unique evolutionary adaptation such that they preferentially respond to infection broadly rather than a pathogen-specific one generated by adults. This unique function of the young immune system is temporally, and possibly mechanistically, tied to the microbiota, as they both develop in coordination early in life. Additional research into the relationship between the developing microbiota and the immune system is needed to develop therapies effective at combating influenza in the youngest and most vulnerable of our population.
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Affiliation(s)
- Sonia Sakleshpur
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Ashley L Steed
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
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