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Szychowski KA, Skóra B. Elastin-derived peptides (EDPs) as a potential pro-malignancy factor in human leukemia cell lines. Immunol Res 2024:10.1007/s12026-024-09511-7. [PMID: 38967692 DOI: 10.1007/s12026-024-09511-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/23/2024] [Indexed: 07/06/2024]
Abstract
The extracellular matrix (ECM) is currently considered to be an important factor influencing the migration and progression of cancer cells. Therefore, the aim of our study was to investigate the mechanism of action of elastin-derived peptides in cancerous cells derived from the immunological system, i.e., HL-60, K562, and MEG-A2 cell lines. Moreover, an attempt to clarify the involvement of c-SRC kinase in EDP mechanism of action was also undertaken. Our data show that the VGVAPG and VVGPGA peptides are not toxic in the studied cell lines. Moreover, due to the involvement of KI67 and PCNA proteins in the cell cycle and proliferation, we can assume that neither peptide stimulates cell proliferation. Our data suggest that both peptides could initiate the differentiation process in all the studied cell lines. However, due to the different origins (HL-60 and K562-leukemic cell line vs. MEG-A2-megakaryoblastic origin) of the cell lines, the mechanism may differ. The increase in the ELANE mRNA expression noted in our experiments may also suggest enhancement of the migration of the tested cells. However, more research is needed to fully explain the mechanism of action of the VGVAPG and VVGPGA peptides in the HL-60, K562, and MEG-A2 cell lines. HIGHLIGHTS: • VGVAPG and VVGPGA peptides do not affect the metabolic activity of HL-60, K562, and MEG-A2 cells. • mTOR and PPARγ proteins are involved in the mechanism of action of VGVAPG and VVGPGA peptides. • Both peptides may initiate differentiation in HL-60, K562, and MEG-A2 cell lines.
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Affiliation(s)
- Konrad A Szychowski
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, Sucharskiego 2, 35-225, Rzeszow, Poland.
| | - Bartosz Skóra
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, Sucharskiego 2, 35-225, Rzeszow, Poland
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Stenhouse C, Halloran KM, Hoskins EC, Moses RM, Wu G, Seo H, Johnson GA, Suva LJ, Gaddy D, Bazer FW. Progesterone regulates tissue non-specific alkaline phosphatase (TNSALP) expression and activity in ovine utero-placental tissues. J Anim Sci Biotechnol 2024; 15:90. [PMID: 38956701 PMCID: PMC11220967 DOI: 10.1186/s40104-024-01048-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/09/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Tissue non-specific alkaline phosphatase (TNSALP; encoded by the ALPL gene) has a critical role in the postnatal regulation of phosphate homeostasis, yet how TNSALP activity and expression are regulated during pregnancy remain largely unknown. This study tested the hypothesis that progesterone (P4) and/or interferon tau (IFNT) regulate TNSALP activity during pregnancy in sheep. METHODS In Exp. 1, ewes were bred and received daily intramuscular injections of either corn oil vehicle (CO) or 25 mg progesterone in CO (P4) for the first 8 days of pregnancy and were hysterectomized on either Day 9, 12, or 125 of gestation. In Exp. 2, ewes were fitted with intrauterine catheters on Day 7 of the estrous cycle and received daily intramuscular injections of 50 mg P4 in CO and/or 75 mg progesterone receptor antagonist (RU486) in CO from Days 8 to 15, and twice daily intrauterine injections of either control proteins (CX) or IFNT (25 µg/uterine horn/d) from Days 11 to 15 (treatment groups: P4 + CX; P4 + IFNT; RU486 + P4 + CX; and RU486 + P4 + IFNT) and were hysterectomized on Day 16. RESULTS In Exp. 1, endometria from ewes administered P4 had greater expression of ALPL mRNA than ewes administered CO on Day 12. TNSALP activity appeared greater in the epithelia, stratum compactum stroma, and endothelium of the blood vessels in the endometrium and myometrium from ewes administered P4 than ewes administered CO on Day 12. On Day 125, TNSALP activity localized to uterine epithelial and endothelial cells, independent of P4 treatment. TNSALP activity in placentomes appeared greater in P4 treated ewes and was detected in endothelial cells and caruncular tissue in P4 treated but not CO treated ewes. In Exp. 2, endometrial homogenates from ewes administered RU486 + P4 + CX had lower TNSALP activity those for P4 + CX and P4 + IFNT ewes. Immunoreactive TNSALP protein appeared greater in the mid- and deep-glandular epithelia in RU486 + P4 + CX treated ewes as compared to the other treatment groups. Enzymatic activity appeared greater on the apical surface of the deep glandular epithelia in endometria from ewes treated with RU486 + P4 + CX compared to the other treatment groups. CONCLUSIONS These results suggest that P4, but not IFNT, regulates the expression and activity of TNSALP in utero-placental tissues and has the potential to contribute to the regulation of phosphate availability that is critical for conceptus development during pregnancy.
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Affiliation(s)
- Claire Stenhouse
- Department of Animal Science, Pennsylvania State University, University Park, PA, 16802, U.S.A..
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A..
| | - Katherine M Halloran
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, 48109, U.S.A
| | - Emily C Hoskins
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN, 37996, U.S.A
| | - Robyn M Moses
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE, 68198, U.S.A
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A
| | - Heewon Seo
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843, U.S.A
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, 20742, U.S.A
| | - Gregory A Johnson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843, U.S.A
| | - Larry J Suva
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, 77843, U.S.A
| | - Dana Gaddy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843, U.S.A
| | - Fuller W Bazer
- Department of Animal Science, Texas A&M University, College Station, Texas, 77843, U.S.A
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Anyona SB, Cheng Q, Wasena SA, Osata SW, Guo Y, Raballah E, Hurwitz I, Onyango CO, Ouma C, Seidenberg PD, McMahon BH, Lambert CG, Schneider KA, Perkins DJ. Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia. Nat Commun 2024; 15:5037. [PMID: 38866743 PMCID: PMC11169501 DOI: 10.1038/s41467-024-48259-4] [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: 07/07/2023] [Accepted: 04/25/2024] [Indexed: 06/14/2024] Open
Abstract
This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, compares the entire expressed whole blood host transcriptome between Kenyan children (3-48 mos.) with non-SMA (Hb ≥ 6.0 g/dL, n = 39) and SMA (n = 18). Differential expression analyses reveal 1403 up-regulated and 279 down-regulated transcripts in SMA, signifying impairments in host inflammasome activation, cell death, and innate immune and cellular stress responses. Immune cell profiling shows decreased memory responses, antigen presentation, and immediate pathogen clearance, suggesting an immature/improperly regulated immune response in SMA. Module repertoire analysis of blood-specific gene signatures identifies up-regulation of erythroid genes, enhanced neutrophil activation, and impaired inflammatory responses in SMA. Enrichment analyses converge on disruptions in cellular homeostasis and regulatory pathways for the ubiquitin-proteasome system, autophagy, and heme metabolism. Pathway analyses highlight activation in response to hypoxic conditions [Hypoxia Inducible Factor (HIF)-1 target and Reactive Oxygen Species (ROS) signaling] as a central theme in SMA. These signaling pathways are also top-ranking in protein abundance measures and a Ugandan SMA cohort with available transcriptomic data. Targeted RNA-Seq validation shows strong concordance with our entire expressed transcriptome data. These findings identify key molecular themes in SMA pathogenesis, offering potential targets for new malaria therapies.
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Affiliation(s)
- Samuel B Anyona
- Department of Medical Biochemistry, School of Medicine, Maseno University, Maseno, 40105, Kenya.
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya.
| | - Qiuying Cheng
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Sharley A Wasena
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, 40105, Kenya
| | - Shamim W Osata
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya
| | - Yan Guo
- Department of Public Health Sciences, University of Miami, Miami, 33136, USA
| | - Evans Raballah
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya
- Department of Medical Laboratory Sciences, School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, 50100, Kenya
| | - Ivy Hurwitz
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Clinton O Onyango
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, 40105, Kenya
| | - Collins Ouma
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya
- Department of Biomedical Sciences and Technology, School of Public Health and Community Development, Maseno University, Maseno, 40105, Kenya
| | - Philip D Seidenberg
- Department of Emergency Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Christophe G Lambert
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico, Albuquerque, NM, 87131-0001, USA
| | - Kristan A Schneider
- Department of Internal Medicine, Division of Translational Informatics, University of New Mexico, Albuquerque, NM, 87131-0001, USA
- Department Applied Computer and Bio-Sciences, University of Applied Sciences Mittweida, Mittweida, 09648, Germany
| | - Douglas J Perkins
- University of New Mexico-Kenya Global Health Programs, Kisumu and Siaya, 40100, Kenya.
- Department of Internal Medicine, Center for Global Health, University of New Mexico, Albuquerque, NM, 87131-0001, USA.
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Lee K, Ko E, Park Y. Adipose Tissue-Derived Mesenchymal Stem Cell Inhibits Osteoclast Differentiation through Tumor Necrosis Factor Stimulated Gene-6. Tissue Eng Regen Med 2024; 21:587-594. [PMID: 38451425 PMCID: PMC11087411 DOI: 10.1007/s13770-023-00619-9] [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: 10/07/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) have been highlighted as a potent therapeutic option for conditions with excessive osteoclast activity such as systemic and local bone loss in rheumatic disease. In addition to their immunomodulatory functions, MSCs also directly suppress osteoclast differentiation and activation by secreting osteoprotegerin (OPG) and IL-10 but the underlying mechanisms are still to be clarified. Tumor necrosis factor-stimulated gene-6 (TSG-6) is a potent anti-inflammatory molecule that inhibits osteoclast activation and has been shown to mediate MSC's immunomodulatory functions. In this study, we aimed to determine whether adipose tissue-derived MSC (ADMSC) inhibits the differentiation from osteoclast precursors to mature osteoclasts through TSG-6. METHODS Human ADMSCs were co-cultured with bone marrow-derived monocyte/macrophage (BMMs) from DBA/1J or B6 mouse in the presence of osteoclastogenic condition (M-CSF 10 ng/mL and RANKL 10 ng/mL). In some co-culture groups, ADMSCs were transfected with siRNA targeting TSG-6 or OPG to determine their role in osteoclastogenesis. Tartrate-resistant acid phosphatase (TRAP) activity in culture supernatant and mRNA expression of osteoclast markers were investigated. TRAP+ multinucleated cells and F-actin ring formation were counted. RESULTS ADMSCs significantly inhibited osteoclast differentiation under osteoclastogenic conditions. Suppression of TSG-6 significantly reversed the inhibition of osteoclast differentiation in a degree similar to that of OPG based on TRAP activity, mRNA expression of osteoclast markers, and numbers of TRAP+ multinucleated cell and F-actin ring formation. CONCLUSION This study demonstrated that ADMSCs inhibit osteoclast differentiation through TSG-6 under osteoclastogenic conditions.
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Affiliation(s)
- Kwanghoon Lee
- Division of Rheumatology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Goyang, 10326, Republic of Korea
| | - Eunhee Ko
- Division of Rheumatology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Yongbeom Park
- Division of Rheumatology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Su EY, Fread K, Goggin S, Zunder ER, Cahan P. Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells. Sci Data 2024; 11:559. [PMID: 38816402 PMCID: PMC11139855 DOI: 10.1038/s41597-024-03399-6] [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: 03/31/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Single-cell methods offer a high-resolution approach for characterizing cell populations. Many studies rely on single-cell transcriptomics to draw conclusions regarding cell state and behavior, with the underlying assumption that transcriptomic readouts largely parallel their protein counterparts and subsequent activity. However, the relationship between transcriptomic and proteomic measurements is imprecise, and thus datasets that probe the extent of their concordance will be useful to refine such conclusions. Additionally, novel single-cell analysis tools often lack appropriate gold standard datasets for the purposes of assessment. Integrative (combining the two data modalities) and predictive (using one modality to improve results from the other) approaches in particular, would benefit from transcriptomic and proteomic data from the same sample of cells. For these reasons, we performed single-cell RNA sequencing, mass cytometry, and flow cytometry on a split-sample of human peripheral blood mononuclear cells. We directly compare the proportions of specific cell types resolved by each technique, and further describe the extent to which protein and mRNA measurements correlate within distinct cell types.
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Affiliation(s)
- Emily Y Su
- Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kristen Fread
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah Goggin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Eli R Zunder
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Patrick Cahan
- Institute for Cell Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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Ramey-Ward AN, Walthall HP, Smith S, Barrows TH. Human keratin matrices promote wound healing by modulating skin cell expression of cytokines and growth factors. Wound Repair Regen 2024; 32:257-267. [PMID: 38111086 DOI: 10.1111/wrr.13137] [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: 06/30/2023] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
A wide variety of biomaterials has been developed to assist in wound healing, including acellular animal and human-derived protein matrices. However, millions of patients worldwide still suffer from non-healing chronic wounds, demonstrating a need for further innovation in wound care. To address this need, a novel biomaterial, the human keratin matrix (HKM), was developed, characterised, and tested in vitro and in vivo. HKM was found to be degradation-resistant, and a proteomics analysis showed it to be greater than 99% human keratin proteins. PCR revealed adult human epidermal keratinocytes (HEKa) grown in contact with HKM showed increased gene expression of keratinocyte activations markers such as Epidermal Growth Factor (EGF). Additionally, a cytokine microarray demonstrated culture on HKM increased the release of cytokines involved in wound inflammatory modulation by both HEKa cells and adult human dermal fibroblasts (HDFa). Finally, in a murine chronic wound model, full-thickness wounds treated weekly with HKM were smaller through the healing process than those treated with human amniotic membrane (AM), bovine dermis (BD), or porcine decellularized small intestinal submucosa (SIS). HKM-treated wounds also closed significantly faster than AM- and SIS-treated wounds. These data suggest that HKM is an effective novel treatment for chronic wounds.
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DelaCuesta-Barrutia J, Hidema S, Caldwell HK, Nishimori K, Erdozain AM, Peñagarikano O. In need of a specific antibody against the oxytocin receptor for neuropsychiatric research: A KO validation study. J Psychiatr Res 2024; 173:260-270. [PMID: 38554622 DOI: 10.1016/j.jpsychires.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/22/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
Antibodies are one of the most utilized tools in biomedical research. However, few of them are rigorously evaluated, as there are no accepted guidelines or standardized methods for determining their validity before commercialization. Often, an antibody is considered validated if it detects a band by Western blot of the expected molecular weight and, in some cases, if blocking peptides result in loss of staining. Neither of these approaches are unquestionable proof of target specificity. Since the oxytocin receptor has recently become a popular target in neuropsychiatric research, the need for specific antibodies to be used in brain has arisen. In this work, we have tested the specificity of six commercially available oxytocin receptor antibodies, indicated by the manufacturers to be suitable for Western blot and with an available image showing the correct size band (45-55 KDa). Antibodies were first tested by Western blot in brain lysates of wild-type and oxytocin receptor knockout mice. Uterus tissue was also tested as control for putative differential tissue specificity. In brain, the six tested antibodies lacked target specificity, as both wild-type and receptor knockout samples resulted in a similar staining pattern, including the expected 45-55 KDa band. Five of the six antibodies detected a selective band in uterus (which disappeared in knockout tissue). These five specific antibodies were also tested for immunohistochemistry in uterus, where only one was specific. However, when the uterine-specific antibody was tested in brain tissue, it lacked specificity. In conclusion, none of the six tested commercial antibodies are suitable to detect oxytocin receptor in brain by either Western blot or immunohistochemistry, although some do specifically detect it in uterus. The present work highlights the need to develop standardized antibody validation methods, including a proper negative control, in order to grant quality and reproducibility of the generated data.
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Affiliation(s)
- Jon DelaCuesta-Barrutia
- Department of Pharmacology, School of Medicine, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Shizu Hidema
- Department of Obesity and Inflammation, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Heather K Caldwell
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Ohio, 44242, USA
| | - Katsuhiko Nishimori
- Department of Obesity and Inflammation, Fukushima Medical University, Fukushima, 960-1295, Japan
| | - Amaia M Erdozain
- Department of Pharmacology, School of Medicine, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain; Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Leioa, 48940, Spain
| | - Olga Peñagarikano
- Department of Pharmacology, School of Medicine, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain; Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Leioa, 48940, Spain.
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9
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Reda GK, Ndunguru SF, Csernus B, Knop R, Lugata JK, Szabó C, Czeglédi L, Lendvai ÁZ. Dietary restriction reveals sex-specific expression of the mTOR pathway genes in Japanese quails. Sci Rep 2024; 14:8314. [PMID: 38594358 PMCID: PMC11004124 DOI: 10.1038/s41598-024-58487-9] [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: 09/20/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Limited resources affect an organism's physiology through the conserved metabolic pathway, the mechanistic target of rapamycin (mTOR). Males and females often react differently to nutritional limitation, but whether it leads to differential mTOR pathway expression remains unknown. Recently, we found that dietary restriction (DR) induced significant changes in the expression of mTOR pathway genes in female Japanese quails (Coturnix japonica). We simultaneously exposed 32 male and female Japanese quails to either 20%, 30%, 40% restriction or ad libitum feeding for 14 days and determined the expression of six key genes of the mTOR pathway in the liver to investigate sex differences in the expression patterns. We found that DR significantly reduced body mass, albeit the effect was milder in males compared to females. We observed sex-specific liver gene expression. DR downregulated mTOR expression more in females than in males. Under moderate DR, ATG9A and RPS6K1 expressions were increased more in males than in females. Like females, body mass in males was correlated positively with mTOR and IGF1, but negatively with ATG9A and RS6K1 expressions. Our findings highlight that sexes may cope with nutritional deficits differently and emphasise the importance of considering sexual differences in studies of dietary restriction.
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Affiliation(s)
- Gebrehaweria K Reda
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary.
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary.
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary.
| | - Sawadi F Ndunguru
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
| | - Brigitta Csernus
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
| | - Renáta Knop
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
| | - James K Lugata
- Doctoral School of Animal Science, University of Debrecen, 4032, Debrecen, Hungary
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Csaba Szabó
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, 4032, Debrecen, Hungary
| | - Levente Czeglédi
- Department of Animal Science, Faculty of Agricultural and Food Sciences and Environmental Management, Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032, Debrecen, Hungary
| | - Ádám Z Lendvai
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032, Debrecen, Hungary
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10
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Todorov-Völgyi K, González-Gallego J, Müller SA, Beaufort N, Malik R, Schifferer M, Todorov MI, Crusius D, Robinson S, Schmidt A, Körbelin J, Bareyre F, Ertürk A, Haass C, Simons M, Paquet D, Lichtenthaler SF, Dichgans M. Proteomics of mouse brain endothelium uncovers dysregulation of vesicular transport pathways during aging. NATURE AGING 2024; 4:595-612. [PMID: 38519806 DOI: 10.1038/s43587-024-00598-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Age-related decline in brain endothelial cell (BEC) function contributes critically to neurological disease. Comprehensive atlases of the BEC transcriptome have become available, but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting-based mouse BEC enrichment protocol compatible with proteomics and resolved the profiles of protein abundance changes during aging. Unsupervised cluster analysis revealed a segregation of age-related protein dynamics with biological functions, including a downregulation of vesicle-mediated transport. We found a dysregulation of key regulators of endocytosis and receptor recycling (most prominently Arf6), macropinocytosis and lysosomal degradation. In gene deletion and overexpression experiments, Arf6 affected endocytosis pathways in endothelial cells. Our approach uncovered changes not picked up by transcriptomic studies, such as accumulation of vesicle cargo and receptor ligands, including Apoe. Proteomic analysis of BECs from Apoe-deficient mice revealed a signature of accelerated aging. Our findings provide a resource for analysing BEC function during aging.
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Affiliation(s)
- Katalin Todorov-Völgyi
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
| | - Judit González-Gallego
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neuroscience (GSN), University Hospital, LMU Munich, Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Nathalie Beaufort
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Rainer Malik
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Mihail Ivilinov Todorov
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
| | - Dennis Crusius
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Sophie Robinson
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Graduate School of Systemic Neuroscience (GSN), University Hospital, LMU Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
| | - Andree Schmidt
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Jakob Körbelin
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florence Bareyre
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center Munich (BMC), Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Ali Ertürk
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Division of Metabolic Biochemistry, Biomedical Center Munich (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mikael Simons
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Martin Dichgans
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany.
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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11
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Haycock J, Maehr T, Dastjerdi A, Steinbach F. Immunostimulation of Asian elephant ( Elephas maximus) blood cells by parapoxvirus ovis and CpG motif-containing bacterial plasmid DNA upregulates innate immune gene expression. Front Immunol 2024; 15:1329820. [PMID: 38590526 PMCID: PMC10999609 DOI: 10.3389/fimmu.2024.1329820] [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: 10/29/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
The immune system of Asian elephants (Elephas maximus) is poorly studied, compared to that of livestock, rodents or humans. The innate immune response has become a focus of interest in relation to Elephant endotheliotropic herpesviruses (EEHVs). EEHVs cause a fatal hemorrhagic disease (EEHV-HD) and are a significant threat to captive Asian elephant populations worldwide. Similar to other herpesvirus infections, nearly all animals become infected, but only some develop disease. As progression to EEHV-HD is often acute, a robust innate immune response is crucial to control EEHV infections. This is invariably true of the host in the first instance, but it can also potentially be modulated by intervention strategies. Here, two immunostimulant veterinary medicinal products, authorized for use in domestic species, were tested for their ability to induce innate anti-viral immune responses in Asian elephant blood cells. Sequence data were obtained for a range of previously unidentified Asian elephant immune genes, including C-X-C motif chemokine ligand 10 (CXCL10), interferon stimulated gene 15 (ISG15) and myxovirus GTPase 1 (Mx1), and were employed in the design of species-specific qPCR assays. These assays were subsequently used in analyses to determine fold changes in gene expression over a period of 24 hours. This study demonstrates that both immunostimulant medications are capable of inducing significant innate anti-viral immune responses which suggests that both could be beneficial in controlling EEHV infections in Asian elephants.
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Affiliation(s)
- Jonathan Haycock
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Virology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Tanja Maehr
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Akbar Dastjerdi
- Department of Virology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Falko Steinbach
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Virology, Animal and Plant Health Agency, Addlestone, United Kingdom
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12
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Yashar WM, Estabrook J, Holly HD, Somers J, Nikolova O, Babur Ö, Braun TP, Demir E. Predicting transcription factor activity using prior biological information. iScience 2024; 27:109124. [PMID: 38455978 PMCID: PMC10918219 DOI: 10.1016/j.isci.2024.109124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hannah D. Holly
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Olga Nikolova
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts, Boston, MA 02125, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Pacific Northwest National Laboratories, Richland, WA 99354, USA
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13
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Devine EA, Imami AS, Eby H, Hamoud AR, Golchin H, Ryan W, Sahay S, Shedroff EA, Arvay T, Joyce AW, Asah SM, Walss-Bass C, O'Donovan S, McCullumsmith RE. Neuronal alterations in AKT isotype expression in schizophrenia. RESEARCH SQUARE 2024:rs.3.rs-3940448. [PMID: 38559131 PMCID: PMC10980160 DOI: 10.21203/rs.3.rs-3940448/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Schizophrenia is characterized by substantial alterations in brain function, and previous studies suggest insulin signaling pathways, particularly involving AKT, are implicated in the pathophysiology of the disorder. This study demonstrates elevated mRNA expression of AKT1-3 in neurons from schizophrenia subjects, contrary to unchanged or diminished total AKT protein expression reported in previous postmortem studies, suggesting a potential decoupling of transcript and protein levels. Sex-specific differential AKT activity was observed, indicating divergent roles in males and females with schizophrenia. Alongside AKT, upregulation of PDPK1, a critical component of the insulin signaling pathway, and several protein phosphatases known to regulate AKT were detected. Moreover, enhanced expression of the transcription factor FOXO1, a regulator of glucose metabolism, hints at possible compensatory mechanisms related to insulin signaling dysregulation. Findings were largely independent of antipsychotic medication use, suggesting inherent alterations in schizophrenia. These results highlight the significance of AKT and related signaling pathways in schizophrenia, proposing that these changes might represent a compensatory response to a primary defect of conical insulin signaling pathways. This research underscores the need for a detailed understanding of these signaling pathways for the development of effective therapeutic strategies.
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Affiliation(s)
- Emily A Devine
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ali S Imami
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hunter Eby
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Abdul-Rizaq Hamoud
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hasti Golchin
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - William Ryan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Smita Sahay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Elizabeth A Shedroff
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Taylen Arvay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Alex W Joyce
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Sophie M Asah
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Consuelo Walss-Bass
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sinead O'Donovan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Robert E McCullumsmith
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Neurosciences Institute, ProMedica, Toledo, OH, USA
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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14
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Eisinger K, Girke P, Buechler C, Krautbauer S. Adipose tissue depot specific expression and regulation of fibrosis-related genes and proteins in experimental obesity. Mamm Genome 2024; 35:13-30. [PMID: 37884762 PMCID: PMC10884164 DOI: 10.1007/s00335-023-10022-3] [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: 10/14/2022] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Transforming growth factor beta (Tgfb) is a well-studied pro-fibrotic cytokine, which upregulates cellular communication network factor 2 (Ccn2), collagen, and actin alpha 2, smooth muscle (Acta2) expression. Obesity induces adipose tissue fibrosis, which contributes to metabolic diseases. This work aimed to analyze the expression of Tgfb, Ccn2, collagen1a1 (Col1a1), Acta2 and BMP and activin membrane-bound inhibitor (Bambi), which is a negative regulator of Tgfb signaling, in different adipose tissue depots of mice fed a standard chow, mice fed a high fat diet (HFD) and ob/ob mice. Principally, these genes were low expressed in brown adipose tissues and this difference was less evident for the ob/ob mice. Ccn2 and Bambi protein as well as mRNA expression, and collagen1a1 mRNA were not induced in the adipose tissues upon HFD feeding whereas Tgfb and Acta2 mRNA increased in the white fat depots. Immunoblot analysis showed that Acta2 protein was higher in subcutaneous and perirenal fat of these mice. In the ob/ob mice, Ccn2 mRNA and Ccn2 protein were upregulated in the fat depots. Here, Tgfb, Acta2 and Col1a1 mRNA levels and serum Tgfb protein were increased. Acta2 protein was, however, not higher in subcutaneous and perirenal fat of these mice. Col6a1 mRNA was shown before to be higher in obese fat tissues. Current analysis proved the Col6a1 protein was induced in subcutaneous fat of HFD fed mice. Notably, Col6a1 was reduced in perirenal fat of ob/ob mice in comparison to the respective controls. 3T3-L1 cells express Ccn2 and Bambi protein, whose levels were not changed by fatty acids, leptin, lipopolysaccharide, tumor necrosis factor and interleukin-6. All of these factors led to higher Tgfb in 3T3-L1 adipocyte media but did not increase its mRNA levels. Free fatty acids induced necrosis whereas apoptosis did not occur in any of the in vitro incubations excluding cell death as a main reason for higher Tgfb in cell media. In summary, Tgfb mRNA is consistently induced in white fat tissues in obesity but this is not paralleled by a clear increase of its target genes. Moreover, discrepancies between mRNA and protein expression of Acta2 were observed. Adipocytes seemingly do not contribute to higher Tgfb mRNA levels in obesity. These cells release more Tgfb protein when challenged with obesity-related metabolites connecting metabolic dysfunction and fibrosis.
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Affiliation(s)
- Kristina Eisinger
- Department of Internal Medicine I, Regensburg University Hospital, 93053, Regensburg, Germany
| | - Philipp Girke
- Department of Genetics, University of Regensburg, 93040, Regensburg, Germany
| | - Christa Buechler
- Department of Internal Medicine I, Regensburg University Hospital, 93053, Regensburg, Germany.
| | - Sabrina Krautbauer
- Department of Internal Medicine I, Regensburg University Hospital, 93053, Regensburg, Germany
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15
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Fadum JM, Borton MA, Daly RA, Wrighton KC, Hall EK. Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 2024; 9:e0105923. [PMID: 38259093 PMCID: PMC10878078 DOI: 10.1128/msystems.01059-23] [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: 10/02/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Nitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.
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Affiliation(s)
- J. M. Fadum
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado, USA
| | - M. A. Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - R. A. Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - K. C. Wrighton
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - E. K. Hall
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado, USA
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Emanuelsson EB, Arif M, Reitzner SM, Perez S, Lindholm ME, Mardinoglu A, Daub C, Sundberg CJ, Chapman MA. Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training. iScience 2024; 27:108638. [PMID: 38213622 PMCID: PMC10783619 DOI: 10.1016/j.isci.2023.108638] [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: 08/30/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Exercise training has tremendous systemic tissue-specific health benefits, but the molecular adaptations to long-term exercise training are not completely understood. We investigated the skeletal muscle proteome of highly endurance-trained, strength-trained, and untrained individuals and performed exercise- and sex-specific analyses. Of the 6,000+ proteins identified, >650 were differentially expressed in endurance-trained individuals compared with controls. Strikingly, 92% of the shared proteins with higher expression in both the male and female endurance groups were known mitochondrial. In contrast to the findings in endurance-trained individuals, minimal differences were found in strength-trained individuals and between females and males. Lastly, a co-expression network and comparative literature analysis revealed key proteins and pathways related to the health benefits of exercise, which were primarily related to differences in mitochondrial proteins. This network is available as an interactive database resource where investigators can correlate clinical data with global gene and protein expression data for hypothesis generation.
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Affiliation(s)
- Eric B. Emanuelsson
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, KTH – Royal Institute of Technology, 171 77 Stockholm, Sweden
| | - Stefan M. Reitzner
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sean Perez
- Department of Biology, Pomona College, Claremont, CA 91711, USA
| | - Maléne E. Lindholm
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH – Royal Institute of Technology, 171 77 Stockholm, Sweden
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London WC2R 2LS, UK
| | - Carsten Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, 171 77 Stockholm, Sweden
- Science for Life Laboratory, 171 65 Solna, Sweden
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mark A. Chapman
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Integrated Engineering, University of San Diego, San Diego, CA 92110, USA
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Goldkamp AK, Hagen DE. Implications of tRNA abundance on translation elongation across bovine tissues. Front Genet 2023; 14:1308048. [PMID: 38174049 PMCID: PMC10763252 DOI: 10.3389/fgene.2023.1308048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Translation is a crucial stage of gene expression. It may also act as an additional layer of regulation that plays an important role in gene expression and function. Highly expressed genes are believed to be codon-biased to support increased protein production, in which quickly translated codons correspond to highly abundant tRNAs. Synonymous SNPs, considered to be silent due to the degeneracy of the genetic code, may shift protein abundance and function through alterations in translational efficiency and suboptimal pairing to lowly abundant tRNAs. Methods: Here, we applied Quantitative Mature tRNA sequencing (QuantM-tRNAseq) and ribosome profiling across bovine tissues in order to investigate the relationship between tRNA expression and slowed translation. Results: Moreover, we have identified genes modulated at transcriptional and/or translational levels underlying tissue-specific biological processes. We have also successfully defined pausing sites that depict the regulatory information encoded within the open reading frame of transcripts, which could be related to translation rate and facilitate proper protein folding. This work offers an atlas of distinctive pausing sites across three bovine tissues, which provides an opportunity to predict codon optimality and understand tissue-specific mechanisms of regulating protein synthesis.
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Affiliation(s)
| | - Darren E. Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
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18
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Shaik SM, Cao Y, Gogola JV, Dodiya HB, Zhang X, Boutej H, Han W, Kriz J, Sisodia SS. Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of cortical microglia/macrophages in APPPS1-21 mice with an antibiotic-perturbed-microbiome. Mol Neurodegener 2023; 18:95. [PMID: 38104136 PMCID: PMC10725591 DOI: 10.1186/s13024-023-00668-7] [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: 04/19/2023] [Accepted: 10/14/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Microglia, the brain-resident macrophages perform immune surveillance and engage with pathological processes resulting in phenotype changes necessary for maintaining homeostasis. In preceding studies, we showed that antibiotic-induced perturbations of the gut microbiome of APPPS1-21 mice resulted in significant attenuation in Aβ amyloidosis and altered microglial phenotypes that are specific to male mice. The molecular events underlying microglial phenotypic transitions remain unclear. Here, by generating 'APPPS1-21-CD11br' reporter mice, we investigated the translational state of microglial/macrophage ribosomes during their phenotypic transition and in a sex-specific manner. METHODS Six groups of mice that included WT-CD11br, antibiotic (ABX) or vehicle-treated APPPS1-21-CD11br males and females were sacrificed at 7-weeks of age (n = 15/group) and used for immunoprecipitation of microglial/macrophage polysomes from cortical homogenates using anti-FLAG antibody. Liquid chromatography coupled to tandem mass spectrometry and label-free quantification was used to identify newly synthesized peptides isolated from polysomes. RESULTS We show that ABX-treatment leads to decreased Aβ levels in male APPPS1-21-CD11br mice with no significant changes in females. We identified microglial/macrophage polypeptides involved in mitochondrial dysfunction and altered calcium signaling that are associated with Aβ-induced oxidative stress. Notably, female mice also showed downregulation of newly-synthesized ribosomal proteins. Furthermore, male mice showed an increase in newly-synthesized polypeptides involved in FcγR-mediated phagocytosis, while females showed an increase in newly-synthesized polypeptides responsible for actin organization associated with microglial activation. Next, we show that ABX-treatment resulted in substantial remodeling of the epigenetic landscape, leading to a metabolic shift that accommodates the increased bioenergetic and biosynthetic demands associated with microglial polarization in a sex-specific manner. While microglia in ABX-treated male mice exhibited a metabolic shift towards a neuroprotective phenotype that promotes Aβ clearance, microglia in ABX-treated female mice exhibited loss of energy homeostasis due to persistent mitochondrial dysfunction and impaired lysosomal clearance that was associated with inflammatory phenotypes. CONCLUSIONS Our studies provide the first snapshot of the translational state of microglial/macrophage cells in a mouse model of Aβ amyloidosis that was subject to ABX treatment. ABX-mediated changes resulted in metabolic reprogramming of microglial phenotypes to modulate immune responses and amyloid clearance in a sex-specific manner. This microglial plasticity to support neuro-energetic homeostasis for its function based on sex paves the path for therapeutic modulation of immunometabolism for neurodegeneration.
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Affiliation(s)
- Shabana M Shaik
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Yajun Cao
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Joseph V Gogola
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hemraj B Dodiya
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Xulun Zhang
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hejer Boutej
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
| | - Weinong Han
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Jasna Kriz
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
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19
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Shimpi AA, Williams ED, Ling L, Tamir T, White FM, Fischbach C. Phosphoproteomic Changes Induced by Cell-Derived Matrix and Their Effect on Tumor Cell Migration and Cytoskeleton Remodeling. ACS Biomater Sci Eng 2023; 9:6835-6848. [PMID: 38015076 DOI: 10.1021/acsbiomaterials.3c01034] [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] [Indexed: 11/29/2023]
Abstract
Increased fibrotic extracellular matrix (ECM) deposition promotes tumor invasion, which is the first step of the metastatic cascade. Yet, the underlying mechanisms are poorly understood as conventional studies of tumor cell migration are often performed in 2D cultures lacking the compositional and structural complexity of native ECM. Moreover, these studies frequently focus on select candidate pathways potentially overlooking other relevant changes in cell signaling. Here, we combine a cell-derived matrix (CDM) model with phosphotyrosine phosphoproteomic analysis to investigate tumor cell migration on fibrotic ECM relative to standard tissue culture plastic (TCP). Our results suggest that tumor cells cultured on CDMs migrate faster and in a more directional manner than their counterparts on TCP. These changes in migration correlate with decreased cell spreading and increased cell elongation. While the formation of phosphorylated focal adhesion kinase (pFAK)+ adhesion complexes did not vary between TCP and CDMs, time-dependent phosphoproteomic analysis identified that the SRC family kinase LYN may be differentially regulated. Pharmacological inhibition of LYN decreased tumor cell migration and cytoskeletal rearrangement on CDMs and also on TCP, suggesting that LYN regulates tumor cell migration on CDMs in combination with other mechanisms. These data highlight how the combination of physicochemically complex in vitro systems with phosphoproteomics can help identify signaling mechanisms by which the fibrotic ECM regulates tumor cell migration.
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Affiliation(s)
- Adrian A Shimpi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Erik D Williams
- Department of Information Science, Cornell University, Ithaca, New York 14853, United States
| | - Lu Ling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Tigist Tamir
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 023139, United States
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York 14853, United States
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20
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Bryant OJ, Lastovka F, Powell J, Chung BYW. The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria. Nat Commun 2023; 14:8167. [PMID: 38071303 PMCID: PMC10710512 DOI: 10.1038/s41467-023-43759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Translational control in pathogenic bacteria is fundamental to gene expression and affects virulence and other infection phenotypes. We used an enhanced ribosome profiling protocol coupled with parallel transcriptomics to capture accurately the global translatome of two evolutionarily distant pathogenic bacteria-the Gram-negative bacterium Salmonella and the Gram-positive bacterium Listeria. We find that the two bacteria use different mechanisms to translationally regulate protein synthesis. In Salmonella, in addition to the expected correlation between translational efficiency and cis-regulatory features such as Shine-Dalgarno (SD) strength and RNA secondary structure around the initiation codon, our data reveal an effect of the 2nd and 3rd codons, where the presence of tandem lysine codons (AAA-AAA) enhances translation in both Salmonella and E. coli. Strikingly, none of these features are seen in efficiently translated Listeria transcripts. Instead, approximately 20% of efficiently translated Listeria genes exhibit 70 S footprints seven nt upstream of the authentic start codon, suggesting that these genes may be subject to a novel translational initiation mechanism. Our results show that SD strength is not a direct hallmark of translational efficiency in all bacteria. Instead, Listeria has evolved additional mechanisms to control gene expression level that are distinct from those utilised by Salmonella and E. coli.
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Affiliation(s)
- Owain J Bryant
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Centre for Structural Biology, National Cancer Institute, 21702, Frederick, MD, USA
| | - Filip Lastovka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Jessica Powell
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Betty Y-W Chung
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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21
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Li X, Li Y, Wei A, Wang Z, Huang H, Huang Q, Yang L, Gao Y, Zhu G, Liu Q, Li Y, Wei S, Wei D. Integrated transcriptomic and proteomic analyses of two sugarcane (Saccharum officinarum Linn.) varieties differing in their lodging tolerance. BMC PLANT BIOLOGY 2023; 23:601. [PMID: 38030995 PMCID: PMC10685470 DOI: 10.1186/s12870-023-04622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Lodging seriously affects sugarcane stem growth and sugar accumulation, reduces sugarcane yield and sucrose content, and impedes mechanization. However, the molecular mechanisms underlying sugarcane lodging tolerance remain unclear. In this study, comprehensive transcriptomic and proteomic analyses were performed to explore the differential genetic regulatory mechanisms between upright (GT42) and lodged (GF98-296) sugarcane varieties. RESULTS The stain test showed that GT42 had more lignin and vascular bundles in the stem than GF98-296. The gene expression analysis revealed that the genes that were differentially expressed between the two varieties were mainly involved in the phenylpropanoid pathway at the growth stage. The protein expression analysis indicated that the proteins that were differentially expressed between the two varieties were related to the synthesis of secondary metabolites, the process of endocytosis, and the formation of aminoacyl-tRNA. Time-series analysis revealed variations in differential gene expression patterns between the two varieties, whereas significant protein expression trends in the two varieties were largely consistent, except for one profile. The expression of CYP84A, 4CL, and CAD from the key phenylpropanoid biosynthetic pathway was enhanced in GT42 at stage 2 but suppressed in GF98-296 at the growth stage. Furthermore, the expression of SDT1 in the nicotinate and nicotinamide metabolism was enhanced in GT42 cells but suppressed in GF98-296 cells at the growth stage. CONCLUSION Our findings provide reference data for mining lodging tolerance-related genes that are expected to facilitate the selective breeding of sugarcane varieties with excellent lodging tolerance.
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Affiliation(s)
- Xiang Li
- Guangxi Subtropical Crops Research Institute, Nanning, 530002, China
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yijie Li
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Ailin Wei
- Baise Institue of Agricultural Sciences, Baise, 533612, China
| | - Zeping Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Hairong Huang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Quyan Huang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Litao Yang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yijing Gao
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Guanghu Zhu
- Center for Applied Mathematics of Guangxi (GUET), Guilin, 541004, China
| | - Qihuai Liu
- Center for Applied Mathematics of Guangxi (GUET), Guilin, 541004, China
| | - Yangrui Li
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Afairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research InstituteGuangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Shaolong Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530002, China.
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Debin Wei
- Baise Institue of Agricultural Sciences, Baise, 533612, China.
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22
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Wang X, Deng K, Tao J, Zou J, Du Y, Dai L. RIPK1 polymorphisms and expression levels: impact on genetic susceptibility and clinical outcome of epithelial ovarian cancer. Cancer Cell Int 2023; 23:290. [PMID: 37996860 PMCID: PMC10668399 DOI: 10.1186/s12935-023-03139-7] [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: 09/15/2021] [Accepted: 10/30/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The aim of this study was to explore the associations of RIPK1 polymorphisms, plasma levels and mRNA expression with susceptibility to epithelial ovarian cancer (EOC) and clinical outcome. METHODS Three hundred and nineteen EOC patients included in a 60-month follow-up program and 376 controls were enrolled. Two tag SNPs (rs6907943 and rs9392453) of RIPK1 were genotyped using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. Plasma levels of RIPK1 and RIPK1 mRNA expression in white blood cells were determined by ELISA and qPCR, respectively. RESULTS For rs9392453, significantly increased EOC risk was found to be associated with C allele (P = 0.002, OR = 1.49, 95%CI 1.15-1.92), and with CT/CC genotypes in the dominant genetic model (P = 0.006, OR = 1.54, 95%CI 1.12-2.08). CC haplotype (rs6907943-rs9392453) was associated with increased EOC susceptibility. CC genotype of rs6907943 and CT/CC genotypes of rs9392453 were associated with early onset (age ≤ 50 years) of EOC (OR = 2.5, 95%CI 1.03-5.88, and OR = 1.64, 95%CI 1.04-2.63, respectively). AC genotype of rs6907943 was associated with better overall survival of EOC patients in the over-dominant genetic model (P = 0.035, HR = 0.41, 95%CI 0.18-0.94). Multivariate survival analysis identified the AC genotype of rs6907943 as an independent protective factor for survival of early onset patients (P = 0.044, HR = 0.12, 95%CI 0.02-0.95). Compared to controls, significantly increased plasma levels of RIPK1 and reduced RIPK1 mRNA expression were observed in patients. CONCLUSIONS Our results suggest that tag SNPs of RIPK1, increased plasma levels of RIPK1 protein and reduced RIPK1 mRNA expression in white blood cells, may influence the susceptibility to EOC. SNP rs6907943 may be a useful marker to distinguish EOC patients with high risk of death.
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Affiliation(s)
- Xuedong Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Chengdu, Sichuan, China
| | - Kui Deng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Chengdu, Sichuan, China
| | - Jing Tao
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Juan Zou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Chengdu, Sichuan, China
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yiting Du
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Chengdu, Sichuan, China
| | - Li Dai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Chengdu, Sichuan, China.
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- Medical Big Data Center, Sichuan University, Chengdu, Sichuan, China.
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Thani AB. DNA supercoiling and regulation of intrinsic β-lactamase in pathogenic Escherichia coli. Arch Microbiol 2023; 205:385. [PMID: 37980630 DOI: 10.1007/s00203-023-03716-4] [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: 07/03/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023]
Abstract
This review addresses the involvement of DNA supercoiling in the development of virulence and antibiotic profiles for uropathogenic Escherichia coli and the emergence of new pathotypes such as strain ST131 (serotype O25:H4). The mechanism suggests a role for topoisomerase enzymes and associated mutations in altering the chromosomal supercoiling state and introducing the required DNA twists for expression of intrinsic β-lactamase by ampC and certain virulence factors. In Escherichia coli, constitutive hyperexpression of intrinsic ampC is associated with specific mutations in the promoter and attenuator regions. However, many reports have documented the involvement of slow growth interventions in the expression of intrinsic resistance determinants. There is evidence that a stationary phase transcriptional switch protein, "BolA," is involved in the expression of the intrinsic ampC gene under starvation conditions. The process involves changes in the activity of the enzyme "gyrase," which leads to a change in the chromosomal DNA topology. Consequently, the DNA is relaxed, and the expression of the bolA gene is upregulated. The evolution of the extraintestinal pathogenic E. coli strain ST131 has demonstrated successful adaptability to various stress conditions and conferred compensatory mutations that endowed the microbe with resistance to fluoroquinolones and β-lactams. The results of this study provided new insights into the evidence for the influence of DNA topology in the expression of virulence genes and various determinants of antibiotic resistance (e.g., the intrinsic ampC gene) in Escherichia coli pathotypes.
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Affiliation(s)
- Ali Bin Thani
- Department of Biology, College of Science, University of Bahrain, Zallaq, Kingdom of Bahrain.
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Li Z, Zhang C, Zhang Q, Dong Y, Sha X, Jiang M, Yan J, Wang W, Li H, Zhang Y, Zhou YL. Identification of a potential bioinformatics-based biomarker in keloids and its correlation with immune infiltration. Eur J Med Res 2023; 28:476. [PMID: 37915086 PMCID: PMC10621210 DOI: 10.1186/s40001-023-01421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/01/2023] [Indexed: 11/03/2023] Open
Abstract
Keloid formation is a pathological consequence resulting from cutaneous irritation and injury, primarily attributed to excessive collagen matrix deposition and fibrous tissue proliferation. Chronic inflammation, left uncontrolled over an extended period, also stands as a substantial contributing factor. The precise mechanisms underlying keloid formation remain unclear. Therefore, this study aimed to identify key genes for diagnostic purposes. To achieve this, we used two Gene Expression Omnibus (GEO) data sets to identify differentially expressed genes. We identified one particular gene, homeobox C9 (HOXC9), using a thorough strategy involving two algorithms (least absolute shrinkage and selection operator and support vector machine-recursive feature elimination) and weighted gene co-expression network analysis. We then assessed its expression in normal and keloid tissues. In addition, we explored its temporal expression patterns via Mfuzz time clustering analysis. In our comprehensive analysis, we observed that immune infiltration, as well as cell proliferation, are crucial to keloid formation. Thus, we investigated immune cell infiltration in the keloid and normal groups, as well as the correlation between HOXC9 and these immune cells. It was found that HOXC9 was closely associated with the immune microenvironment of keloids. This shows that HOXC9 can serve as a potential biomarker and therapeutic target for keloids.
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Affiliation(s)
- Zihan Li
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University, Nantong, China
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Chuwei Zhang
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University, Nantong, China
| | - Qingrong Zhang
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yipeng Dong
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University, Nantong, China
| | - Xinyu Sha
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Ming Jiang
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University, Nantong, China
| | - Jun Yan
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China
- Nantong University, Nantong, China
| | - Wenmiao Wang
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Houqiang Li
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Yi Zhang
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China.
| | - You Lang Zhou
- Department of Burn and Plastic Surgery, Affiliated Hospital of Nantong University, Nantong, China.
- The Hand Surgery Research Center, Department of Hand Surgery, Affiliated Hospital of Nantong University, Nantong, China.
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25
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Proschinger S, Schenk A, Weßels I, Donath L, Rappelt L, Metcalfe AJ, Zimmer P. Intensity- and time-matched acute interval and continuous endurance exercise similarly induce an anti-inflammatory environment in recreationally active runners: focus on PD-1 expression in T regs and the IL-6/IL-10 axis. Eur J Appl Physiol 2023; 123:2575-2584. [PMID: 37336816 PMCID: PMC10615943 DOI: 10.1007/s00421-023-05251-y] [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: 12/16/2022] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
PURPOSE Acute exercise elicits a transient anti-inflammatory state during the early recovery period. Since recent studies reported on regimen-specific effects on immune-related humoral factors and cellular subsets, this study compared the effects of intensity- and time-matched acute interval and continuous exercise on peripheral anti-inflammatory cellular and humoral immune parameters with a particular focus on the PD-1 expression in CD4+ regulatory T cells (Tregs). METHODS Twenty-four recreationally active runners (age: 29.7 ± 4.3 years, BMI: 22.2 ± 2.4, VO2peak: 56.6 ± 6.4 ml × kg-1 × min-1) participated in this crossover RCT. Each subject conducted a moderate continuous (MCE) and a high-intensity interval exercise (HIIE) session in a counterbalanced design. Blood was drawn before, immediately after, and 1 h after exercise. Treg subsets and levels of PD-1 and Foxp3 were assessed by flow cytometry. Serum levels of IL-10 and IL-6 were quantified by ELISA. RESULTS PD-1 levels on Tregs increased within the recovery period after HIIE (p < .001) and MCE (p < 0.001). Total counts of Tregs (HIIE: p = 0.044; MCE: p = .021), naïve Tregs (HIIE: p < 0.001; MCE: p < 0.001), and PD-1+ effector Tregs (eTregs) (HIIE: p = .002) decreased 1 h after exercise. IL-10 increased 1 h after HIIE (p < 0.001) and MCE (p = 0.018), while IL-6 increased immediately after both HIIE (p = 0.031) and MCE (p = 0.021). Correlations between changes in IL-6 and IL-10 (p = 0.017, r = 0.379) and baseline VO2peak and Treg frequency (p = 0.002, r = 0.660) were identified. CONCLUSION This is the first study that investigates PD-1 expression in circulating Tregs after acute exercise, revealing an increase in PD-1 levels on eTregs during the early recovery period after intensity- and time-matched HIIE and MCE. Future studies are needed to investigate the PD-1 signalosome in eTregs, together with the expression of key effector molecules (i.e., IL-10, TGF-β, IL-35, CTLA-4) to elucidate PD-1-dependent changes in cellular function. Based on changes in serum cytokines, this study further reveals a regimen-independent establishment of an anti-inflammatory milieu and underpins the role of the IL-6/IL-10 axis.
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Affiliation(s)
- Sebastian Proschinger
- Division of Performance and Health (Sports Medicine), TU Dortmund University, Institute for Sport and Sport Science, 44227, Dortmund, Germany
| | - Alexander Schenk
- Division of Performance and Health (Sports Medicine), TU Dortmund University, Institute for Sport and Sport Science, 44227, Dortmund, Germany
| | - Inga Weßels
- Faculty of Medicine, RWTH Aachen University, Institute of Immunology, 52074, Aachen, Germany
| | - Lars Donath
- Department of Intervention Research in Exercise Training, German Sport University Cologne, Cologne, Germany
| | - Ludwig Rappelt
- Department of Intervention Research in Exercise Training, German Sport University Cologne, Cologne, Germany
| | - Alan J Metcalfe
- Department for Molecular and Cellular Sports Medicine, Institute of Cardiovascular Research and Sports Medicine, German Sport University Cologne, Cologne, Germany
| | - Philipp Zimmer
- Division of Performance and Health (Sports Medicine), TU Dortmund University, Institute for Sport and Sport Science, 44227, Dortmund, Germany.
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Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023; 24:739-754. [PMID: 37365273 DOI: 10.1038/s41576-023-00618-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The interplay between chromatin, transcription factors and genes generates complex regulatory circuits that can be represented as gene regulatory networks (GRNs). The study of GRNs is useful to understand how cellular identity is established, maintained and disrupted in disease. GRNs can be inferred from experimental data - historically, bulk omics data - and/or from the literature. The advent of single-cell multi-omics technologies has led to the development of novel computational methods that leverage genomic, transcriptomic and chromatin accessibility information to infer GRNs at an unprecedented resolution. Here, we review the key principles of inferring GRNs that encompass transcription factor-gene interactions from transcriptomics and chromatin accessibility data. We focus on the comparison and classification of methods that use single-cell multimodal data. We highlight challenges in GRN inference, in particular with respect to benchmarking, and potential further developments using additional data modalities.
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Affiliation(s)
- Pau Badia-I-Mompel
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Lorna Wessels
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty, MannHeim Heidelberg University, Mannheim, Germany
| | - Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Rémi Trimbour
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, Paris, France
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
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Harman JC, Pivodic A, Nilsson AK, Boeck M, Yagi H, Neilsen K, Ko M, Yang J, Kinter M, Hellström A, Fu Z. Postnatal hyperglycemia alters amino acid profile in retinas (model of Phase I ROP). iScience 2023; 26:108021. [PMID: 37841591 PMCID: PMC10568433 DOI: 10.1016/j.isci.2023.108021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/03/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023] Open
Abstract
Nutritional deprivation occurring in most preterm infants postnatally can induce hyperglycemia, a significant and independent risk factor for suppressing physiological retinal vascularization (Phase I retinopathy of prematurity (ROP)), leading to compensatory but pathological neovascularization. Amino acid supplementation reduces retinal neovascularization in mice. Little is known about amino acid contribution to Phase I ROP. In mice modeling hyperglycemia-associated Phase I ROP, we found significant changes in retinal amino acids (including most decreased L-leucine, L-isoleucine, and L-valine). Parenteral L-isoleucine suppressed physiological retinal vascularization. In premature infants, severe ROP was associated with a higher mean intake of parenteral versus enteral amino acids in the first two weeks of life after adjustment for treatment group, gestational age at birth, birth weight, and sex. The number of days with parenteral amino acids support independently predicted severe ROP. Further understanding and modulating amino acids may help improve nutritional intervention and prevent Phase I ROP.
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Affiliation(s)
- Jarrod C. Harman
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aldina Pivodic
- The Sahlgrenska Centre for Pediatric Ophthalmology Research, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders K. Nilsson
- The Sahlgrenska Centre for Pediatric Ophthalmology Research, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Myriam Boeck
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Hitomi Yagi
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Katherine Neilsen
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Minji Ko
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jay Yang
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Kinter
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Ann Hellström
- The Sahlgrenska Centre for Pediatric Ophthalmology Research, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Zhongjie Fu
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Kjær C, Palasca O, Barzaghi G, Bak LK, Durhuus RKJ, Jakobsen E, Pedersen L, Bartels ED, Woldbye DPD, Pinborg LH, Jensen LJ. Differential Expression of the β3 Subunit of Voltage-Gated Ca 2+ Channel in Mesial Temporal Lobe Epilepsy. Mol Neurobiol 2023; 60:5755-5769. [PMID: 37341859 PMCID: PMC10471638 DOI: 10.1007/s12035-023-03426-4] [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: 12/21/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
The purpose of this study was to identify and validate new putative lead drug targets in drug-resistant mesial temporal lobe epilepsy (mTLE) starting from differentially expressed genes (DEGs) previously identified in mTLE in humans by transcriptome analysis. We identified consensus DEGs among two independent mTLE transcriptome datasets and assigned them status as "lead target" if they (1) were involved in neuronal excitability, (2) were new in mTLE, and (3) were druggable. For this, we created a consensus DEG network in STRING and annotated it with information from the DISEASES database and the Target Central Resource Database (TCRD). Next, we attempted to validate lead targets using qPCR, immunohistochemistry, and Western blot on hippocampal and temporal lobe neocortical tissue from mTLE patients and non-epilepsy controls, respectively. Here we created a robust, unbiased list of 113 consensus DEGs starting from two lists of 3040 and 5523 mTLE significant DEGs, respectively, and identified five lead targets. Next, we showed that CACNB3, a voltage-gated Ca2+ channel subunit, was significantly regulated in mTLE at both mRNA and protein level. Considering the key role of Ca2+ currents in regulating neuronal excitability, this suggested a role for CACNB3 in seizure generation. This is the first time changes in CACNB3 expression have been associated with drug-resistant epilepsy in humans, and since efficient therapeutic strategies for the treatment of drug-resistant mTLE are lacking, our finding might represent a step toward designing such new treatment strategies.
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Affiliation(s)
- Christina Kjær
- Biomedical Laboratory Science, Department of Technology, Faculty of Health and Technology, University College Copenhagen, Sigurdsgade 26, 1St, 2200 Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Oana Palasca
- Disease Systems Biology Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Guido Barzaghi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Lasse K. Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
| | - Rúna K. J. Durhuus
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Specific Pharma A/S, Borgmester Christiansens Gade 40, 2450 Copenhagen, SV Denmark
| | - Emil Jakobsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Takeda Pharma A/S, Delta Park 45, 2665 Vallensbaek Strand, Denmark
| | - Louise Pedersen
- Biomedical Laboratory Science, Department of Technology, Faculty of Health and Technology, University College Copenhagen, Sigurdsgade 26, 1St, 2200 Copenhagen, Denmark
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
| | - Emil D. Bartels
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David P. D. Woldbye
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars H. Pinborg
- Epilepsy Clinic & Neurobiology Research Unit, Copenhagen University Hospital, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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Díaz-Dinamarca DA, Salazar ML, Escobar DF, Castillo BN, Valdebenito B, Díaz P, Manubens A, Salazar F, Troncoso MF, Lavandero S, Díaz J, Becker MI, Vásquez AE. Surface immunogenic protein from Streptococcus agalactiae and Fissurella latimarginata hemocyanin are TLR4 ligands and activate MyD88- and TRIF dependent signaling pathways. Front Immunol 2023; 14:1186188. [PMID: 37790926 PMCID: PMC10544979 DOI: 10.3389/fimmu.2023.1186188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023] Open
Abstract
The development of vaccine adjuvants is of interest for the management of chronic diseases, cancer, and future pandemics. Therefore, the role of Toll-like receptors (TLRs) in the effects of vaccine adjuvants has been investigated. TLR4 ligand-based adjuvants are the most frequently used adjuvants for human vaccines. Among TLR family members, TLR4 has unique dual signaling capabilities due to the recruitment of two adapter proteins, myeloid differentiation marker 88 (MyD88) and interferon-β adapter inducer containing the toll-interleukin-1 receptor (TIR) domain (TRIF). MyD88-mediated signaling triggers a proinflammatory innate immune response, while TRIF-mediated signaling leads to an adaptive immune response. Most studies have used lipopolysaccharide-based ligands as TLR4 ligand-based adjuvants; however, although protein-based ligands have been proven advantageous as adjuvants, their mechanisms of action, including their ability to undergo structural modifications to achieve optimal immunogenicity, have been explored less thoroughly. In this work, we characterized the effects of two protein-based adjuvants (PBAs) on TLR4 signaling via the recruitment of MyD88 and TRIF. As models of TLR4-PBAs, we used hemocyanin from Fissurella latimarginata (FLH) and a recombinant surface immunogenic protein (rSIP) from Streptococcus agalactiae. We determined that rSIP and FLH are partial TLR4 agonists, and depending on the protein agonist used, TLR4 has a unique bias toward the TRIF or MyD88 pathway. Furthermore, when characterizing gene products with MyD88 and TRIF pathway-dependent expression, differences in TLR4-associated signaling were observed. rSIP and FLH require MyD88 and TRIF to activate nuclear factor kappa beta (NF-κB) and interferon regulatory factor (IRF). However, rSIP and FLH have a specific pattern of interleukin 6 (IL-6) and interferon gamma-induced protein 10 (IP-10) secretion associated with MyD88 and TRIF recruitment. Functionally, rSIP and FLH promote antigen cross-presentation in a manner dependent on TLR4, MyD88 and TRIF signaling. However, FLH activates a specific TRIF-dependent signaling pathway associated with cytokine expression and a pathway dependent on MyD88 and TRIF recruitment for antigen cross-presentation. Finally, this work supports the use of these TLR4-PBAs as clinically useful vaccine adjuvants that selectively activate TRIF- and MyD88-dependent signaling to drive safe innate immune responses and vigorous Th1 adaptive immune responses.
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Affiliation(s)
- Diego A. Díaz-Dinamarca
- Sección de Biotecnología, Subdepartamento, Innovación, Desarrollo, Transferencia Tecnológica (I+D+T) y Evaluación de Tecnologías Sanitarias (ETESA), Instituto de Salud Pública, Santiago, Chile
- Laboratorio de Inmunología, Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile
- Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Michelle L. Salazar
- Laboratorio de Inmunología, Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile
| | - Daniel F. Escobar
- Sección de Biotecnología, Subdepartamento, Innovación, Desarrollo, Transferencia Tecnológica (I+D+T) y Evaluación de Tecnologías Sanitarias (ETESA), Instituto de Salud Pública, Santiago, Chile
| | - Byron N. Castillo
- Laboratorio de Inmunología, Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile
| | - Bastián Valdebenito
- Sección de Biotecnología, Subdepartamento, Innovación, Desarrollo, Transferencia Tecnológica (I+D+T) y Evaluación de Tecnologías Sanitarias (ETESA), Instituto de Salud Pública, Santiago, Chile
| | - Pablo Díaz
- Sección de Biotecnología, Subdepartamento, Innovación, Desarrollo, Transferencia Tecnológica (I+D+T) y Evaluación de Tecnologías Sanitarias (ETESA), Instituto de Salud Pública, Santiago, Chile
| | | | - Fabián Salazar
- Laboratorio de Inmunología, Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile
- Investigación y Desarrollo, BIOSONDA S.A., Santiago, Chile
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
| | - Mayarling F. Troncoso
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Químicas y Farmacéuticas and Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Químicas y Farmacéuticas and Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Janepsy Díaz
- Departamento Agencia Nacional de Dispositivos Médicos, Innovación y Desarrollo, Instituto de Salud Pública de Chile, Santiago, Chile
| | - María Inés Becker
- Laboratorio de Inmunología, Fundación Ciencia y Tecnología para el Desarrollo (FUCITED), Santiago, Chile
- Investigación y Desarrollo, BIOSONDA S.A., Santiago, Chile
| | - Abel E. Vásquez
- Sección de Biotecnología, Subdepartamento, Innovación, Desarrollo, Transferencia Tecnológica (I+D+T) y Evaluación de Tecnologías Sanitarias (ETESA), Instituto de Salud Pública, Santiago, Chile
- Facultad de Ciencias de la Salud, Escuela de Medicina, Universidad del Alba, Santiago, Chile
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Stenberg K, Novotny GW, Lutz TA, Mandrup-Poulsen T, Bjørnvad CR. Obesity-induced changes in gene expression in feline adipose and skeletal muscle tissue. J Anim Physiol Anim Nutr (Berl) 2023; 107:1262-1278. [PMID: 36591865 DOI: 10.1111/jpn.13802] [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: 03/21/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Indoor-confined cats are prone to developing obesity due to a sedentary life and an energy intake exceeding energy requirements. As in humans, feline obesity decreases insulin sensitivity and increases the risk of developing feline diabetes mellitus, but the pathophysiological mechanisms are currently poorly understood. Human obesity-related metabolic alterations seem to relate to changes in the expression of genes involved in glucose metabolism, insulin action and inflammation. The objective of the current study was to investigate changes in the expression of genes relating to obesity, glucose metabolism and inflammation in cats with non-experimentally induced obesity. Biopsies from the sartorius muscle and subcutaneous adipose tissue were obtained from 73 healthy, neutered, indoor-confined domestic shorthaired cats ranging from lean to obese. Quantification of obesity-related gene expression levels relative to glyceraldehyde-3-phosphate dehydrogenase was performed by quantitative real-time polymerase chain reaction. A negative association between obesity and adiponectin expression was observed in the adipose tissue (mean ± SD; normal weight, 27.30 × 10-3 ± 77.14 × 10-3 ; overweight, 2.89 × 10-3 ± 0.38 × 10-3 and obese, 2.93 × 10-3 ± 4.20 × 10-3 , p < 0.05). In muscle, the expression of peroxisome proliferative activated receptor-γ2 and plasminogen activator inhibitor-1 was increased in the obese compared to the normal-weight cats, and resistin was increased in the normal-weight compared to the overweight cats. There were no detectable obesity-related changes in the messenger RNA levels of inflammatory cytokines. In conclusion, a possible obesity-related low-grade inflammation caused by increased expression of key proinflammatory regulators was not observed. This could imply that the development of feline obesity and ensuing insulin resistance may not be based on tissue-derived inflammation, but caused by several determining factors, many of which still need further investigation.
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Affiliation(s)
- Kathrine Stenberg
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guy W Novotny
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Departments of Hematology/Pathology, Herlev Hospital, Herlev, Denmark
| | - Thomas A Lutz
- Institute of Veterinary Physiology, Vetsuisse-Faculty University of Zurich, Zurich, Switzerland
| | | | - Charlotte Reinhard Bjørnvad
- Department of Veterinary Clinical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Zlatic SA, Werner E, Surapaneni V, Lee CE, Gokhale A, Singleton K, Duong D, Crocker A, Gentile K, Middleton F, Dalloul JM, Liu WLY, Patgiri A, Tarquinio D, Carpenter R, Faundez V. Systemic Proteome Phenotypes Reveal Defective Metabolic Flexibility in Mecp2 Mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535431. [PMID: 37066332 PMCID: PMC10103972 DOI: 10.1101/2023.04.03.535431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Genes mutated in monogenic neurodevelopmental disorders are broadly expressed. This observation supports the concept that monogenic neurodevelopmental disorders are systemic diseases that profoundly impact neurodevelopment. We tested the systemic disease model focusing on Rett syndrome, which is caused by mutations in MECP2. Transcriptomes and proteomes of organs and brain regions from Mecp2-null mice as well as diverse MECP2-null male and female human cells were assessed. Widespread changes in the steady-state transcriptome and proteome were identified in brain regions and organs of presymptomatic Mecp2-null male mice as well as mutant human cell lines. The extent of these transcriptome and proteome modifications was similar in cortex, liver, kidney, and skeletal muscle and more pronounced than in the hippocampus and striatum. In particular, Mecp2- and MECP2-sensitive proteomes were enriched in synaptic and metabolic annotated gene products, the latter encompassing lipid metabolism and mitochondrial pathways. MECP2 mutations altered pyruvate-dependent mitochondrial respiration while maintaining the capacity to use glutamine as a mitochondrial carbon source. We conclude that mutations in Mecp2/MECP2 perturb lipid and mitochondrial metabolism systemically limiting cellular flexibility to utilize mitochondrial fuels.
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Affiliation(s)
| | - Erica Werner
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Veda Surapaneni
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Chelsea E. Lee
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Kaela Singleton
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Duc Duong
- Department of Biochemistry, Emory University, Atlanta, GA, USA, 30322
| | - Amanda Crocker
- Program in Neuroscience, Middlebury College, Middlebury, Vermont 05753
| | - Karen Gentile
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Frank Middleton
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Joseph Martin Dalloul
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | - William Li-Yun Liu
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | - Anupam Patgiri
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | | | | | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
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Fang K, Ma J, Wang X, Xu Z, Zhang Z, Li P, Wang R, Wang J, Sun C, Dong Z. Flow-cytometric cell sorting coupled with UV mutagenesis for improving pectin lyase expression. Front Bioeng Biotechnol 2023; 11:1251342. [PMID: 37720319 PMCID: PMC10502208 DOI: 10.3389/fbioe.2023.1251342] [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: 07/01/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction: Alkaline pectin lyase is an important enzyme with a wide range of applications in industrial production, It has been widely used in many important fields such as fruit juice processing and extraction, the dyeing and processing of cotton and linen textiles, degumming plant fibers, environmental industrial wastewater treatment, and pulp and paper production. PGLA-rep4 was previously generated as a modified alkaline pectin lyase with high specific activity at pH 11.0°C and 70°C. However, the pre-constructed high-activity pectin lyase expression strains are still difficult to apply in industrial production due to their limited enzymatic activity. We hope to solve these problems by combining modern breeding techniques with high-throughput equipment to rapidly screen alkaline pectin lyase with higher enzymatic activity and lower cost. Methods: We fused the genes encoding PGLA-rep4 and fluorescent protein egfp using a flexible linker peptide and ligated them into a temperature-sensitive plasmid, pKD46. The constructed screening plasmid pKD46-PGLA-rep4-egfp was then transformed into an expression host and screened via flow-cytometric cell sorting coupled with UV mutagenesis. Results: Following mutagenesis, primary screening, and secondary screening, the high-expression strain, named Escherichia coli BL21/1G3, was obtained. The screening plasmid pKD46-PGLA-rep4-egfp was eliminated, and the original expression plasmid pET28a-PGLA-rep4 was then retransformed into the mutant strains. After induction and fermentation, pectin lyase activity in E. coli BL21/1G3 was significantly increased (1.37-fold relative to that in the parental E. coli BL21/PGLA-rep4 strain, p < 0.001), and the highest activity was 230, 240 U/mL at 144 h. Genome sequencing revealed that genes encoding ribonuclease E (RNase E) and diadenosine tetraphosphatase (ApaH) of E. coli BL21/1G3 were mutated compared to the sequence in the original E. coli BL21 (DE3) strain, which could be associated with increased enzyme expression. Discussion: Our work provides an effective method for the construction of strains expressing pectin lyase at high levels.
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Affiliation(s)
- Ke Fang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Jun Ma
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Xinyu Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziting Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziyang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Chuying Sun
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
| | - Ziyang Dong
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- School of Bioengineering, Qilu University of Technology, Jinan, Shandong, China
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33
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Saastad SA, Skjervold AH, Ytterhus B, Engstrøm MJ, Bofin AM. PD-L1 protein expression in breast cancer. J Clin Pathol 2023:jcp-2023-208942. [PMID: 37553245 DOI: 10.1136/jcp-2023-208942] [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: 04/25/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
AIMS The immune checkpoint marker, Programmed cell death-ligand 1 (PD-L1), is expressed by both cancer epithelial cells and tumour-infiltrating immune cells (TICs) thus constituting a potential target for immunotherapy. This is of particular interest in triple negative breast cancer. In this study, we assessed the prognostic value of PD-L1 expression in tumour epithelial cells and TICs in a series of patients with breast cancer with long-term follow-up, and associations between PD-L1 expression and histopathological type and grade, proliferation and molecular subtype. METHODS Using immunohistochemistry for PD-L1 in tissue microarrays, we assessed PD-L1 expression in 821 tumours. Expression of PD-L1 was assessed separately in the epithelial and stromal compartments and classified as <1%, ≥1% to <10% or ≥10% positive staining cells. We correlated PD-L1 expression in tumour epithelial cells and TICs with tumour characteristics using Pearson's χ2 test, and prognosis by cumulative incidence of death from breast cancer and Cox regression analyses. RESULTS We found membranous staining in ≥1% of tumour epithelial cells in 53/821 cases (6.5%). Of these, 21 (2.6%) were ≥10%. Among TICs, staining (≥1%) was seen in 144/821 cases (17.6%). Of these, 62 were ≥10% (7.6%). PD-L1 was associated with high histopathological grade and proliferation, and the medullary and metaplastic patterns. In TICs, PD-L1 ≥1% found in 22/34 (34.4%) human epidermal growth factor receptor 2 type and 29/58 (50%) basal phenotype. An independent association between PD-L1 expression and prognosis was not observed. CONCLUSIONS PD-L1 is expressed more frequently in TICs than tumour epithelial cells. Expression in TICs is associated with aggressive tumour characteristics and non-luminal tumours but not with prognosis.
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Affiliation(s)
- Sigurd A Saastad
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anette H Skjervold
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Borgny Ytterhus
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Monica Jernberg Engstrøm
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Sugrery, St. Olav's Hospital Trondheim University Hospital, Trondheim, Norway
| | - Anna M Bofin
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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34
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Masson SWC, Madsen S, Cooke KC, Potter M, Vegas AD, Carroll L, Thillainadesan S, Cutler HB, Walder KR, Cooney GJ, Morahan G, Stöckli J, James DE. Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance. eLife 2023; 12:RP86961. [PMID: 37494090 PMCID: PMC10371229 DOI: 10.7554/elife.86961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. 'Diversity Outbred in Australia (DOz)' is a population of genetically unique mice with profound metabolic heterogeneity. We leveraged this variance to explore skeletal muscle's contribution to whole-body insulin action through metabolic phenotyping and skeletal muscle proteomics of 215 DOz mice. Linear modelling identified 553 proteins that associated with whole-body insulin sensitivity (Matsuda Index) including regulators of endocytosis and muscle proteostasis. To enrich for causality, we refined this network by focusing on negatively associated, genetically regulated proteins, resulting in a 76-protein fingerprint of insulin resistance. We sought to perturb this network and restore insulin action with small molecules by integrating the Broad Institute Connectivity Map platform and in vitro assays of insulin action using the Prestwick chemical library. These complementary approaches identified the antibiotic thiostrepton as an insulin resistance reversal agent. Subsequent validation in ex vivo insulin-resistant mouse muscle and palmitate-induced insulin-resistant myotubes demonstrated potent insulin action restoration, potentially via upregulation of glycolysis. This work demonstrates the value of a drug-centric framework to validate systems-level analysis by identifying potential therapeutics for insulin resistance.
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Affiliation(s)
- Stewart W C Masson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Kristen C Cooke
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Alexis Diaz Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Luke Carroll
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, Australia
| | - Senthil Thillainadesan
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Harry B Cutler
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Ken R Walder
- School of Medicine, Deakin University, Geelong, Australia
| | - Gregory J Cooney
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Murdoch, Australia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Camperdown, Australia
- School of Medical Sciences University of Sydney, Sydney, Australia
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35
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Wei J, Dai S, Yan Y, Li S, Yang P, Zhu R, Huang T, Li X, Duan Y, Wang Z, Ji W, Si W. Spatiotemporal proteomic atlas of multiple brain regions across early fetal to neonatal stages in cynomolgus monkey. Nat Commun 2023; 14:3917. [PMID: 37400444 PMCID: PMC10317979 DOI: 10.1038/s41467-023-39411-7] [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: 10/14/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
Fetal stages are critical periods for brain development. However, the protein molecular signature and dynamics of the human brain remain unclear due to sampling difficulty and ethical limitations. Non-human primates present similar developmental and neuropathological features to humans. This study constructed a spatiotemporal proteomic atlas of cynomolgus macaque brain development from early fetal to neonatal stages. Here we showed that (1) the variability across stages was greater than that among brain regions, and comparisons of cerebellum vs. cerebrum and cortical vs. subcortical regions revealed region-specific dynamics across early fetal to neonatal stages; (2) fluctuations in abundance of proteins associated with neural disease suggest the risk of nervous disorder at early fetal stages; (3) cross-species analysis (human, monkey, and mouse) and comparison between proteomic and transcriptomic data reveal the proteomic specificity and genes with mRNA/protein discrepancy. This study provides insight into fetal brain development in primates.
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Affiliation(s)
- Jingkuan Wei
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Shaoxing Dai
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Yaping Yan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Shulin Li
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Pengpeng Yang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Ran Zhu
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
| | - Tianzhuang Huang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Xi Li
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Yanchao Duan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China
| | - Zhengbo Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
- Chinese Primate Biomedical Research Alliance (CPBRA), 650500, Kunming, Yunnan, China.
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, 650500, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Primate Biomedical Research, 650500, Kunming, Yunnan, China.
- Chinese Primate Biomedical Research Alliance (CPBRA), 650500, Kunming, Yunnan, China.
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36
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Zeng H, Huang J, Ren J, Wang CK, Tang Z, Zhou H, Zhou Y, Shi H, Aditham A, Sui X, Chen H, Lo JA, Wang X. Spatially resolved single-cell translatomics at molecular resolution. Science 2023; 380:eadd3067. [PMID: 37384709 PMCID: PMC11146668 DOI: 10.1126/science.add3067] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/07/2023] [Indexed: 07/01/2023]
Abstract
The precise control of messenger RNA (mRNA) translation is a crucial step in posttranscriptional gene regulation of cellular physiology. However, it remains a challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of ribosome-bound mRNA mapping (RIBOmap), a highly multiplexed three-dimensional in situ profiling method to detect cellular translatome. RIBOmap profiling of 981 genes in HeLa cells revealed cell cycle-dependent translational control and colocalized translation of functional gene modules. We mapped 5413 genes in mouse brain tissues, yielding spatially resolved single-cell translatomic profiles for 119,173 cells and revealing cell type-specific and brain region-specific translational regulation, including translation remodeling during oligodendrocyte maturation. Our method detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks.
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Affiliation(s)
- Hu Zeng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiahao Huang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jingyi Ren
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Zefang Tang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Haowen Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yiming Zhou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hailing Shi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Aditham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Sui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hongyu Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer A. Lo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiao Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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37
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Burns J, Wilding CP, Krasny L, Zhu X, Chadha M, Tam YB, Ps H, Mahalingam AH, Lee ATJ, Arthur A, Guljar N, Perkins E, Pankova V, Jenks A, Djabatey V, Szecsei C, McCarthy F, Ragulan C, Milighetti M, Roumeliotis TI, Crosier S, Finetti M, Choudhary JS, Judson I, Fisher C, Schuster EF, Sadanandam A, Chen TW, Williamson D, Thway K, Jones RL, Cheang MCU, Huang PH. The proteomic landscape of soft tissue sarcomas. Nat Commun 2023; 14:3834. [PMID: 37386008 PMCID: PMC10310735 DOI: 10.1038/s41467-023-39486-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Soft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research.
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Affiliation(s)
- Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Xixuan Zhu
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Yuen Bun Tam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Hari Ps
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Alexander T J Lee
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Nafia Guljar
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Emma Perkins
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Valeriya Pankova
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Andrew Jenks
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Vanessa Djabatey
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Cornelia Szecsei
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Frank McCarthy
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chanthirika Ragulan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Martina Milighetti
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Martina Finetti
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ian Judson
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Cyril Fisher
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Eugene F Schuster
- Ralph Lauren Centre for Breast Cancer Research, The Royal Marsden NHS Foundation Trust, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Tom W Chen
- Department of Oncology, National Taiwan University Hospital, Taipei City, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine Taipei, Taipei City, Taiwan
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Robin L Jones
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Maggie C U Cheang
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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38
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Barros GC, Guerrero S, Silva GM. The central role of translation elongation in response to stress. Biochem Soc Trans 2023; 51:959-969. [PMID: 37318088 PMCID: PMC11160351 DOI: 10.1042/bst20220584] [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: 02/06/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Protein synthesis is essential to support homeostasis, and thus, must be highly regulated during cellular response to harmful environments. All stages of translation are susceptible to regulation under stress, however, the mechanisms involved in translation regulation beyond initiation have only begun to be elucidated. Methodological advances enabled critical discoveries on the control of translation elongation, highlighting its important role in translation repression and the synthesis of stress-response proteins. In this article, we discuss recent findings on mechanisms of elongation control mediated by ribosome pausing and collisions and the availability of tRNAs and elongation factors. We also discuss how elongation intersects with distinct modes of translation control, further supporting cellular viability and gene expression reprogramming. Finally, we highlight how several of these pathways are reversibly regulated, emphasizing the dynamics of translation control during stress-response progression. A comprehensive understanding of translation regulation under stress will produce fundamental knowledge of protein dynamics while opening new avenues and strategies to overcome dysregulated protein production and cellular sensitivity to stress.
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Affiliation(s)
| | | | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC, USA
- Lead contact
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39
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Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
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40
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Zhao T, Cheng F, Zhan D, Li J, Zheng C, Lu Y, Qin W, Liu Z. The Glomerulus Multiomics Analysis Provides Deeper Insights into Diabetic Nephropathy. J Proteome Res 2023. [PMID: 37191251 DOI: 10.1021/acs.jproteome.2c00794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Although diabetic nephropathy (DN) is the leading cause of the end-stage renal disease, the exact regulation mechanisms remain unknown. In this study, we integrated the transcriptomics and proteomics profiles of glomeruli isolated from 50 biopsy-proven DN patients and 25 controls to investigate the latest findings about DN pathogenesis. First, 1152 genes exhibited differential expression at the mRNA or protein level, and 364 showed significant association. These strong correlated genes were divided into four different functional modules. Moreover, a regulatory network of the transcription factors (TFs)-target genes (TGs) was constructed, with 30 TFs upregulated at the protein levels and 265 downstream TGs differentially expressed at the mRNA levels. These TFs are the integration centers of several signal transduction pathways and have tremendous therapeutic potential for regulating the aberrant production of TGs and the pathological process of DN. Furthermore, 29 new DN-specific splice-junction peptides were discovered with high confidence; these peptides may play novel functions in the pathological course of DN. So, our in-depth integrative transcriptomics-proteomics analysis provided deeper insights into the pathogenesis of DN and opened the potential avenue for finding new therapeutic interventions. MS raw files were deposited into the proteomeXchange with the dataset identifier PXD040617.
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Affiliation(s)
- Tingting Zhao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Fang Cheng
- Department of Bioinformatics, Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Dongdong Zhan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jin'e Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Weisong Qin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
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41
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Johnson LC, Vo AA, Clancy JC, Myles KM, Pooranachithra M, Aguilera J, Levenson MT, Wohlenberg C, Rechtsteiner A, Ragle JM, Chisholm AD, Ward JD. NHR-23 activity is necessary for C. elegans developmental progression and apical extracellular matrix structure and function. Development 2023; 150:dev201085. [PMID: 37129010 PMCID: PMC10233720 DOI: 10.1242/dev.201085] [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: 07/07/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Nematode molting is a remarkable process where animals must repeatedly build a new apical extracellular matrix (aECM) beneath a previously built aECM that is subsequently shed. The nuclear hormone receptor NHR-23 (also known as NR1F1) is an important regulator of C. elegans molting. NHR-23 expression oscillates in the epidermal epithelium, and soma-specific NHR-23 depletion causes severe developmental delay and death. Tissue-specific RNAi suggests that nhr-23 acts primarily in seam and hypodermal cells. NHR-23 coordinates the expression of factors involved in molting, lipid transport/metabolism and remodeling of the aECM. NHR-23 depletion causes dampened expression of a nas-37 promoter reporter and a loss of reporter oscillation. The cuticle collagen ROL-6 and zona pellucida protein NOAH-1 display aberrant annular localization and severe disorganization over the seam cells after NHR-23 depletion, while the expression of the adult-specific cuticle collagen BLI-1 is diminished and frequently found in patches. Consistent with these localization defects, the cuticle barrier is severely compromised when NHR-23 is depleted. Together, this work provides insight into how NHR-23 acts in the seam and hypodermal cells to coordinate aECM regeneration during development.
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Affiliation(s)
- Londen C. Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John C. Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Aguilera
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chloe Wohlenberg
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew D. Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Ziff OJ, Neeves J, Mitchell J, Tyzack G, Martinez-Ruiz C, Luisier R, Chakrabarti AM, McGranahan N, Litchfield K, Boulton SJ, Al-Chalabi A, Kelly G, Humphrey J, Patani R. Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology. Nat Commun 2023; 14:2176. [PMID: 37080969 PMCID: PMC10119258 DOI: 10.1038/s41467-023-37630-6] [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: 09/09/2022] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) causes motor neuron degeneration, with 97% of cases exhibiting TDP-43 proteinopathy. Elucidating pathomechanisms has been hampered by disease heterogeneity and difficulties accessing motor neurons. Human induced pluripotent stem cell-derived motor neurons (iPSMNs) offer a solution; however, studies have typically been limited to underpowered cohorts. Here, we present a comprehensive compendium of 429 iPSMNs from 15 datasets, and 271 post-mortem spinal cord samples. Using reproducible bioinformatic workflows, we identify robust upregulation of p53 signalling in ALS in both iPSMNs and post-mortem spinal cord. p53 activation is greatest with C9orf72 repeat expansions but is weakest with SOD1 and FUS mutations. TDP-43 depletion potentiates p53 activation in both post-mortem neuronal nuclei and cell culture, thereby functionally linking p53 activation with TDP-43 depletion. ALS iPSMNs and post-mortem tissue display enrichment of splicing alterations, somatic mutations, and gene fusions, possibly contributing to the DNA damage response.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamie Mitchell
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Carlos Martinez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Raphaelle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland
| | | | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, WC1N 3BG, UK.
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43
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Chen W, Pilling D, Gomer RH. The mRNA-binding protein DDX3 mediates TGF-β1 upregulation of translation and promotes pulmonary fibrosis. JCI Insight 2023; 8:e167566. [PMID: 36821384 PMCID: PMC10132153 DOI: 10.1172/jci.insight.167566] [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: 11/28/2022] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Pulmonary fibrosis is potentiated by a positive feedback loop involving the extracellular sialidase enzyme neuraminidase 3 (NEU3) causing release of active TGF-β1 and TGF-β1 upregulating NEU3 by increasing translation without affecting mRNA levels. In this report, we elucidate the TGF-β1 upregulation of the translation mechanism. In human lung fibroblasts, TGF-β1 increased levels of proteins, including NEU3, by increasing translation of the encoding mRNAs without significantly affecting levels of these mRNAs. A total of 180 of these mRNAs shared a common 20-nucleotide motif. Deletion of this motif from NEU3 mRNA eliminated the TGF-β1 upregulation of NEU3 translation, while insertion of this motif in 2 mRNAs insensitive to TGF-β1 caused TGF-β1 to upregulate their translation. RNA-binding proteins including DEAD box helicase 3, X-linked (DDX3), bind the RNA motif, and TGF-β1 regulates their protein levels and/or binding to the motif. We found that DDX3 was upregulated in the fibrotic lesions in patients with pulmonary fibrosis, and inhibiting DDX3 in fibroblasts reduced TGF-β1 upregulation of NEU3 levels. In the mouse bleomycin model of pulmonary fibrosis, injections of the DDX3 inhibitor RK-33 potentiated survival and reduced lung inflammation, fibrosis, and tissue levels of DDX3, TGF-β1, and NEU3. These results suggest that inhibiting an mRNA-binding protein that mediates TGF-β1 upregulation of translation can reduce pulmonary fibrosis.
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44
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da Costa LCO, Gardinassi LG, Veras FP, Milanezi C, Ramalho LNZ, Benevides L, Alves-Filho JC, da Silva JS, da Silva Souza C. Expression of B lymphocyte-induced maturation protein 1 (Blimp-1) in keratinocyte and cytokine signalling drives human Th17 response in psoriasis. Arch Dermatol Res 2023; 315:481-490. [PMID: 36042041 DOI: 10.1007/s00403-022-02379-3] [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: 12/04/2021] [Revised: 06/30/2022] [Accepted: 08/01/2022] [Indexed: 11/02/2022]
Abstract
Transcriptional factor B lymphocyte-induced maturation protein 1 (Blimp-1) is pivotally implicated in T helper 17 (Th17) cell differentiation. This study investigated expression of the Blimp-1 protein, positive regulatory domain 1 (PRDM1), and cytokine genes in psoriasis (PsO). Affected (AS-PsO) and non-affected skin (nAS-PsO) samples were used to assess gene and protein expressions by reverse transcription-quantitative PCR (RT-qPCR), and immunostaining and confocal microscopy, respectively; the normalised public transcriptomic data permitted differential gene expression analyses. On RT-qPCR, PRDM1 and IL17A transcripts showed higher expression in AS-PsO than in nAS-PsO (n = 34) (p < 0.001; p < 0.0001, respectively). Confocal microscopy showed Blimp-1 protein expression in epidermal layer keratinocytes in AS-PsO, but not in nAS-PsO. Bioinformatic analysis of the transcriptomic dataset GSE13355 corroborated the increased PRDM1, signal transducer and activator of transcription 3 (STAT3), IL12B, TNF, IL17A, IL6, IL1B, IL22, and IL10 gene expression in AS-PsO, when compared to normal skin and nAS-PsO (p < 0.001). PRDM1 expression correlated positively (p < 0.0001) with that of IL17A (r = 0.7), IL1B (r = 0.67), IL12B (r = 0.6), IL6 (r = 0.59), IL22 (r = 0.53), IL23A (r = 0.47), IL21 (r = 0.47), IL27 (r = 0.34), IL23R (r = 0.32), S100 calcium binding protein A9 (r = 0.63), and lipocalin 2 (r = 0.50), and negatively with that of TGFB1 (r = - 0.28) and RORC (r = - 0.60). Blimp-1 may be critical in the pathogenesis of PsO dysregulation involving the Th17 inflammatory pathway. This knowledge may accelerate the development of new treatments.
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Affiliation(s)
- Lorena Carla Oliveira da Costa
- Dermatology Division, Department of Internal Medicine, Ribeirão Preto Medical School, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14048-900, Brazil
| | - Luiz Gustavo Gardinassi
- Department of Biosciences and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Flávio Protásio Veras
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cristiane Milanezi
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Luciana Benevides
- Fiocruz-Bi-Institutional Translational Medicine Plataform, Ribeirão Preto, São Paulo, Brazil
| | - José Carlos Alves-Filho
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Santana da Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Fiocruz-Bi-Institutional Translational Medicine Plataform, Ribeirão Preto, São Paulo, Brazil
| | - Cacilda da Silva Souza
- Dermatology Division, Department of Internal Medicine, Ribeirão Preto Medical School, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14048-900, Brazil.
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45
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Yao K, Zhou E, Schaafsma E, Zhang B, Cheng C. Immune checkpoint gene VSIR predicts patient prognosis in acute myeloid leukemia and myelodysplastic syndromes. Cancer Med 2023; 12:5590-5602. [PMID: 36394080 PMCID: PMC10028170 DOI: 10.1002/cam4.5409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Immune checkpoint proteins play critical functions during the immune response to cancer and have been targeted by immune checkpoint blockade therapy. V-domain Ig suppressor of T cell activation (VSIR) is one of these immune checkpoint genes and has been investigated extensively in recent years due to its conflicting roles in cancer immunity. Specifically, in acute myeloid leukemia (AML), the prognostic value of VSIR is debated. RESULTS In both patient tumor samples and cancer cell lines we find that VSIR has the highest expression in AML out of all cancer types and, in AML, has the highest expression out of all other immune checkpoint genes. Survival analysis indicated that AML patients with higher VSIR expression have significantly shorter survival than those patients with lower expression, even within established AML subgroups (e.g., FAB subtypes). Importantly, VSIR expression is predictive of progression from myelodysplastic syndromes (MDS) patients into AML, suggesting its potential role during the very early stage of AML development and progression. In addition to AML, VSIR also demonstrates prognostic values in other cancer types, including multiple myeloma and mesothelioma. CONCLUSION In summary, our analyses revealed the prognostic value of VSIR and its potential as a target for immunotherapy, especially in AML.
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Affiliation(s)
- Kevin Yao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA
| | - Emily Zhou
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Evelien Schaafsma
- Department of Molecular and Systems Biology, Dartmouth College, Lebanon, New Hampshire, USA
- Department of Biomedical Data Science, The Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire, USA
| | - Baoyi Zhang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Institute for Clinical and Transcriptional Research, Baylor College of Medicine, Houston, Texas, USA
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46
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [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: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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47
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Computational approaches to understand transcription regulation in development. Biochem Soc Trans 2023; 51:1-12. [PMID: 36695505 PMCID: PMC9988001 DOI: 10.1042/bst20210145] [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: 10/28/2022] [Revised: 01/07/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Gene regulatory networks (GRNs) serve as useful abstractions to understand transcriptional dynamics in developmental systems. Computational prediction of GRNs has been successfully applied to genome-wide gene expression measurements with the advent of microarrays and RNA-sequencing. However, these inferred networks are inaccurate and mostly based on correlative rather than causative interactions. In this review, we highlight three approaches that significantly impact GRN inference: (1) moving from one genome-wide functional modality, gene expression, to multi-omics, (2) single cell sequencing, to measure cell type-specific signals and predict context-specific GRNs, and (3) neural networks as flexible models. Together, these experimental and computational developments have the potential to significantly impact the quality of inferred GRNs. Ultimately, accurately modeling the regulatory interactions between transcription factors and their target genes will be essential to understand the role of transcription factors in driving developmental gene expression programs and to derive testable hypotheses for validation.
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48
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Tanrıverdi LH, Özhan O, Ulu A, Yıldız A, Ateş B, Vardı N, Acet HA, Parlakpinar H. Activation of the Mas receptors by AVE0991 and MrgD receptor using alamandine to limit the deleterious effects of Ang II-induced hypertension. Fundam Clin Pharmacol 2023; 37:60-74. [PMID: 36117326 DOI: 10.1111/fcp.12829] [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: 07/04/2022] [Revised: 08/16/2022] [Accepted: 09/06/2022] [Indexed: 01/27/2023]
Abstract
The MrgD receptor agonist, alamandine (ALA) and Mas receptor agonist, AVE0991 have recently been identified as protective components of the renin-angiotensin system. We evaluated the effects of ALA and AVE0991 on cardiovascular function and remodeling in angiotensin (Ang) II-induced hypertension in rats. Sprague Dawley rats were subject to 4-week subcutaneous infusions of Ang II (80 ng/kg/min) or saline after which they were treated with ALA (50 μg/kg), AVE0991 (576 μg/kg), or ALA+AVE0991 during the last 2 weeks. Systolic blood pressure (SBP) and heart rate (HR) values were recorded with tail-cuff plethysmography at 1, 15, and 29 days post-treatment. After euthanization, the heart and thoracic aorta were removed for further analysis and vascular responses. SBP significantly increased in the Ang II group when compared to the control group. Furthermore, Ang II also caused an increase in cardiac and aortic cyclophilin-A (CYP-A), monocyte chemoattractant protein-1 (MCP-1), and cardiomyocyte degeneration but produced a decrease in vascular relaxation. HR, matrix metalloproteinase-2 and -9, NADPH oxidase-4, and lysyl oxidase levels were comparable among groups. ALA, AVE0991, and the drug combination produced antihypertensive effects and alleviated vascular responses. The inflammatory and oxidative stress related to cardiac MCP-1 and CYP-A levels decreased in the Ang II+ALA+AVE0991 group. Vascular but not cardiac angiotensin-converting enzyme-2 levels decreased with Ang II administration but were similar to the Ang II+ALA+AVE0991 group. Our experimental data showed the combination of ALA and AVE0991 was found beneficial in Ang II-induced hypertension in rats by reducing SBP, oxidative stress, inflammation, and improving vascular responses.
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Affiliation(s)
| | - Onural Özhan
- Department of Medical Pharmacology, Faculty of Medicine, İnönü University, Malatya, Türkiye
| | - Ahmet Ulu
- Biochemistry and Biomaterials Research Laboratory, Department of Chemistry, Faculty of Science, İnönü University, Malatya, Türkiye
| | - Azibe Yıldız
- Department of Histology and Medical Embryology, Faculty of Medicine, İnönü University, Malatya, Türkiye
| | - Burhan Ateş
- Biochemistry and Biomaterials Research Laboratory, Department of Chemistry, Faculty of Science, İnönü University, Malatya, Türkiye
| | - Nigar Vardı
- Department of Histology and Medical Embryology, Faculty of Medicine, İnönü University, Malatya, Türkiye
| | - Hacı Ahmet Acet
- Department of Medical Pharmacology, Faculty of Medicine, İnönü University, Malatya, Türkiye
| | - Hakan Parlakpinar
- Department of Medical Pharmacology, Faculty of Medicine, İnönü University, Malatya, Türkiye
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49
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Virgolini N, Hagan R, Correia R, Silvano M, Fernandes S, Alves PM, Clarke C, Roldão A, Isidro IA. Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno-associated virus. Biotechnol J 2023; 18:e2200466. [PMID: 36401834 DOI: 10.1002/biot.202200466] [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: 09/12/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022]
Abstract
The insect cell-baculovirus expression vector system (IC-BEVS) has emerged as an alternative time- and cost-efficient production platform for recombinant Adeno-associated virus (AAV) for gene therapy. However, a better understanding of the underlying biological mechanisms of IC-BEVS is fundamental to further optimize this expression system toward increased product titer and quality. Here, gene expression of Sf9 insect cells producing recombinant AAV through a dual baculovirus expression system, with low multiplicity of infection (MOI), was profiled by RNA-seq. An 8-fold increase in reads mapping to either baculovirus or AAV transgene sequences was observed between 24 and 48 h post-infection (hpi), confirming a take-over of the host cell transcriptome by the baculovirus. A total of 336 and 4784 genes were identified as differentially expressed at 24 hpi (vs non-infected cells) and at 48 hpi (vs. infected cells at 24 hpi), respectively, including dronc, birc5/iap5, and prp1. Functional annotation found biological processes such as cell cycle, cell growth, protein folding, and cellular amino acid metabolic processes enriched along infection. This work uncovers transcriptional changes in Sf9 in response to baculovirus infection, which provide new insights into cell and/or metabolic engineering targets that can be leveraged for rational bioprocess engineering of IC-BEVS for AAV production.
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Affiliation(s)
- Nikolaus Virgolini
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ryan Hagan
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Ricardo Correia
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marco Silvano
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Fernandes
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Colin Clarke
- National Institute for Bioprocessing Research and Training, Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - António Roldão
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A Isidro
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.,ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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50
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Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles. Proc Natl Acad Sci U S A 2023; 120:e2216851120. [PMID: 36701367 PMCID: PMC9945961 DOI: 10.1073/pnas.2216851120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The phase transition from solitary to gregarious locusts is crucial in outbreaks of locust plague, which threaten agricultural yield and food security. Research on the regulatory mechanisms of phase transition in locusts has focused primarily on the transcriptional or posttranslational level. However, the translational regulation of phase transition is unexplored. Here, we show a phase-dependent pattern at the translation level, which exhibits different polysome profiles between gregarious and solitary locusts. The gregarious locusts exhibit significant increases in 60S and polyribosomes, while solitary locusts possess higher peaks of the monoribosome and a specific "halfmer." The polysome profiles, a molecular phenotype, respond to changes in population density. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. The high expression of large ribosomal protein 7 at the translational level promotes accumulation of the free 60S ribosomal subunit in gregarious locusts, while solitary locusts employ mitochondrial small ribosomal protein 18c to induce the assembly of mitochondrial ribosomes, causing divergence of the translational profiles and behavioral transition. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.
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