251
|
Sharma V, Ali MF, Kawashima T. Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102566. [PMID: 38830335 DOI: 10.1016/j.pbi.2024.102566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
The endosperm, a product of double fertilization, is one of the keys to the evolution and success of angiosperms in conquering the land. While there are differences in endosperm development among flowering plants, the most common form is coenocytic growth, where the endosperm initially undergoes nuclear division without cytokinesis and eventually becomes cellularized. This complex process requires interplay among networks of transcription factors such as MADS-box, auxin response factors (ARFs), and phytohormones. The role of cytoskeletal elements in shaping the coenocytic endosperm and influencing seed growth also becomes evident. This review offers a recent understanding of the molecular and cellular dynamics in coenocytic endosperm development and their contributions to the final seed size.
Collapse
Affiliation(s)
- Vijyesh Sharma
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Mohammad Foteh Ali
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA.
| |
Collapse
|
252
|
Cho Y, Kim YK. CARM1 phosphorylation at S595 by p38γ MAPK drives ROS-mediated cellular senescence. Redox Biol 2024; 76:103344. [PMID: 39265499 PMCID: PMC11415932 DOI: 10.1016/j.redox.2024.103344] [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: 08/08/2024] [Accepted: 09/04/2024] [Indexed: 09/14/2024] Open
Abstract
CARM1 is predominantly localized in the nucleus and plays a pivotal role in maintaining mitochondrial homeostasis by regulating gene expression. It suppresses mitochondrial biogenesis by downregulating PGC-1α and TFAM expression, while promoting mitochondrial fission through increased DNM1L expression. Under oxidative stress, CARM1 translocates to the cytoplasm, where it directly methylates DRP1 and accelerates mitochondrial fission, enhancing reactive oxygen species (ROS) production. Cytoplasmic localization of CARM1 is facilitated by its phosphorylation at S595 by ROS-activated p38γ MAPK, creating a positive feedback loop. Consequently, cytoplasmic CARM1 contributes to cellular senescence by altering mitochondrial dynamics and increasing ROS levels. This observation was supported by the increased cytoplasmic CARM1 levels and disrupted mitochondrial dynamics in the transformed 10T1/2 cells. Moreover, CARM1 inhibitors not only inhibit the proliferation of cancer cells but also induce apoptotic death in senescent cells. These findings highlight the potential of CARM1 inhibitors, particularly those targeting cytoplasmic functions, as novel strategies for eliminating cancer and senescent cells.
Collapse
Affiliation(s)
- Yena Cho
- Muscle Physiome Research Center and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea; College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Yong Kee Kim
- Muscle Physiome Research Center and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea; College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
| |
Collapse
|
253
|
Ospina Cardona D, Rodriguez-Pinto I, Iosim S, Bonet N, Mensa-Vilaro A, Wong MK, Ho G, Tormo M, Yagüe J, Shon W, Wallace DJ, Casals F, Beck DB, Abuav R, Arostegui JI. Description of a novel splice site variant in UBA1 gene causing VEXAS syndrome. Rheumatology (Oxford) 2024; 63:2897-2902. [PMID: 38552317 PMCID: PMC11443021 DOI: 10.1093/rheumatology/keae201] [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: 12/14/2023] [Accepted: 03/19/2024] [Indexed: 10/02/2024] Open
Abstract
OBJECTIVE Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome is a complex immune disorder consequence of somatic UBA1 variants. Most reported pathogenic UBA1 variants are missense or splice site mutations directly impairing the translational start site at p.Met41, with recent studies showing that these variants are frequent causes of recurrent inflammation in older individuals. Here we aimed to characterize a novel UBA1 variant found in two patients clinically presenting with VEXAS syndrome. METHODS Patients' data were collected from direct assessments and from their medical charts. Genomics analyses were undertaken by both Sanger and amplicon-based deep sequencing, and mRNA studies were undertaken by both cDNA subcloning and mRNA sequencing. RESULTS We report a novel, somatic variant in a canonical splice site of the UBA1 gene (c.346-2A>G), which was identified in two unrelated adult male patients with late-onset, unexplained inflammatory manifestations including recurrent fever, Sweet syndrome-like neutrophilic dermatosis, and lung inflammation responsive only to glucocorticoids. RNA analysis of the patients' samples indicated aberrant mRNA splicing leading to multiple in-frame transcripts, including a transcript retaining the full sequence of intron 4 and a different transcript with the deletion of the first 15 nucleotides of exon 5. CONCLUSION Here we describe abnormal UBA1 transcription as a consequence of the novel c.346-2A>G variant, identified in two patients with clinical features compatible with VEXAS syndrome. Overall, these results further demonstrate the expanding spectrum of variants in UBA1 leading to pathology and provide support for a complete gene evaluation in those patients considered candidates for VEXAS syndrome.
Collapse
Affiliation(s)
- Daniela Ospina Cardona
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
| | | | - Sonia Iosim
- Department of Pediatrics, New York University School of Medicine, New York, NY, USA
| | - Nuria Bonet
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Anna Mensa-Vilaro
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Mei-Kay Wong
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gary Ho
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Marc Tormo
- Genomics Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Scientific Computing Core Facility, Departament de Medicina i Ciències de la Vida (MELIS), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Wonwoo Shon
- Department Pathology & Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel J Wallace
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ferran Casals
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - David B Beck
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Rachel Abuav
- Department Pathology & Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Juan I Arostegui
- Department of Immunology, Hospital Clínic, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- School of Medicine, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
254
|
Qin X, Tape CJ. Functional analysis of cell plasticity using single-cell technologies. Trends Cell Biol 2024; 34:854-864. [PMID: 38355348 DOI: 10.1016/j.tcb.2024.01.006] [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: 11/02/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
Metazoan organisms are heterocellular systems composed of hundreds of different cell types, which arise from an isogenic genome through differentiation. Cellular 'plasticity' further enables cells to alter their fate in response to exogenous cues and is involved in a variety of processes, such as wound healing, infection, and cancer. Recent advances in cellular model systems, high-dimensional single-cell technologies, and lineage tracing have sparked a renaissance in plasticity research. Here, we discuss the definition of cell plasticity, evaluate state-of-the-art model systems and techniques to study cell-fate dynamics, and explore the application of single-cell technologies to obtain functional insights into cell plasticity in healthy and diseased tissues. The integration of advanced biomimetic model systems, single-cell technologies, and high-throughput perturbation studies is enabling a new era of research into non-genetic plasticity in metazoan systems.
Collapse
Affiliation(s)
- Xiao Qin
- MRC Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK.
| | - Christopher J Tape
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK.
| |
Collapse
|
255
|
Ge J, Wang Y, Li X, Lu Q, Yu H, Liu H, Ma K, Deng X, Luo ZQ, Liu X, Qiu J. Phosphorylation of caspases by a bacterial kinase inhibits host programmed cell death. Nat Commun 2024; 15:8464. [PMID: 39349471 PMCID: PMC11442631 DOI: 10.1038/s41467-024-52817-1] [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: 03/25/2024] [Accepted: 09/20/2024] [Indexed: 10/02/2024] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila utilizes the Dot/Icm system to translocate over 330 effectors into the host cytosol. These virulence factors modify a variety of cell processes, including pathways involved in cell death and survival, to promote bacterial proliferation. Here, we show that the effector LegK3 is a eukaryotic-like Ser/Thr kinase that functions to suppress host apoptosis. Mechanistically, LegK3 directly phosphorylates multiple caspases involved in apoptosis signaling, including Caspase-3, Caspase-7, and Caspase-9. LegK3-induced phosphorylation of these caspases occurs at serine (Ser29 in Caspase-3 and Ser199 in Caspase-7) or threonine (Thr102 in Caspase-9) residues located in the prodomain or interdomain linkers. These modifications interfere with the suitability of the caspases as the substrates of initiator caspases or upstream regulators without impacting their proteolytic activity. Collectively, our study reveals a novel strategy used by L. pneumophila to maintain the integrity of infected cells for its intracellular growth.
Collapse
Affiliation(s)
- Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ying Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xueyu Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Qian Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hangqian Yu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
| |
Collapse
|
256
|
Rodríguez-Pastor R, Knossow N, Shahar N, Hasik AZ, Deatherage DE, Gutiérrez R, Harrus S, Zaman L, Lenski RE, Barrick JE, Hawlena H. Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host. PLoS Pathog 2024; 20:e1012591. [PMID: 39348417 DOI: 10.1371/journal.ppat.1012591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 09/13/2024] [Indexed: 10/02/2024] Open
Abstract
Parasites, including pathogens, can adapt to better exploit their hosts on many scales, ranging from within an infection of a single individual to series of infections spanning multiple host species. However, little is known about how the genomes of parasites in natural communities evolve when they face diverse hosts. We investigated how Bartonella bacteria that circulate in rodent communities in the dunes of the Negev Desert in Israel adapt to different species of rodent hosts. We propagated 15 Bartonella populations through infections of either a single host species (Gerbillus andersoni or Gerbillus pyramidum) or alternating between the two. After 20 rodent passages, strains with de novo mutations replaced the ancestor in most populations. Mutations in two mononucleotide simple sequence repeats (SSRs) that caused frameshifts in the same adhesin gene dominated the evolutionary dynamics. They appeared exclusively in populations that encountered G. andersoni and altered the dynamics of infections of this host. Similar SSRs in other genes are conserved and exhibit ON/OFF variation in Bartonella isolates from the Negev Desert dunes. Our results suggest that SSR-based contingency loci could be important not only for rapidly and reversibly generating antigenic variation to escape immune responses but that they may also mediate the evolution of host specificity.
Collapse
Affiliation(s)
- Ruth Rodríguez-Pastor
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Nadav Knossow
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Naama Shahar
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Adam Z Hasik
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ricardo Gutiérrez
- National Reference Center for Bacteriology, Costa Rican Institute for Research and Teaching in Nutrition and Health (Inciensa), Cartago, Costa Rica
- Ross University School of Veterinary Medicine, Basseterre, St. Kitts and Nevis, West Indies
| | - Shimon Harrus
- Koret School of Veterinary Medicine, Faculty of Agricultural, Nutritional and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Luis Zaman
- Department of Ecology and Evolutionary Biology, Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard E Lenski
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Hadas Hawlena
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| |
Collapse
|
257
|
Hoffmann MH, Kirchner H, Krönke G, Riemekasten G, Bonelli M. Inflammatory tissue priming: novel insights and therapeutic opportunities for inflammatory rheumatic diseases. Ann Rheum Dis 2024; 83:1233-1253. [PMID: 38702177 DOI: 10.1136/ard-2023-224092] [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: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Due to optimised treatment strategies and the availability of new therapies during the last decades, formerly devastating chronic inflammatory diseases such as rheumatoid arthritis or systemic sclerosis (SSc) have become less menacing. However, in many patients, even state-of-the-art treatment cannot induce remission. Moreover, the risk for flares strongly increases once anti-inflammatory therapy is tapered or withdrawn, suggesting that underlying pathological processes remain active even in the absence of overt inflammation. It has become evident that tissues have the ability to remember past encounters with pathogens, wounds and other irritants, and to react more strongly and/or persistently to the next occurrence. This priming of the tissue bears a paramount role in defence from microbes, but on the other hand drives inflammatory pathologies (the Dr Jekyll and Mr Hyde aspect of tissue adaptation). Emerging evidence suggests that long-lived tissue-resident cells, such as fibroblasts, macrophages, long-lived plasma cells and tissue-resident memory T cells, determine inflammatory tissue priming in an interplay with infiltrating immune cells of lymphoid and myeloid origin, and with systemically acting factors such as cytokines, extracellular vesicles and antibodies. Here, we review the current state of science on inflammatory tissue priming, focusing on tissue-resident and tissue-occupying cells in arthritis and SSc, and reflect on the most promising treatment options targeting the maladapted tissue response during these diseases.
Collapse
Affiliation(s)
| | - Henriette Kirchner
- Institute for Human Genetics, Epigenetics and Metabolism Lab, University of Lübeck, Lübeck, Germany
| | - Gerhard Krönke
- Department of Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Michael Bonelli
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
| |
Collapse
|
258
|
Szwarc S, Le Pogam P, Beniddir MA. Emerging trends in plant natural products biosynthesis: a chemical perspective. CURRENT OPINION IN PLANT BIOLOGY 2024; 82:102649. [PMID: 39353262 DOI: 10.1016/j.pbi.2024.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 09/09/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024]
Abstract
Biosynthetic pathways are multistep processes transforming simple substrates into more complex structures. Over the past two decades, our understanding of these pathways, especially for specialized plant metabolites, has significantly increased. This surge is due to numerous scientific advancements such as next-generation sequencing, improved analytical platforms, and metabolite-transcript networks. The uprising of data sharing through public databases has also fostered collaboration and knowledge dissemination. Growing concerns about the supply of therapeutic natural products and their environmental impact have led to exploring sustainable alternatives like heterologous expression, which requires extensive knowledge of these pathways. Herein, we review emerging approaches in biosynthetic pathway elucidations and their prospects for their efficient integration.
Collapse
Affiliation(s)
- Sarah Szwarc
- Université Paris-Saclay, CNRS, BioCIS, 91400 Orsay, France
| | | | | |
Collapse
|
259
|
Kumano S, Tanaka K, Akahori R, Yanagiya A, Nojima A. Using peptide barcodes for simultaneous profiling of protein expression from mRNA. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9867. [PMID: 38973066 DOI: 10.1002/rcm.9867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
RATIONALE mRNA technology has begun to play a significant role in the areas of therapeutic intervention and vaccine development. However, optimizing the mRNA sequence that influences protein expression levels is a resource-intensive and time-consuming process. This study introduces a new method to accelerate the selection of sequences of mRNA for optimal protein expression. METHODS We designed the mRNA sequences in such a way that a unique peptide barcode, corresponding to each mRNA sequence, is attached to the expressed protein. These barcodes, cleaved off by a protease and simultaneously quantified by mass spectrometry, reflect the protein expression, enabling a parallel analysis. We validated this method using two mRNAs, each with different untranslated regions (UTRs) but encoding enhanced green fluorescence protein (eGFP), and investigated whether the peptide barcodes could analyze the differential eGFP expression levels. RESULTS The fluorescence intensity of eGFP, a marker of its expression level, has shown noticeable changes between the two UTR sequences in mRNA-transfected cells when measured using flow cytometry. This suggests alterations in the expression level of eGFP due to the influence of different UTR sequences. Furthermore, the quantified amount of peptide barcodes that were released from eGFP showed consistent patterns with these changes. CONCLUSIONS The experimental findings suggest that peptide barcodes serve as a valuable tool for assessing protein expression levels. The process of mRNA sequence selection, aimed at maximizing protein expression, can be enhanced by the parallel analysis of peptide barcodes using mass spectrometry.
Collapse
Affiliation(s)
- Shun Kumano
- Research & Development Group, Hitachi Ltd, Tokyo, Japan
| | - Kazuki Tanaka
- Research & Development Group, Hitachi Ltd, Tokyo, Japan
| | - Rena Akahori
- Research & Development Group, Hitachi Ltd, Tokyo, Japan
- CMC Development, ARCALIS Inc., Fukushima, Japan
| | | | | |
Collapse
|
260
|
Chen H, Gridnev A, Schlamowitz N, Hu W, Dey K, Zheng G, Misra JR. Targeted degradation of specific TEAD paralogs by small molecule degraders. Heliyon 2024; 10:e37829. [PMID: 39328531 PMCID: PMC11425103 DOI: 10.1016/j.heliyon.2024.e37829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/28/2024] Open
Abstract
The transcription factors, TEAD1-4 together with their co-activator YAP/TAZ function as key downstream effectors of the Hippo pathway. Hyperactivation of TEAD-YAP/TAZ activity is observed in many human cancers. TEAD1-4 possess distinct physiological and pathological functions, with conserved sequences and structures. Targeting specific isoforms within TEAD1-4 can serve as valuable chemical probes for investigating TEAD-related functions in both development and diseases. We report the TEAD-targeting proteolysis targeting chimera (PROTAC), HC278, which achieves effective and specific targeting of TEAD1 and TEAD3 at low nanomolar doses while weakly degrading TEAD2 and TEAD4 at higher doses. Proteomic analysis of >6000 proteins confirmed their highly selective TEAD1 and TEAD3 degradation. Consistently, HC278 can suppress the proliferation of YAP-dependent NCI-H226 mesothelioma cells. Mechanistic exploration revealed that both CRBN and proteasome systems are involved in the TEAD degradation induced by HC278. Moreover, RNA-seq and Gene Set Enrichment Analysis (GSEA) revealed that the YAP signature genes such as CTGF, CYR61, and ANKRD1 are significantly downregulated by HC278 treatment. Overall, HC278 serves as a valuable chemical tool for unraveling the intricate biological roles of TEAD1 and TEAD3 and holds the potential as a lead compound for developing targeted therapy for TEAD1/3-driven pathologies.
Collapse
Affiliation(s)
- Hui Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Artem Gridnev
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
- Graduate School of Biomedical Sciences, Oregon Health & Sciences University, Portland, OR, USA
| | - Netanya Schlamowitz
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
- Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wanyi Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Kuntala Dey
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
| | - Jyoti R. Misra
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, 11794, USA
| |
Collapse
|
261
|
Fernández P, Porrini L, Pereyra JI, Albanesi D, Mansilla MC. Unveiling the Coordinated Action of DesK/DesR and YvfT/YvfU to Control the Expression of an ABC Transporter in Bacillus subtilis. Mol Microbiol 2024. [PMID: 39344851 DOI: 10.1111/mmi.15320] [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: 02/15/2024] [Revised: 09/04/2024] [Accepted: 09/07/2024] [Indexed: 10/01/2024]
Abstract
Two-component systems (TCSs) are vital signal transduction pathways ubiquitous among bacteria, facilitating their responses to diverse environmental stimuli. In Bacillus subtilis, the DesK histidine kinase thermosensor, together with the response regulator DesR, constitute a TCS dedicated to membrane lipid homeostasis maintenance. This TCS orchestrates the transcriptional regulation of the des gene, encoding the sole desaturase in these bacteria, Δ5-Des. Additionally, B. subtilis possesses a paralog TCS, YvfT/YvfU, with unknown target gene(s). In this work, we show that YvfT/YvfU controls the expression of the yvfRS operon that codes for an ABC transporter. Interestingly, we found that this regulation also involves the action of DesK/DesR. Notably, opposite to des, yvfRS transcription is induced at 37°C and not at 25°C. Our in vivo and in vitro experiments demonstrate that both YvfU and DesR directly bind to the operon promoter region, with DesR exerting its control over yvfRS expression in its unphosphorylated state. Our study uncovers an intriguing case of cross-regulation where two homologous TCSs interact closely to finely tune gene expression in response to environmental cues. These findings shed light on the complexity of bacterial signal transduction systems and their critical role in bacterial adaptability.
Collapse
Affiliation(s)
- Pilar Fernández
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
- Departamento de Microbiología Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lucía Porrini
- Departamento de Microbiología Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Daniela Albanesi
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
- Departamento de Microbiología Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Cecilia Mansilla
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
- Departamento de Microbiología Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| |
Collapse
|
262
|
Zhou RW, Manisa B, Wang B. A Binuclear Metallohydrolase Model for RelA/SpoT-Homolog (RSH) Hydrolases. J Biol Chem 2024:107841. [PMID: 39357826 DOI: 10.1016/j.jbc.2024.107841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/31/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
When challenged by starvation, bacterial organisms synthesize guanosine penta- and tetraphosphate, collectively denoted as (p)ppGpp, as second messengers to reprogram metabolism towards slower growth and enhanced stress tolerance. When starvation is alleviated, the RelA-SpoT homolog (RSH) hydrolases down-regulate (p)ppGpp, cleaving the 3'-diphosphate to produce GTP or GDP. Metazoan RSH hydrolases (MESH) possess phosphatase activity responsible for converting cytoplasmic NADPH to NADH in mammalian cells. Inhibitor development for this family may therefore provide therapies to combat bacterial infection or metabolic dysregulation. Despite the availability of dozens of high-resolution structures, catalytic mechanisms of RSH hydrolases have remained poorly understood. All RSH hydrolases tightly bind a Mn2+ near its active center, which is believed sufficient for hydrolase activity. In contrast to this notion, we demonstrate, using the (p)ppGpp hydrolase SpoT from Acinetobacter baumannii, that a second divalent cation, presumably a Mg2+ under physiological conditions, is required for efficient catalysis. We also show that SpoT preferentially cleaves 3'-diphosphate over 3'-phosphate substrates, likely due to a key coordination between the β-phosphate and the second metal center. MESH replaces this β-phosphate with the side chain of an aspartate residue, thereby functioning as a phosphatase. We propose a binuclear metallohydrolase model where an invariant ED (Glu-Asp) diad, previously believed to activate the water nucleophile, instead coordinates to a Mg2+ center. The refined molecular and evolutionary blueprint of RSH hydrolases will provide a more reliable foundation for the development of small-molecule inhibitors of this important enzyme family.
Collapse
Affiliation(s)
- Rich W Zhou
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Berti Manisa
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boyuan Wang
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
263
|
Peesapati RS, Austin-Byler BL, Nawaz FZ, Stevenson JB, Mais SA, Kaya RN, Hassan MG, Khanal N, Wells AC, Ghiai D, Garikapati AK, Selhub J, Kipreos ET. A specific folate activates serotonergic neurons to control C. elegans behavior. Nat Commun 2024; 15:8471. [PMID: 39349491 PMCID: PMC11442744 DOI: 10.1038/s41467-024-52738-z] [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: 11/28/2023] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
Folates are B-group vitamins that function in one-carbon metabolism. Here we show that a specific folate can activate serotonergic neurons in C. elegans to modulate behavior through a pathway that requires the folate receptor FOLR-1 and the GON-2 calcium channel. FOLR-1 and GON-2 physically interact in a heterologous system, and both are expressed in the HSN and NSM serotonergic neurons. Both the folate 10-formyl-THF and a non-metabolic pteroate induce increases in the number of Ca2+ transients in the HSN neurons and egg laying in an FOLR-1- and GON-2-dependent manner. FOLR-1 and GON-2 are required for the activation of the NSM neurons in response to 10-formyl-THF, and for full NSM-mediated stoppage of movement when starved animals encounter bacteria. Our results demonstrate that FOLR-1 acts independently of one-carbon metabolism and suggest that 10-formyl-THF acts as a dietary signal that activates serotonergic neurons to impact behavior through a pathway that involves calcium entry.
Collapse
Affiliation(s)
- Ria S Peesapati
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | | | | | | | - Stanelle A Mais
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Rabia N Kaya
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Michael G Hassan
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Nabraj Khanal
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Alexandra C Wells
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Deena Ghiai
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Anish K Garikapati
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA
| | - Jacob Selhub
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Edward T Kipreos
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA.
| |
Collapse
|
264
|
Hardy PB, Wang BY, Chan KM, Webber CA, Senger JLB. The use of electrical stimulation to enhance recovery following peripheral nerve injury. Muscle Nerve 2024. [PMID: 39347555 DOI: 10.1002/mus.28262] [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: 01/17/2024] [Revised: 09/04/2024] [Accepted: 09/07/2024] [Indexed: 10/01/2024]
Abstract
Peripheral nerve injury is common and can have devastating consequences. In severe cases, functional recovery is often poor despite surgery. This is primarily due to the exceedingly slow rate of nerve regeneration at only 1-3 mm/day. The local environment in the distal nerve stump supportive of nerve regrowth deteriorates over time and the target end organs become atrophic. To overcome these challenges, investigations into treatments capable of accelerating nerve regrowth are of great clinical relevance and are an active area of research. One intervention that has shown great promise is perioperative electrical stimulation. Postoperative stimulation helps to expedite the Wallerian degeneration process and reduces delays caused by staggered regeneration at the site of nerve injury. By contrast, preoperative "conditioning" stimulation increases the rate of nerve regrowth along the nerve trunk. Over the past two decades, a rich body of literature has emerged that provides molecular insights into the mechanism by which electrical stimulation impacts nerve regeneration. The end result is upregulation of regeneration-associated genes in the neuronal body and accelerated transport to the axon front for regrowth. The efficacy of brief electrical stimulation on patients with peripheral nerve injuries was demonstrated in a number of randomized controlled trials on compressive, transection and traction injuries. As approved equipment to deliver this treatment is becoming available, it may be feasible to deploy this novel treatment in a wide range of clinical settings.
Collapse
Affiliation(s)
- Paige B Hardy
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Bonnie Y Wang
- Division of Physical Medicine and Rehabilitation, University of Alberta, Edmonton, Alberta, Canada
| | - K Ming Chan
- Division of Physical Medicine and Rehabilitation, University of Alberta, Edmonton, Alberta, Canada
| | | | - Jenna-Lynn B Senger
- Division of Plastic & Reconstructive Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
265
|
Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling MC, Adams DJ, Bradley A, Braun RE, Brown SD, Caulder A, Codner GF, DeMayo FJ, Dickinson ME, Doe B, Duddy G, Gertsenstein M, Goodwin LO, Hérault Y, Lintott LG, Lloyd KCK, Lorenzo I, Mackenzie M, Mallon AM, McKerlie C, Parkinson H, Ramirez-Solis R, Seavitt JR, Sedlacek R, Skarnes WC, Smedley D, Wells S, White JK, Wood JA, Murray SA, Heaney JD, Nutter LMJ. Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines. Sci Rep 2024; 14:22626. [PMID: 39349521 PMCID: PMC11443006 DOI: 10.1038/s41598-024-72418-8] [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: 04/03/2024] [Accepted: 09/06/2024] [Indexed: 10/02/2024] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps - generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease.
Collapse
Affiliation(s)
- Hillary Elrick
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | | | - Brandon J Willis
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
| | - Denise G Lanza
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elif F Acar
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Statistics, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- LGC Assure, Fordham, CB7 5WW, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marie-Christine Birling
- CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Allan Bradley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Trinity Lane, Cambridge, CB2 1TN, UK
| | | | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | - Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Francesco J DeMayo
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Reproductive and Developmental Biology Laboratory, NIEHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brendan Doe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | | | - Yann Hérault
- CNRS, INSERM, CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
- Department of Surgery, School of Medicine, University of California Davis, Davis, CA, 95618, USA
| | - Isabel Lorenzo
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew Mackenzie
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | | | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ramiro Ramirez-Solis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- UT Health San Antonio, San Antonio, TX, 78229, USA
| | - John R Seavitt
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - William C Skarnes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Damien Smedley
- William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell Campus, Didcot, Oxon, OX11 0RD, UK
| | | | - Joshua A Wood
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Mouse Biology Program, University of California-Davis, Davis, CA, 95618, USA
| | | | - Jason D Heaney
- Department of Molecular and Human Genetic, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.
- The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
| |
Collapse
|
266
|
Wan Y, Li S, Xu W, Wang K, Guo W, Yang C, Li X, Zhou J, Wang J. Terminal Chemical Modifications of crRNAs Enable Improvement in the Performance of CRISPR-Cas for Point-of-Care Nucleic Acid Detection. Anal Chem 2024. [PMID: 39348463 DOI: 10.1021/acs.analchem.4c03698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
CRISPR-Cas systems, harnessing their precise nucleic acid recognition via CRISPR RNA (crRNA), offer promise for the accurate testing of nucleic acids in the field. However, the inherent susceptibility of crRNA to degradation poses challenges for accurate detection in low-resource settings. Here, we utilized the chemically modified crRNA for the CRISPR-Cas-based assay (CM-CRISPR). We found that the extension and chemical modification to crRNA significantly enhanced the trans-cleavage activity of LbCas12a. The chemically modified crRNA was resistant to degradation, and CM-CRISPR showed superior detection capability in complex environments. CM-CRISPR could be combined with recombinase polymerase amplification (RPA) and applied in a droplet digital platform, enabling attomolar-level sensitivity. We also developed a portable and automated device for a digital CRISPR assay, which is amenable to point-of-care testing (POCT). The extraction-free procedure was integrated with this assay to streamline the workflow, and clinical samples were successfully detected. This work finds a simple and efficient way to improve the performance of CRISPR-Cas and develops a portable platform for POCT, representing a significant advance toward practical applications of CRISPR-based diagnostics.
Collapse
Affiliation(s)
- Yunzhu Wan
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Wenfei Xu
- Zhejiang Key Laboratory of Multiomics and Molecular Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Zhejiang 314006, China
| | - Ke Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Wenlong Guo
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, Guangdong Province, China
| | - Xuhui Li
- Zhejiang Key Laboratory of Multiomics and Molecular Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, Zhejiang 314006, China
| | - Jianhua Zhou
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
267
|
Zhang C, Wang H, Ablimit A, Zhao Y, Sun Q, Dong H, Zhang B, Liu C, Wang C. Functional Verification of Transcription Factor comp54181_c0 in Monascus purpureus. J Basic Microbiol 2024:e2400469. [PMID: 39344177 DOI: 10.1002/jobm.202400469] [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: 07/27/2024] [Revised: 09/04/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024]
Abstract
Monacolin K is a valuable secondary metabolite produced after a period of fermentation by Monascus purpureus; however, our current understanding of the regulatory mechanisms of its synthesis remains incomplete. This study conducted functional analysis on the key transcription factor, comp54181_c0, that is involved in the synthesis of monacolin K in Monascus. Mutant strains with either knockout or overexpression of comp54181_c0 were constructed using CRISPR/Cas9. A comparison between the knockout and overexpression strains revealed changes in fungal morphology and growth, with a significant increase in the production of Monascus pigments and monacolin K when comp54181_c0 was absent. Real-time fluorescence quantitative PCR analysis revealed that comp54181_c0 significantly influenced the transcription of key genes related to monacolin K biosynthesis in Monascus. In conclusion, our study elucidates the crucial role of comp54181_c0 in Monascus, enriches our understanding of fungal secondary metabolite development and regulation, and provides a foundation for the development and regulation of Monascus and monacolin K production.
Collapse
Affiliation(s)
- Chan Zhang
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| | - Haijiao Wang
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
| | - Arzugul Ablimit
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
| | - Yufei Zhao
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
| | - Qing Sun
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
| | - HuiJun Dong
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
| | - Bobo Zhang
- School of Science, Shantou University, Shantou, Guangdong, China
| | - Chengjian Liu
- Shandong Fanhui Pharmaceutical Co. Ltd., Jinan, Shandong, China
| | - Chengtao Wang
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing, China
| |
Collapse
|
268
|
Guo S, Su Q, Yang Z, Mo W. Development and validation of a novel liquid-liquid phase separation gene signature for bladder cancer. Sci Rep 2024; 14:22552. [PMID: 39343809 PMCID: PMC11439906 DOI: 10.1038/s41598-024-73422-8] [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: 07/13/2023] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
Bladder carcinoma (BLCA) represents a common urinary tract malignancy, characterized by aggressive behavior and high recurrence rates. The biological response regulation during tumor proliferation and metastasis is intimately associated with liquid-liquid phase separation (LLPS). For the purpose of enhancing early detection and treatment, this study employed transcriptomic data to examine the prognostic implications of LLPS-associated genes and formulate a predictive model. Clinical and transcriptomic data of bladder cancer patients were sourced from the GEO and TCGA databases. This study applied a clustering algorithm using non-negative matrix factorization (NMF) to classify samples, which were systematically compared based on their liquid-liquid phase separation characteristics. Prognostic models were developed using multivariate Cox regression and the Least Absolute Shrinkage Selection Operator (LASSO) algorithm to establish risk formulas for nine genes. The gene signature's validity was tested across the entire TCGA cohort (406 cases), the TCGA testing cohort (120 cases), and the external validation dataset GSE13507. The predictive accuracy of the signature system was assessed using receiver operating characteristic (ROC) and Kaplan-Meier curves. Additionally, decision curve analysis incorporating clinicopathological parameters and the genetic signature was employed to predict individual survival. This study identified two distinct molecular subtypes, C1 and C2. Patients with the C1 subtype exhibited significantly better prognoses than those with the C2 subtype. Low-risk group patients consistently showed superior prognoses compared to high-risk groups across the entire TCGA, GEO, and TCGA training cohorts. Furthermore, the LLPS-related gene model demonstrated prognostic value independent of other clinical traits. This study identifies LLPS-associated gene clusters and establishes an independent, accurate prognostic model for BLCA. The model holds potential for clinical application in BLCA prognosis assessment.
Collapse
Affiliation(s)
- Sufan Guo
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Department of Clinical Laboratory, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
| | - Qisheng Su
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zheng Yang
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wuning Mo
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
| |
Collapse
|
269
|
Sun B, Li Q, Mei Y, Zhang Y, Zheng Y, Huang Y, Xiao X, Zhang J, Jian G, Cao X. Chromosome-scale and haplotype-resolved genome assembly of the autotetraploid Misgurnus anguillicaudatus. Sci Data 2024; 11:1059. [PMID: 39341798 PMCID: PMC11438953 DOI: 10.1038/s41597-024-03891-z] [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: 04/09/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
In nature, diploids and tetraploids are two common types of polyploid evolution. Misgurnus anguillicaudatus (mud loach) is a remarkable fish species that exhibits both diploid and tetraploid forms. However, reconstructing the four haplotypes of its autotetraploid genome remains unresolved. Here, we generated the first haplotype-resolved, chromosome-level genome of autotetraploid M. anguillicaudatus with a size of 4.76 Gb, contig N50 of 6.78 Mb, and scaffold N50 of 44.11 Mb. We identified approximately 2.9 Gb (61.03% of genome) of repetitive sequences and predicted 91,485 protein-coding genes. Moreover, allelic gene expression levels indicated the absence of significant dominant haplotypes within the autotetraploid loach genome. This genome will provide a valuable biological model for unraveling the mechanisms of polyploid formation and evolution, adaptation to environmental changes, and benefit for aquaculture applications and biodiversity conservation.
Collapse
Affiliation(s)
- Bing Sun
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingshan Li
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuxuan Zheng
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwei Huang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Xiao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gao Jian
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
270
|
Jiang L, Tian J, Yang J, Luo R, Zhang Y, Shao C, Guo B, Wu X, Dan J, Luo Y. p21 Regulates Wnt-Notch balance via DREAM/MMB/Rb-E2F1 and maintains intestinal stem cell homeostasis. Cell Death Discov 2024; 10:413. [PMID: 39341834 PMCID: PMC11438959 DOI: 10.1038/s41420-024-02192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024] Open
Abstract
The crosstalk and balance regulation of Wnt-Notch have been known to be essential for cell fate decision and tissue regeneration, however, how this balance is maintained and how the Wnt-Notch pathways are connected with cell cycle regulation is still not clear. By analyzing the molecular alterations in mouse model with accelerated aging phenotypes due to loss of p21 function in a Werner syndrome background, we observed that Wnt3 and β-Catenin were down-regulated, while Notch1 and Hes1 were up-regulated. This disruption in Wnt-Notch signaling was accompanied by the loss of intestinal stem cell compartment, increase in Bmi1 positive cells, loss of Olfm4/Lgr5 positive cells, and reduced secretory Paneth cells and goblet cells in the intestinal crypts of p21TKO mice. BrdU incorporation, cleaved caspase 3, and Tunel assay results revealed the fast turnover of intestinal epithelia, which may result in abnormal stem cell mobilization and exhaustion of the stem cell reservoir in the intestinal crypts. We further identified shift of DREAM complex towards MMB complex due to the loss of p21 as the cause for faster turnover of intestinal epithelia. Importantly, we identified the E2F1 as the transcriptional regulator for Notch1, which linked the p21-DREAM/MMB/Rb-E2F1 pathway with Wnt-Notch pathway. The overexpression of p21 rescued the DREAM pathway, as well as the imbalance of Wnt-Notch pathway. In summary, our data identify p21 as an important factor in maintaining sequential mobilization, proliferation, and homeostasis of intestinal stem cells.
Collapse
Affiliation(s)
- Liangxia Jiang
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jie Tian
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jun Yang
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronggang Luo
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yongjin Zhang
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chihao Shao
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Bing Guo
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoming Wu
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Juhua Dan
- Laboratory of Molecular Genetics of Aging & Tumor, Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying Luo
- Department of Pathophysiology, School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China.
| |
Collapse
|
271
|
Zhou B, Arthur JG, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo JXJ, Lee H, Nachun DC, Purmann C, Monte EM, Weimer AK, Qu PP, Shi M, Jiang L, Yang X, Fullard JF, Bendl J, Girdhar K, Kim M, Chen X, Greenleaf WJ, Duncan L, Ji HP, Zhu X, Song G, Montgomery SB, Palejev D, Zu Dohna H, Roussos P, Kundaje A, Hallmayer JF, Snyder MP, Wong WH, Urban AE. Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell 2024:S0092-8674(24)01032-8. [PMID: 39353437 DOI: 10.1016/j.cell.2024.09.014] [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: 09/12/2023] [Revised: 07/01/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024]
Abstract
Complex structural variations (cxSVs) are often overlooked in genome analyses due to detection challenges. We developed ARC-SV, a probabilistic and machine-learning-based method that enables accurate detection and reconstruction of cxSVs from standard datasets. By applying ARC-SV across 4,262 genomes representing all continental populations, we identified cxSVs as a significant source of natural human genetic variation. Rare cxSVs have a propensity to occur in neural genes and loci that underwent rapid human-specific evolution, including those regulating corticogenesis. By performing single-nucleus multiomics in postmortem brains, we discovered cxSVs associated with differential gene expression and chromatin accessibility across various brain regions and cell types. Additionally, cxSVs detected in brains of psychiatric cases are enriched for linkage with psychiatric GWAS risk alleles detected in the same brains. Furthermore, our analysis revealed significantly decreased brain-region- and cell-type-specific expression of cxSV genes, specifically for psychiatric cases, implicating cxSVs in the molecular etiology of major neuropsychiatric disorders.
Collapse
Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Joseph G Arthur
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Hanmin Guo
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Taeyoung Kim
- School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Tao Wang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Jay X J Luo
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma M Monte
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Annika K Weimer
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ping-Ping Qu
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Minyi Shi
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lixia Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xinqiong Yang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minsu Kim
- School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea
| | - Xi Chen
- Department of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Xiang Zhu
- Department of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Giltae Song
- School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea; Center for Artificial Intelligence Research, Pusan National University, Busan 46241, South Korea
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Dean Palejev
- Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Heinrich Zu Dohna
- Department of Biology, American University of Beirut, Beirut 11-0236, Lebanon
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA; Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Joachim F Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wing H Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
272
|
Pizzioli E, Minutolo A, Balestrieri E, Matteucci C, Magiorkinis G, Horvat B. Crosstalk between human endogenous retroviruses and exogenous viruses. Microbes Infect 2024:105427. [PMID: 39349096 DOI: 10.1016/j.micinf.2024.105427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 09/11/2024] [Accepted: 09/26/2024] [Indexed: 10/02/2024]
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections of human germ-line cells, which are mostly silenced during evolution, but could be de-repressed and play a pathological role. Infection with some exogenous viruses, including herpesviruses, HIV-1 and SARS-CoV-2, was demonstrated to induce the expression of HERV RNAs and proteins.
Collapse
Affiliation(s)
- Edoardo Pizzioli
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, France
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Branka Horvat
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, France.
| |
Collapse
|
273
|
Kyriacou E, Lingner J. TERRA long noncoding RNA: At the interphase of telomere damage, rescue and signaling. Curr Opin Cell Biol 2024; 91:102437. [PMID: 39342869 DOI: 10.1016/j.ceb.2024.102437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/07/2024] [Accepted: 09/09/2024] [Indexed: 10/01/2024]
Abstract
TERRA long noncoding RNAs play key roles in telomere function and maintenance. They can orchestrate telomeric chromatin remodeling, regulate telomere maintenance by telomerase and homology-directed repair, and they participate in the telomeric DNA damage response. TERRA associates with chromosome ends through base-pairing forming R-loops, which are mediated by the RAD51 DNA recombinase and its partner RAD51AP1. Telomeric R-loops interfere with replication fork progression, stimulating a switch of telomere maintenance from semiconservative DNA replication to homology-directed repair (HDR). The latter mechanism is exploited by a subset of cancer cells that lack telomerase, referred to as ALT. In addition, TERRA stimulates HDR at short telomeres during aging, delaying cellular senescence. During carcinogenesis, when cells with eroded telomeres enter replicative crisis, TERRA acts as a signaling molecule to mediate autophagic cell death.
Collapse
Affiliation(s)
- Eftychia Kyriacou
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| |
Collapse
|
274
|
Moran HR, Nyarko OO, O'Rourke R, Ching RCK, Riemslagh FW, Peña B, Burger A, Sucharov CC, Mosimann C. The pericardium forms as a distinct structure during heart formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613484. [PMID: 39345600 PMCID: PMC11429720 DOI: 10.1101/2024.09.18.613484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The heart integrates diverse cell lineages into a functional unit, including the pericardium, a mesothelial sac that supports heart movement, homeostasis, and immune responses. However, despite its critical roles, the developmental origins of the pericardium remain uncertain due to disparate models. Here, using live imaging, lineage tracking, and single-cell transcriptomics in zebrafish, we find the pericardium forms within the lateral plate mesoderm from dedicated anterior mesothelial progenitors and distinct from the classic heart field. Imaging of transgenic reporters in zebrafish documents lateral plate mesoderm cells that emerge lateral of the classic heart field and among a continuous mesothelial progenitor field. Single-cell transcriptomics and trajectories of hand2-expressing lateral plate mesoderm reveal distinct populations of mesothelial and cardiac precursors, including pericardial precursors that are distinct from the cardiomyocyte lineage. The mesothelial gene expression signature is conserved in mammals and carries over to post-natal development. Light sheet-based live-imaging and machine learning-supported cell tracking documents that during heart tube formation, pericardial precursors that reside at the anterior edge of the heart field migrate anteriorly and medially before fusing, enclosing the embryonic heart to form a single pericardial cavity. Pericardium formation proceeds even upon genetic disruption of heart tube formation, uncoupling the two structures. Canonical Wnt/β-catenin signaling modulates pericardial cell number, resulting in a stretched pericardial epithelium with reduced cell number upon canonical Wnt inhibition. We connect the pathological expression of secreted Wnt antagonists of the SFRP family found in pediatric dilated cardiomyopathy to increased pericardial stiffness: sFRP1 in the presence of increased catecholamines causes cardiomyocyte stiffness in neonatal rats as measured by atomic force microscopy. Altogether, our data integrate pericardium formation as an independent process into heart morphogenesis and connect disrupted pericardial tissue properties such as pericardial stiffness to pediatric cardiomyopathies.
Collapse
|
275
|
Zhang CX, Hou YC. Short-homology-mediated PCR-based method for gene introduction in the fission yeast Schizosaccharomyces pombe. Brief Funct Genomics 2024; 23:672-678. [PMID: 38669080 DOI: 10.1093/bfgp/elae016] [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: 02/20/2024] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Schizosaccharomyces pombe is a commonly utilized model organism for studying various aspects of eukaryotic cell physiology. One reason for its widespread use as an experimental system is the ease of genetic manipulations, leveraging the natural homology-targeted repair mechanism to accurately modify the genome. We conducted a study to assess the feasibility and efficiency of directly introducing exogenous genes into the fission yeast S. pombe using Polymerase Chain Reaction (PCR) with short-homology flanking sequences. Specifically, we amplified the NatMX6 gene (which provides resistance to nourseothricin) using PCR with oligonucleotides that had short flanking regions of 20 bp, 40 bp, 60 bp and 80 bp to the target gene. By using this purified PCR product, we successfully introduced the NatMX6 gene at position 171 385 on chromosome III in S. pombe. We have made a simple modification to the transformation procedure, resulting in a significant increase in transformation efficiency by at least 5-fold. The success rate of gene integration at the target position varied between 20% and 50% depending on the length of the flanking regions. Additionally, we discovered that the addition of dimethyl sulfoxide and boiled carrier DNA increased the number of transformants by ~60- and 3-fold, respectively. Furthermore, we found that the removal of the pku70+ gene improved the transformation efficiency to ~5% and reduced the formation of small background colonies. Overall, our results demonstrate that with this modified method, even very short stretches of homologous regions (as short as 20 bp) can be used to effectively target genes at a high frequency in S. pombe. This finding greatly facilitates the introduction of exogenous genes in this organism.
Collapse
|
276
|
Rafiei N, Ronceret A. The plant early recombinosome: a high security complex to break DNA during meiosis. PLANT REPRODUCTION 2024:10.1007/s00497-024-00509-7. [PMID: 39331138 DOI: 10.1007/s00497-024-00509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
KEY MESSAGE The formacion of numerous unpredictable DNA Double Strand Breaks (DSBs) on chromosomes iniciates meiotic recombination. In this perspective, we propose a 'multi-key lock' model to secure the risky but necesary breaks as well as a 'one per pair of cromatids' model for the topoisomerase-like early recombinosome. During meiosis, homologous chromosomes recombine at few sites of crossing-overs (COs) to ensure correct segregation. The initiation of meiotic recombination involves the formation of DNA double strand breaks (DSBs) during prophase I. Too many DSBs are dangerous for genome integrity: if these DSBs are not properly repaired, it could potentially lead to chromosomal fragmentation. Too few DSBs are also problematic: if the obligate CO cannot form between bivalents, catastrophic unequal segregation of univalents lead to the formation of sterile aneuploid spores. Research on the regulation of the formation of these necessary but risky DSBs has recently advanced in yeast, mammals and plants. DNA DSBs are created by the enzymatic activity of the early recombinosome, a topoisomerase-like complex containing SPO11. This opinion paper reviews recent insights on the regulation of the SPO11 cofactors necessary for the introduction of temporally and spatially controlled DSBs. We propose that a 'multi-key-lock' model for each subunit of the early recombinosome complex is required to secure the formation of DSBs. We also discuss the hypothetical implications that the established topoisomerase-like nature of the SPO11 core-complex can have in creating DSB in only one of the two replicated chromatids of early prophase I meiotic chromosomes. This hypothetical 'one per pair of chromatids' DSB formation model could optimize the faithful repair of the self-inflicted DSBs. Each DSB could use three potential intact homologous DNA sequences as repair template: one from the sister chromatid and the two others from the homologous chromosomes.
Collapse
Affiliation(s)
- Nahid Rafiei
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Arnaud Ronceret
- Department of Plant Molecular Biology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México.
| |
Collapse
|
277
|
Rojas-Ríos P, Chartier A, Enjolras C, Cremaschi J, Garret C, Boughlita A, Ramat A, Simonelig M. piRNAs are regulators of metabolic reprogramming in stem cells. Nat Commun 2024; 15:8405. [PMID: 39333531 PMCID: PMC11437085 DOI: 10.1038/s41467-024-52709-4] [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: 09/28/2023] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Stem cells preferentially use glycolysis instead of oxidative phosphorylation and this metabolic rewiring plays an instructive role in their fate; however, the underlying molecular mechanisms remain largely unexplored. PIWI-interacting RNAs (piRNAs) and PIWI proteins have essential functions in a range of adult stem cells across species. Here, we show that piRNAs and the PIWI protein Aubergine (Aub) are instrumental in activating glycolysis in Drosophila female germline stem cells (GSCs). Higher glycolysis is required for GSC self-renewal and aub loss-of-function induces a metabolic switch in GSCs leading to their differentiation. Aub directly binds glycolytic mRNAs and Enolase mRNA regulation by Aub depends on its 5'UTR. Furthermore, mutations of a piRNA target site in Enolase 5'UTR lead to GSC loss. These data reveal an Aub/piRNA function in translational activation of glycolytic mRNAs in GSCs, and pinpoint a mechanism of regulation of metabolic reprogramming in stem cells based on small RNAs.
Collapse
Affiliation(s)
- Patricia Rojas-Ríos
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Aymeric Chartier
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Camille Enjolras
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Julie Cremaschi
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Céline Garret
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Adel Boughlita
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Anne Ramat
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, Université de Montpellier, CNRS, Montpellier, France.
| |
Collapse
|
278
|
Gordon S, Rodriguez AA, Gu Y, Corbett KD, Lee CF, Rog O. The synaptonemal complex aligns meiotic chromosomes by wetting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607092. [PMID: 39149313 PMCID: PMC11326210 DOI: 10.1101/2024.08.07.607092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
During meiosis, the parental chromosomes are drawn together to enable exchange of genetic information. Chromosomes are aligned through the assembly of a conserved interface, the synaptonemal complex, composed of a central region that forms between two parallel chromosomal backbones called axes. Here we identify the axis-central region interface in C. elegans , containing a conserved positive patch on the axis component HIM-3 and the C-terminus of the central region protein SYP-5. Crucially, the canonical ultrastructure of the synaptonemal complex is altered upon weakening this interface. We developed a thermodynamic model that recapitulates our experimental observations, indicating that the liquid-like central region can assemble by wetting the axes without active energy consumption. More broadly, our data show that condensation drives tightly regulated nuclear reorganization during sexual reproduction.
Collapse
|
279
|
Fan K, Li Y, Chen Z, Fan L. GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes. BMC Bioinformatics 2024; 25:309. [PMID: 39333857 PMCID: PMC11438159 DOI: 10.1186/s12859-024-05934-z] [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: 12/20/2023] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND The study of codon usage bias is important for understanding gene expression, evolution and gene design, providing critical insights into the molecular processes that govern the function and regulation of genes. Codon Usage Bias (CUB) indices are valuable metrics for understanding codon usage patterns across different organisms without extensive experiments. Considering that there is no one-fits-all index for all species, a comprehensive platform supporting the calculation and analysis of multiple CUB indices for codon optimization is greatly needed. RESULTS Here, we release GenRCA, an updated version of our previous Rare Codon Analysis Tool, as a free and user-friendly website for all-inclusive evaluation of codon usage preferences of coding sequences. In this study, we manually reviewed and implemented up to 31 codon preference indices, with 65 expression host organisms covered and batch processing of multiple gene sequences supported, aiming to improve the user experience and provide more comprehensive and efficient analysis. CONCLUSIONS Our website fills a gap in the availability of comprehensive tools for species-specific CUB calculations, enabling researchers to thoroughly assess the protein expression level based on a comprehensive list of 31 indices and further guide the codon optimization.
Collapse
Affiliation(s)
- Kunjie Fan
- Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd., Shanghai, China
| | - Yuanyuan Li
- Production and R&D Center I of LSS, GenScript Biotech Corporation, Nanjing, China
| | - Zhiwei Chen
- Production and R&D Center I of LSS, GenScript Biotech Corporation, Nanjing, China
| | - Long Fan
- Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd., Shanghai, China.
| |
Collapse
|
280
|
Rapps K, Weller A, Meiri N. Epigenetic Regulation is involved in Reversal of Obesity. Neurosci Biobehav Rev 2024:105906. [PMID: 39343077 DOI: 10.1016/j.neubiorev.2024.105906] [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: 07/01/2024] [Revised: 09/10/2024] [Accepted: 09/23/2024] [Indexed: 10/01/2024]
Abstract
Epigenetic processes play a crucial role in mediating the impact of environmental energetic challenges, from overconsumption to starvation. Over-nutrition of energy-dense foods and sedentary lifestyles contribute to the development of obesity, characterized by excessive fat storage and impaired metabolic signaling, stemming from disrupted brain signaling. Conversely, dieting and physical activity facilitate body weight rebalancing and trigger adaptive neural responses. These adaptations involve the upregulation of neurogenesis, synaptic plasticity and optimized brain function and energy homeostasis, balanced hormone signaling, normal metabolism, and reduced inflammation. The transition of the brain from a maladaptive to an adaptive state is partially guided by epigenetic mechanisms. While epigenetic mechanisms underlying obesity-related brain changes have been described, their role in mediating the reversal of maladaptation/obesity through lifestyle interventions remains less explored. This review focuses on elucidating epigenetic mechanisms involved in hypothalamic adaptations induced by lifestyle interventions. Given that lifestyle interventions are widely prescribed and accessible approaches for weight loss and maintenance, it is our challenge to uncover epigenetic mechanisms moderating these hypothalamic-functional beneficial changes.
Collapse
Affiliation(s)
- Kayla Rapps
- Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel; Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel; Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan, Israel
| | - Aron Weller
- Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan, Israel; Department of Psychology, Bar Ilan University, Ramat-Gan, Israel
| | - Noam Meiri
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
| |
Collapse
|
281
|
Hoffman JI, Vendrami DLJ, Hench K, Chen RS, Stoffel MA, Kardos M, Amos W, Kalinowski J, Rickert D, Köhrer K, Wachtmeister T, Goebel ME, Bonin CA, Gulland FMD, Dasmahapatra KK. Genomic and fitness consequences of a near-extinction event in the northern elephant seal. Nat Ecol Evol 2024:10.1038/s41559-024-02533-2. [PMID: 39333394 DOI: 10.1038/s41559-024-02533-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/07/2024] [Indexed: 09/29/2024]
Abstract
Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability. However, actual outcomes are complex and depend on how a species' unique demography affects its genetic load. We used population genetic and veterinary pathology data, demographic modelling, whole-genome resequencing and forward genetic simulations to investigate the genomic and fitness consequences of a near-extinction event in the northern elephant seal. We found no evidence of inbreeding depression within the contemporary population for key fitness components, including body mass, blubber thickness and susceptibility to parasites and disease. However, we detected a genomic signature of a recent extreme bottleneck (effective population size = 6; 95% confidence interval = 5.0-7.5) that will have purged much of the genetic load, potentially leading to the lack of observed inbreeding depression in our study. Our results further suggest that deleterious genetic variation strongly impacted the post-bottleneck population dynamics of the northern elephant seal. Our study provides comprehensive empirical insights into the intricate dynamics underlying species-specific responses to anthropogenic bottlenecks.
Collapse
Affiliation(s)
- Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- British Antarctic Survey, Cambridge, UK.
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany.
| | - David L J Vendrami
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
| | - Kosmas Hench
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Rebecca S Chen
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Martin A Stoffel
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Alan Turing Institute, British Library, London, UK
| | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - William Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jörn Kalinowski
- Department of Microbial Genomics and Biotechnology, CeBiTec, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Rickert
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wachtmeister
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Mike E Goebel
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Carolina A Bonin
- Department of Marine and Environmental Sciences, Hampton University, Hampton, VA, USA
| | - Frances M D Gulland
- Karen C. Drayer Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | | |
Collapse
|
282
|
Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024; 23:579-594. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [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: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
Collapse
Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
283
|
Wu X, Xu M, Yang JR, Lu J. Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster. Nat Commun 2024; 15:8329. [PMID: 39333102 PMCID: PMC11437122 DOI: 10.1038/s41467-024-52660-4] [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: 09/26/2023] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Accuracy and efficiency are fundamental to mRNA translation. Codon usage bias is widespread across species. Despite the long-standing association between optimized codon usage and improved translation, our understanding of its evolutionary basis and functional effects remains limited. Drosophila is widely used to study codon usage bias, but genome-scale experimental data are scarce. Using high-resolution mass spectrometry data from Drosophila melanogaster, we show that optimal codons have lower translation errors than nonoptimal codons after accounting for these biases. Genomic-scale analysis of ribosome profiling data shows that optimal codons are translated more rapidly than nonoptimal codons. Although we find no long-term selection favoring synonymous mutations in D. melanogaster after diverging from D. simulans, we identify signatures of positive selection driving codon optimization in the D. melanogaster population. These findings expand our understanding of the functional consequences of codon optimization and serve as a foundation for future investigations.
Collapse
Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Mengze Xu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
284
|
Harris SE, Alexis MS, Giri G, Cavazos FF, Hu Y, Murn J, Aleman MM, Burge CB, Dominguez D. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Nat Commun 2024; 15:8400. [PMID: 39333159 PMCID: PMC11436793 DOI: 10.1038/s41467-024-52231-7] [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: 12/20/2023] [Accepted: 08/28/2024] [Indexed: 09/29/2024] Open
Abstract
While evolution is often considered from a DNA- and protein-centric view, RNA-based regulation can also impact gene expression and protein sequences. Here we examine interspecies differences in RNA-protein interactions using the conserved neuronal RNA-binding protein, Unkempt (UNK) as model. We find that roughly half of mRNAs bound in human are also bound in mouse. Unexpectedly, even when transcript-level binding was conserved across species differential motif usage was prevalent. To understand the biochemical basis of UNK-RNA interactions, we reconstitute the human and mouse UNK-RNA interactomes using a high-throughput biochemical assay. We uncover detailed features driving binding, show that in vivo patterns are captured in vitro, find that highly conserved sites are the strongest bound, and associate binding strength with downstream regulation. Furthermore, subtle sequence differences surrounding motifs are key determinants of species-specific binding. We highlight the complex features driving protein-RNA interactions and how these evolve to confer species-specific regulation.
Collapse
Affiliation(s)
- Sarah E Harris
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Maria S Alexis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Remix Therapeutics, Cambridge, MA, USA
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Francisco F Cavazos
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Yue Hu
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Dominguez
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA.
- RNA Discovery Center, University of North Carolina, Chapel Hill, NC, USA.
| |
Collapse
|
285
|
Zhu X, Liang Z, Ma J, Huang J, Wang L, Yao H, Wu Z. The cadDX operon contributes to cadmium resistance, oxidative stress resistance, and virulence in zoonotic streptococci. Vet Res 2024; 55:119. [PMID: 39334407 PMCID: PMC11430099 DOI: 10.1186/s13567-024-01371-1] [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: 07/01/2024] [Accepted: 08/13/2024] [Indexed: 09/30/2024] Open
Abstract
Mobile genetic elements (MGEs) enable bacteria to acquire novel genes and traits. However, the functions of cargo genes within MGEs remain poorly understood. The cadmium resistance operon cadDX is present in many gram-positive bacteria. Although cadDX has been reported to be involved in metal detoxification, its regulatory mechanisms and functions in bacterial pathogenesis are poorly understood. This study revealed that cadDX contributes to cadmium resistance, oxidative stress resistance, and virulence in Streptococcus suis, an important zoonotic pathogen in pigs and humans. CadX represses cadD expression by binding to the cadDX promoter. Notably, cadX responds to H2O2 stress through an additional promoter within the cadDX operon, mitigating the harmful effect of excessive cadD expression during oxidative stress. cadDX resides within an 11 K integrative and mobilizable element that can autonomously form circular structures. Moreover, cadDX is found in diverse MGEs, accounting for its widespread distribution across various bacteria, especially among pathogenic streptococci. Transferring cadDX into another zoonotic pathogen, Streptococcus agalactiae, results in similar phenotypes, including resistance to cadmium and oxidative stresses and increased virulence of S. agalactiae in mice. The new functions and regulatory mechanisms of cadDX shed light on the importance of the cadDX system in driving evolutionary adaptations and survival strategies across diverse gram-positive bacteria.
Collapse
Affiliation(s)
- Xinchi Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, 210014, China
| | - Zijing Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, 210014, China
| | - Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, 210014, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210014, China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, 210014, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210014, China.
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210014, China.
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, 210014, China.
- Guangdong Provincial Key Laboratory of Research On the Technology of Pig Breeding and Pig Disease Prevention, Guangzhou, 511400, China.
| |
Collapse
|
286
|
Kikuchi S, Sakamoto T, Matsunaga S, Sugiyama M, Iwamoto A. Plant chromosome polytenization contributes to suppression of root growth in high polyploids. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5703-5716. [PMID: 38970333 DOI: 10.1093/jxb/erae288] [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: 12/29/2023] [Accepted: 07/04/2024] [Indexed: 07/08/2024]
Abstract
Autopolyploidization, which refers to a polyploidization via genome duplication without hybridization, promotes growth in autotetraploids, but suppresses growth in high polyploids (autohexaploids or auto-octoploids). The mechanism underlying this growth suppression (i.e. 'high-ploidy syndrome') has not been comprehensively characterized. In this study, we conducted a kinematic analysis of the root apical meristem cells in Arabidopsis thaliana autopolyploids (diploid, tetraploid, hexaploid, and octoploid) to determine the effects of the progression of genome duplication on root growth. The results of the root growth analysis showed that tetraploidization increases the cell volume, but decreases cell proliferation. However, cell proliferation and volume growth are suppressed in high polyploids. Whole-mount fluorescence in situ hybridization analysis revealed extensive chromosome polytenization in the region where cell proliferation does not usually occur in the roots of high polyploids, which is likely to be at least partly correlated with the suppression of endoreduplication. The study findings indicate that chromosome polytenization is important for the suppressed growth of high polyploids.
Collapse
Affiliation(s)
- Suzuka Kikuchi
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuou-ku, Kumamoto-shi, Kumamoto, 860-8555, Japan
| | - Takuya Sakamoto
- Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama-shi, Kanagawa, 221-8686, Japan
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan
| | - Sachihiro Matsunaga
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8561, Japan
| | - Munetaka Sugiyama
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akitoshi Iwamoto
- Faculty of Science, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama-shi, Kanagawa, 221-8686, Japan
| |
Collapse
|
287
|
Maeda AE, Matsuo H, Muranaka T, Nakamichi N. Cold-induced degradation of core clock proteins implements temperature compensation in the Arabidopsis circadian clock. SCIENCE ADVANCES 2024; 10:eadq0187. [PMID: 39331704 PMCID: PMC11430399 DOI: 10.1126/sciadv.adq0187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024]
Abstract
The period of circadian clocks is maintained at close to 24 hours over a broad range of physiological temperatures due to temperature compensation of period length. Here, we show that the quantitative control of the core clock proteins TIMING OF CAB EXPRESSION 1 [TOC1; also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)] and PRR5 is crucial for temperature compensation in Arabidopsis thaliana. The prr5 toc1 double mutant has a shortened period at higher temperatures, resulting in weak temperature compensation. Low ambient temperature reduces amounts of PRR5 and TOC1. In low-temperature conditions, PRR5 and TOC1 interact with LOV KELCH PROTEIN 2 (LKP2), a component of the E3 ubiquitin ligase Skp, Cullin, F-box (SCF) complex. The lkp2 mutations attenuate low temperature-induced decrease of PRR5 and TOC1, and the mutants display longer period only at lower temperatures. Our findings reveal that the circadian clock maintains its period length despite ambient temperature fluctuations through temperature- and LKP2-dependent control of PRR5 and TOC1 abundance.
Collapse
Affiliation(s)
- Akari E. Maeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Tomoaki Muranaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| |
Collapse
|
288
|
Deng X, Yu YV, Jin YN. Non-canonical translation in cancer: significance and therapeutic potential of non-canonical ORFs, m 6A-modification, and circular RNAs. Cell Death Discov 2024; 10:412. [PMID: 39333489 PMCID: PMC11437038 DOI: 10.1038/s41420-024-02185-y] [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: 05/12/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
Translation is a decoding process that synthesizes proteins from RNA, typically mRNA. The conventional translation process consists of four stages: initiation, elongation, termination, and ribosome recycling. Precise control over the translation mechanism is crucial, as dysregulation in this process is often linked to human diseases such as cancer. Recent discoveries have unveiled translation mechanisms that extend beyond typical well-characterized components like the m7G cap, poly(A)-tail, or translation factors like eIFs. These mechanisms instead utilize atypical elements, such as non-canonical ORF, m6A-modification, and circular RNA, as key components for protein synthesis. Collectively, these mechanisms are classified as non-canonical translations. It is increasingly clear that non-canonical translation mechanisms significantly impact the various regulatory pathways of cancer, including proliferation, tumorigenicity, and the behavior of cancer stem cells. This review explores the involvement of a variety of non-canonical translation mechanisms in cancer biology and provides insights into potential therapeutic strategies for cancer treatment.
Collapse
Affiliation(s)
- Xiaoyi Deng
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Yanxun V Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China
| | - Youngnam N Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
289
|
Kumar S, Singh A, Bist CMS, Sharma M. Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability. Brief Funct Genomics 2024; 23:607-623. [PMID: 38679487 DOI: 10.1093/bfgp/elae017] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.
Collapse
Affiliation(s)
- Surender Kumar
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Anupama Singh
- Department of Biotechnology, College of Horticulture, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
| | - Chander Mohan Singh Bist
- Indian Council of Agricultural Research (ICAR)-Central Potato Research Institute, Shimla-171001, Himachal Pradesh, India
| | - Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Dharamshala-176215, Himachal Pradesh, India
| |
Collapse
|
290
|
Martin Říhová J, Gupta S, Nováková E, Hypša V. Fur microbiome as a putative source of symbiotic bacteria in sucking lice. Sci Rep 2024; 14:22326. [PMID: 39333204 PMCID: PMC11436785 DOI: 10.1038/s41598-024-73026-2] [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: 05/13/2024] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment. Since lice are permanent ectoparasites, often specific to the particular host, we screened various microbiomes associated with three rodent species (Microtus arvalis, Clethrionomys glareolus, and Apodemus flavicollis). The analyzed samples included fur, skin, spleen, and other ectoparasites sampled from these rodents. The fur microbiome data revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. The draft genomes of the environmental Neisseriaceae, assembled from all three rodent hosts, converged to a remarkably small size of approximately 1.4 Mbp, being even smaller than the genomes of the related symbionts. Our results suggest that the rodent fur microbiome can serve as a source for independent establishment of bacterial symbiosis in associated louse species. We further propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.
Collapse
Affiliation(s)
- Jana Martin Říhová
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Shruti Gupta
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, ASCR, v.v.i, České Budějovice, Czech Republic
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, ASCR, v.v.i, České Budějovice, Czech Republic.
| |
Collapse
|
291
|
Gallardo-Dodd CJ, Kutter C. The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer. Hum Genomics 2024; 18:109. [PMID: 39334294 PMCID: PMC11437681 DOI: 10.1186/s40246-024-00678-6] [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: 04/28/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
Collapse
Affiliation(s)
- Carlos J Gallardo-Dodd
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
| |
Collapse
|
292
|
Olagunju TA, Rosen BD, Neibergs HL, Becker GM, Davenport KM, Elsik CG, Hadfield TS, Koren S, Kuhn KL, Rhie A, Shira KA, Skibiel AL, Stegemiller MR, Thorne JW, Villamediana P, Cockett NE, Murdoch BM, Smith TPL. Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nat Commun 2024; 15:8277. [PMID: 39333471 PMCID: PMC11436988 DOI: 10.1038/s41467-024-52384-5] [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: 03/07/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024] Open
Abstract
Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosomal regions are similar in length, but the total chromosome size is substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity is accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 19MYA. The centromeres also differ dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosomes have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.
Collapse
Affiliation(s)
- Temitayo A Olagunju
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory (AGIL), ARS, USDA, Beltsville, MD, USA
| | - Holly L Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Gabrielle M Becker
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA
| | | | - Christine G Elsik
- Divisions of Animal Sciences and Plant Science & Technology, University of Missouri, Columbia, MO, USA
| | - Tracy S Hadfield
- Animal, Dairy and Veterinary Sciences (ADVS), Utah State University, Logan, UT, USA
| | - Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center (USMARC), ARS, USDA, Clay Center, NE, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katie A Shira
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA
| | - Amy L Skibiel
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA
| | - Morgan R Stegemiller
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA
| | | | - Patricia Villamediana
- Department of Dairy and Food Science, South Dakota State University, Brookings, SD, USA
| | - Noelle E Cockett
- Animal, Dairy and Veterinary Sciences (ADVS), Utah State University, Logan, UT, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Sciences (AVFS), University of Idaho, Moscow, ID, USA.
| | - Timothy P L Smith
- U.S. Meat Animal Research Center (USMARC), ARS, USDA, Clay Center, NE, USA.
| |
Collapse
|
293
|
Ai L, Qi Y, Hu Y, Zhu C, Liu K, Li F, Ye F, Dai H, Wu Y, Kuai Q, Nie D, Shan L, Zhang Y, Wang C, Tan W. The epidemiological and infectious characteristics of novel types of Coxiella burnetii co-infected with Coxiella-like microorganisms from Xuyi County, Jiangsu province, China. BMC Infect Dis 2024; 24:1041. [PMID: 39333956 PMCID: PMC11430510 DOI: 10.1186/s12879-024-09924-7] [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: 02/24/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Coxiella burnetii (C. burnetii) is the causative agent of Q fever, a type of zoonoses withwidespread distribution. In 2019, a case of Q fever was diagnosed by metagenomic next-generation sequencing (mNGS) method in Xuyi County (Jiangsu province, China). The seroprevalence of previous fever patients and the molecular epidemiology of Coxiella in wild hedgehogs and harbouring ticks around the confirmed patient were detected to reveal the genetic characteristics and pathogenicity of the Coxiella strains. Four of the 90 serum samples (4.44%) were positive for specific C. burnetii IgM antibody, suggesting that local humans are at risk of Q fever. The positive rates of C. burnetii in hedgehogs and ticks were 21.9% (7/32) and 70.5% (122/173), respectively. At least 3 strains of Coxiella were found prevalent in the investigated area, including one new genotype of pathogenic C. burnetii (XYHT29) and two non-pathogenic Coxiella-like organisms (XYHT19 and XYHT3). XYHT29 carried by ticks and wild hedgehogs successfully infected mice, imposing a potential threat to local humans. XYHT19, a novel Coxiella-like microorganism, was first discovered in the world to co-infect with C. burnetii in Haemaphysalis flava. The study provided significant epidemic information that could be used for prevention and control strategies against Q fever for local public health departments and medical institutions.
Collapse
Affiliation(s)
- Lele Ai
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Yong Qi
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Yue Hu
- Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Changqiang Zhu
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Kangle Liu
- Institute of Rocket Force Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Feng Li
- Yancheng Center for Disease Control and Prevention, Yancheng, China
| | - Fuqiang Ye
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Han Dai
- Eastern Theater General Hospital, Nanjing, China
| | - Yifan Wu
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Qiyuan Kuai
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Danyue Nie
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China
| | - Laiyou Shan
- Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yan Zhang
- Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Changjun Wang
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Weilong Tan
- Nanjing Bioengineer (Gene) Center for Medicines, Nanjing, China.
| |
Collapse
|
294
|
Komza M, Chipuk JE. Mitochondrial metabolism: A moving target in hepatocellular carcinoma therapy. J Cell Physiol 2024:e31441. [PMID: 39324415 DOI: 10.1002/jcp.31441] [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: 05/01/2024] [Revised: 08/21/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024]
Abstract
Mitochondria are pivotal contributors to cancer mechanisms due to their homeostatic and pathological roles in cellular bioenergetics, biosynthesis, metabolism, signaling, and survival. During transformation and tumor initiation, mitochondrial function is often disrupted by oncogenic mutations, leading to a metabolic profile distinct from precursor cells. In this review, we focus on hepatocellular carcinoma, a cancer arising from metabolically robust and nutrient rich hepatocytes, and discuss the mechanistic impact of altered metabolism in this setting. We provide distinctions between normal mitochondrial activity versus disease-related function which yielded therapeutic opportunities, along with highlighting recent preclinical and clinical efforts focused on targeting mitochondrial metabolism. Finally, several novel strategies for exploiting mitochondrial programs to eliminate hepatocellular carcinoma cells in metabolism-specific contexts are presented to integrate these concepts and gain foresight into the future of mitochondria-focused therapeutics.
Collapse
Affiliation(s)
- Monika Komza
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jerry Edward Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, New York, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn School of Medicine at Mount Sinai, The Diabetes, Obesity, and Metabolism Institute, New York, New York, USA
| |
Collapse
|
295
|
Goldfeld EI, Kelly BE, Ring KL. What About the Others? Clinical Management of Gynecologic Cancer Risk in Patients With Moderate-Risk Hereditary Cancer Genes (ATM, BRIP1, RAD51C, RAD51D, and PALB2). Clin Obstet Gynecol 2024:00003081-990000000-00172. [PMID: 39324947 DOI: 10.1097/grf.0000000000000897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Hereditary cancer syndromes associated with gynecologic malignancies account for up to 18% of all cases of ovarian, uterine, and cervical cancers, and identification of these syndromes has implications for cancer screening and risk reduction techniques in affected patients. The associated cancer risks with moderate-penetrance genes are rapidly evolving and present variable risks for the provider counseling the patient. In this review, we detail the cancer risk and management of patients with germline PV in the moderate-risk hereditary cancer genes ATM, BRIP1, RAD51C, RAD51D, and PALB2.
Collapse
Affiliation(s)
- Ester I Goldfeld
- Department of Obstetrics and Gynecology, University of Virginia Health System, Charlottesville, Virginia
| | | | | |
Collapse
|
296
|
Hawley RS, Salz HK, McKim KS, Sekelsky J. The passing of the last oracle: Adelaide Carpenter and Drosophila meiosis. Chromosoma 2024:10.1007/s00412-024-00825-x. [PMID: 39325143 DOI: 10.1007/s00412-024-00825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Affiliation(s)
- R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
| | - Helen K Salz
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Kim S McKim
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| |
Collapse
|
297
|
De-Paula RB, Bacolla A, Syed A, Tainer JA. Enriched G4 forming repeats in the human genome are associated with robust well-coordinated transcription and reduced cancer transcriptome variation. J Biol Chem 2024:107822. [PMID: 39341500 DOI: 10.1016/j.jbc.2024.107822] [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: 05/24/2024] [Revised: 09/01/2024] [Accepted: 09/21/2024] [Indexed: 10/01/2024] Open
Abstract
Non-B DNA G-quadruplex (G4) structures with guanine (G) runs of 2-4 repeats can trigger opposing experimental transcriptional impacts. Here, we employed bioinformatic algorithms to comprehensively assess correlations of steady-state RNA transcript levels with all putative G4 sequence (pG4) locations genome-wide in three mammalian genomes and in normal and tumor human tissues. The human pG4-containing gene set displays higher expression levels than the set without pG4, supporting and extending some prior observations. pG4 enrichment at transcription start sites (TSS) in human, but not chimpanzee and mouse genomes, suggests possible positive selection pressure for pG4 at human TSS, potentially driving genome rewiring and gene expression divergence between human and chimpanzee. Comprehensive bioinformatic analyses revealed lower pG4-containing gene set variability in humans and among different pG4 genes in tumors. As G4 stabilizers are under therapeutic consideration for cancer and pathogens, such distinctions between human normal and tumor G4s along with other species merit attention. Furthermore, in germline and cancer sequences, the most mutagenic pG4 mapped to regions promoting alternative DNA structures. Overall findings establish high pG4 at TSS as a human genome attribute statistically associated with robust well-coordinated transcription and reduced cancer transcriptome variation with implications for biology, model organisms, and medicine.
Collapse
Affiliation(s)
- Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| |
Collapse
|
298
|
Gawande PS, Manigandan V, Ganesh R S, Kannan VR, Ramu K, Murthy MVR. Metagenomic analysis of pathogenic bacteria and virulence factor genes in coastal sediments from highly urbanized cities of India. Microb Pathog 2024; 196:106984. [PMID: 39341578 DOI: 10.1016/j.micpath.2024.106984] [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: 05/15/2024] [Revised: 09/25/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
A metagenomic approach was employed to investigate the diversity and distribution of Virulence Factors Genes (VFGs) and Pathogenic Bacteria (PB) in sediment samples collected from highly urbanized cities along the Indian coastline. Among the study locations, Mumbai, Veraval and Paradeep showed a higher abundance of PB, with Vibrio and Pseudomonas as dominant at the genus level, and Escherichia coli and Pseudomonas aeruginosa at the species level. In total, 295 VFGs were detected across all sediment samples, of which 40 VFGs showed a similarity of ≥90 % with the Virulence Database (VFDB) and were focused in this study. Among the virulent proteins, twitching motility protein and flagellar P-ring were found to be prevalent and significantly associated with Vibrio spp., and Pseudomonas spp., indicating potential bacterial pathogenicity. This investigation serves as the basis for future studies and provides insights into the comprehensive taxonomic profiles of PB, VFGs and their associated PB in the coastal sediments of India.
Collapse
Affiliation(s)
- Pradip Sahebrao Gawande
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, Tamil Nadu, India; Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
| | - Vajravelu Manigandan
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, Tamil Nadu, India
| | - Sankar Ganesh R
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, Tamil Nadu, India
| | - V Rajesh Kannan
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - K Ramu
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, Tamil Nadu, India.
| | - M V Ramana Murthy
- National Centre for Coastal Research, Ministry of Earth Sciences, Chennai, Tamil Nadu, India
| |
Collapse
|
299
|
Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024; 88:e0000624. [PMID: 38995044 PMCID: PMC11426024 DOI: 10.1128/mmbr.00006-24] [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: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
Collapse
Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| |
Collapse
|
300
|
Merlin JPJ, Abrahamse H. Optimizing CRISPR/Cas9 precision: Mitigating off-target effects for safe integration with photodynamic and stem cell therapies in cancer treatment. Biomed Pharmacother 2024; 180:117516. [PMID: 39332185 DOI: 10.1016/j.biopha.2024.117516] [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: 07/12/2024] [Revised: 09/22/2024] [Accepted: 09/25/2024] [Indexed: 09/29/2024] Open
Abstract
CRISPR/Cas9 precision genome editing has revolutionized cancer treatment by introducing specific alterations to the cancer genome. But the therapeutic potential of CRISPR/Cas9 is limited by off-target effects, which can cause undesired changes to genomic regions and create major safety concerns. The primary emphasis lies in their implications within the realm of cancer photodynamic therapy (PDT), where precision is paramount. PDT is a promising cancer treatment method; nevertheless, its effectiveness is severely limited and readily leads to recurrence due to the therapeutic resistance of cancer stem cells (CSCs). With a focus on targeted genome editing into cancer cells during PDT and stem cell treatment (SCT), the review aims to further the ongoing search for safer and more accurate CRISPR/Cas9-mediated methods. At the core of this exploration are recent advancements and novel techniques that offer promise in mitigating the risks associated with off-target effects. With a focus on cancer PDT and SCT, this review critically assesses the landscape of off-target effects in CRISPR/Cas9 applications, offering a comprehensive knowledge of their nature and prevalence. A key component of the review is the assessment of cutting-edge delivery methods, such as technologies based on nanoparticles (NPs), to optimize the distribution of CRISPR components. Additionally, the study delves into the intricacies of guide RNA design, focusing on advancements that bolster specificity and minimize off-target effects, crucial elements in ensuring the precision required for effective cancer PDT and SCT. By synthesizing insights from various methodologies, including the exploration of innovative genome editing tools and leveraging robust validation methods and bioinformatics tools, the review aspires to chart a course towards more reliable and precise CRISPR-Cas9 applications in cancer PDT and SCT. For safe PDT and SCT integration in cancer therapy, CRISPR/Cas9 precision optimization is essential. Utilizing sophisticated molecular and computational techniques to address off-target effects is crucial to realizing the therapeutic promise of these technologies, which will ultimately lead to the development of individualized and successful cancer treatment strategies. Our long-term goals are to improve precision genome editing for more potent cancer therapy approaches by refining the way CRISPR/Cas9 is integrated with photodynamic and stem cell therapies.
Collapse
Affiliation(s)
- J P Jose Merlin
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa.
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, South Africa
| |
Collapse
|