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Tang Z, Zhang T, Yang B, Su J, Song Q. spaCI: deciphering spatial cellular communications through adaptive graph model. Brief Bioinform 2023; 24:bbac563. [PMID: 36545790 PMCID: PMC9851335 DOI: 10.1093/bib/bbac563] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Cell-cell communications are vital for biological signalling and play important roles in complex diseases. Recent advances in single-cell spatial transcriptomics (SCST) technologies allow examining the spatial cell communication landscapes and hold the promise for disentangling the complex ligand-receptor (L-R) interactions across cells. However, due to frequent dropout events and noisy signals in SCST data, it is challenging and lack of effective and tailored methods to accurately infer cellular communications. Herein, to decipher the cell-to-cell communications from SCST profiles, we propose a novel adaptive graph model with attention mechanisms named spaCI. spaCI incorporates both spatial locations and gene expression profiles of cells to identify the active L-R signalling axis across neighbouring cells. Through benchmarking with currently available methods, spaCI shows superior performance on both simulation data and real SCST datasets. Furthermore, spaCI is able to identify the upstream transcriptional factors mediating the active L-R interactions. For biological insights, we have applied spaCI to the seqFISH+ data of mouse cortex and the NanoString CosMx Spatial Molecular Imager (SMI) data of non-small cell lung cancer samples. spaCI reveals the hidden L-R interactions from the sparse seqFISH+ data, meanwhile identifies the inconspicuous L-R interactions including THBS1-ITGB1 between fibroblast and tumours in NanoString CosMx SMI data. spaCI further reveals that SMAD3 plays an important role in regulating the crosstalk between fibroblasts and tumours, which contributes to the prognosis of lung cancer patients. Collectively, spaCI addresses the challenges in interrogating SCST data for gaining insights into the underlying cellular communications, thus facilitates the discoveries of disease mechanisms, effective biomarkers and therapeutic targets.
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Affiliation(s)
- Ziyang Tang
- Department of Computer and Information Technology, Purdue University, Indiana, USA
| | - Tonglin Zhang
- Department of Statistics, Purdue University, Indiana, USA
| | - Baijian Yang
- Department of Computer and Information Technology, Purdue University, Indiana, USA
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indiana, USA
| | - Qianqian Song
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Atrium Health Wake Forest Baptist, Winston Salem, NC, USA
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA
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Naidu A, Lulu S S. Mucosal and systemic immune responses to Vibrio cholerae infection and oral cholera vaccines (OCVs) in humans: a systematic review. Expert Rev Clin Immunol 2022; 18:1307-1318. [PMID: 36255170 DOI: 10.1080/1744666x.2022.2136650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Cholera is an enteric disease caused by Vibrio cholerae, a water-borne pathogen, and characterized by severe diarrhea. Vaccines have been recommended for use by the WHO in resource-limited settings. Efficacies of the currently licensed cholera vaccines are not optimal in endemic settings and low in children below the age of five, a section of the population most susceptible to the disease. Development of next generation of cholera vaccines would require a detailed understanding of the required protective immune responses. AREA COVERED In this review, we revisit clinical trials which are focused on the early transcriptional mucosal responses elicited during Vibrio cholerae infection and upon vaccination along with summarizing various components of the effector immune response against Vibrio cholerae. EXPERT OPINION The inability of currently licensed killed/inactivated vaccines to elicit key inflammatory pathways locally may explain their restricted efficacy in endemic settings. More studies are required to understand the immunogenicity of the live attenuated cholera vaccine in these regions. Various extrinsic and intrinsic factors influence anti-cholera immunity and need to be considered to develop region-specific next generation vaccines.
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Affiliation(s)
- Akshayata Naidu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sajitha Lulu S
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
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Teng Z, Meng LY, Yang JK, He Z, Chen XG, Liu Y. Bridging nanoplatform and vaccine delivery, a landscape of strategy to enhance nasal immunity. J Control Release 2022; 351:456-475. [PMID: 36174803 DOI: 10.1016/j.jconrel.2022.09.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
Vaccination is an urgently needed and effective option to address epidemic, cancers, allergies, and other diseases. Nasal administration of vaccines offers many benefits over needle-based injection including high compliance and less risk of infection. Inactivated or attenuated vaccines as convention vaccine present potential risks of pathogenic virulence reversal, the focus of nasal vaccine development has shifted to the use of next-generation (subunit and nucleic acid) vaccines. However, subunit and nucleic acid vaccine intranasally have numerous challenges in development and utilization due to mucociliary clearance, mucosal epithelial tight junction, and enzyme/pH degradation. Nanoplatforms as ideal delivery systems, with the ability to enhance the retention, penetration, and uptake of nasal mucosa, shows great potential in improving immunogenic efficacy of nasal vaccine. This review provides an overview of delivery strategies for overcoming nasal barrier, including mucosal adhesion, mucus penetration, targeting of antigen presenting cells (APCs), enhancement of paracellular transportation. We discuss methods of enhancing antigen immunogenicity by nanoplatforms as immune-modulators or multi-antigen co-delivery. Meanwhile, we describe the application status and development prospect of nanoplatforms for nasal vaccine administration. Development of nanoplatforms for vaccine delivery via nasal route will facilitate large-scale and faster global vaccination, helping to address the threat of epidemics.
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Affiliation(s)
- Zhuang Teng
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Ling-Yang Meng
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Jian-Ke Yang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Zheng He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China
| | - Xi-Guang Chen
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, PR China
| | - Ya Liu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, PR China.
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Overgaard E, Morris B, Mohammad Mousa O, Price E, Rodriguez A, Cufurovic L, Beard RS, Tinker JK. Cellular Activity of Salmonella Typhimurium ArtAB Toxin and Its Receptor-Binding Subunit. Toxins (Basel) 2021; 13:toxins13090599. [PMID: 34564603 PMCID: PMC8472264 DOI: 10.3390/toxins13090599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022] Open
Abstract
Salmonellosis is among the most reported foodborne illnesses in the United States. The Salmonellaenterica Typhimurium DT104 phage type, which is associated with multidrug-resistant disease in humans and animals, possesses an ADP-ribosylating toxin called ArtAB. Full-length artAB has been found on a number of broad-host-range non-typhoidal Salmonella species and serovars. ArtAB is also homologous to many AB5 toxins from diverse Gram-negative pathogens, including cholera toxin (CT) and pertussis toxin (PT), and may be involved in Salmonella pathogenesis, however, in vitro cellular toxicity of ArtAB has not been characterized. artAB was cloned into E. coli and initially isolated using a histidine tag (ArtABHIS) and nickel chromatography. ArtABHIS was found to bind to African green monkey kidney epithelial (Vero) cells using confocal microscopy and to interact with glycans present on fetuin and monosialotetrahexosylganglioside (GM1) using ELISA. Untagged, or native, holotoxin (ArtAB), and the pentameric receptor-binding subunit (ArtB) were purified from E. coli using fetuin and d-galactose affinity chromatography. ArtAB and ArtB metabolic and cytotoxic activities were determined using Vero and Chinese hamster ovary (CHO) epithelial cells. Vero cells were more sensitive to ArtAB, however, incubation with both cell types revealed only partial cytotoxicity over 72 h, similar to that induced by CT. ArtAB induced a distinctive clustering phenotype on CHO cells over 72 h, similar to PT, and an elongated phenotype on Vero cells, similar to CT. The ArtB binding subunit alone also had a cytotoxic effect on CHO cells and induced morphological rounding. Results indicate that this toxin induces distinctive cellular outcomes. Continued biological characterization of ArtAB will advance efforts to prevent disease caused by non-typhoidal Salmonella.
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Affiliation(s)
- Elise Overgaard
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA;
| | - Brad Morris
- Department of Biology, Boise State University, Boise, ID 83725, USA; (B.M.); (O.M.M.); (A.R.); (L.C.)
| | - Omid Mohammad Mousa
- Department of Biology, Boise State University, Boise, ID 83725, USA; (B.M.); (O.M.M.); (A.R.); (L.C.)
| | - Emily Price
- Idaho Veterans Research and Education Foundation, Infectious Diseases Section, Boise, ID 83702, USA;
| | - Adriana Rodriguez
- Department of Biology, Boise State University, Boise, ID 83725, USA; (B.M.); (O.M.M.); (A.R.); (L.C.)
| | - Leyla Cufurovic
- Department of Biology, Boise State University, Boise, ID 83725, USA; (B.M.); (O.M.M.); (A.R.); (L.C.)
| | - Richard S. Beard
- Biomolecular Research Center, Boise State University, Boise, ID 83725, USA;
| | - Juliette K. Tinker
- Biomolecular Sciences Graduate Program, Boise State University, Boise, ID 83725, USA;
- Department of Biology, Boise State University, Boise, ID 83725, USA; (B.M.); (O.M.M.); (A.R.); (L.C.)
- Correspondence: ; Tel.: +1-208-426-5472
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Baek Y, Lee D, Lee J, Yoon Y, Nair GB, Kim DW, Kim EJ. Cholera Toxin Production in Vibrio cholerae O1 El Tor Biotype Strains in Single-Phase Culture. Front Microbiol 2020; 11:825. [PMID: 32431681 PMCID: PMC7214932 DOI: 10.3389/fmicb.2020.00825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/07/2020] [Indexed: 11/23/2022] Open
Abstract
Vibrio cholerae O1 serogroup strains have been classified into classical and El Tor biotypes. Cholera, a life-threatening diarrheal disease, can be caused by either biotype through the cholera toxin (CT) that they produce. To increase our knowledge of the pathogenicity of bacteria, we must understand the toxigenicity of bacteria. CT production by classical biotype strains in simple single-phase cell cultures has been established; however, special culture media and growth conditions that are not appropriate for mass production of CT are required to facilitate CT production in El Tor biotype strains. In this report, we produced CT in El Tor biotype strains using simple media and single-phase culture conditions. A single point mutation in ToxT, a transcriptional activator of toxin co-regulated pilus (TCP) and CT, enabled the El Tor biotype strains to produce CT in similar quantities as classical biotype strains in single-phase laboratory culture conditions. CT production capacity varied between El Tor biotype strains. Wave 2 and 3 atypical El Tor strains tended to produce more CT than prototype Wave 1 strains. Wave 2 and 3 strains lack neutral fermentation; however, the capacity for neutral fermentation was not associated with significant differences in CT production by El Tor biotype strains. The Wave 3 strain that caused the 2010 cholera outbreak in Haiti produced CT only when neutral fermentation was abolished. The disparity in CT production between the seventh cholera pandemic strains highlight the differences in virulence between strains and the cause of population changes in V. cholerae.
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Affiliation(s)
- Yeongjun Baek
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
| | - Donghyun Lee
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
| | - Jiwon Lee
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
| | - Youngbae Yoon
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
| | - G Balakrish Nair
- Microbiome Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, South Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, South Korea
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Ivanov K, Garanina E, Rizvanov A, Khaiboullina S. Inflammasomes as Targets for Adjuvants. Pathogens 2020; 9:E252. [PMID: 32235526 PMCID: PMC7238254 DOI: 10.3390/pathogens9040252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 11/16/2022] Open
Abstract
Inflammasomes are an essential part of the innate immune system. They are necessary for the development of a healthy immune response against infectious diseases. Inflammasome activation leads to the secretion of pro-inflammatory cytokines such as IL-1β and IL-18, which stimulate the adaptive immune system. Inflammasomes activators can be used as adjuvants to provide and maintain the strength of the immune response. This review is focused on the mechanisms of action and the effects of adjuvants on inflammasomes. The therapeutic and prophylaxis significance of inflammasomes in infectious diseases is also discussed.
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Affiliation(s)
- Konstantin Ivanov
- Kazan Federal University, 420008 Kazan, Russia; (K.I.); (E.G.); (A.R.)
| | - Ekaterina Garanina
- Kazan Federal University, 420008 Kazan, Russia; (K.I.); (E.G.); (A.R.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Albert Rizvanov
- Kazan Federal University, 420008 Kazan, Russia; (K.I.); (E.G.); (A.R.)
| | - Svetlana Khaiboullina
- Kazan Federal University, 420008 Kazan, Russia; (K.I.); (E.G.); (A.R.)
- University of Nevada, Reno, NV 89557, USA
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