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Zhang L, Chai D, Chen C, Li C, Qiu Z, Kuang T, Parveena M, Dong K, Yu J, Deng W, Wang W. Mycobiota and C-Type Lectin Receptors in Cancers: Know thy Neighbors. Front Microbiol 2022; 13:946995. [PMID: 35910636 PMCID: PMC9326027 DOI: 10.3389/fmicb.2022.946995] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 11/15/2022] Open
Abstract
Numerous studies have demonstrated the importance of gut bacteria in the development of malignancy, while relatively little research has been done on gut mycobiota. As a part of the gut microbiome, the percentage of gut mycobiota is negligible compared to gut bacteria. However, the effect of gut fungi on human health and disease is significant. This review systematically summarizes the research progress on mycobiota, especially gut fungi, in patients with head and neck cancer (HNC), esophageal cancer (EC), gastric cancer (GC), colorectal cancer (CRC), hepatocellular carcinoma (HCC), pancreatic cancer, melanoma, breast cancer, and lung carcinoma-induced cachexia. Moreover, we also describe, for the first time in detail, the role of the fungal recognition receptors, C-type lectin receptors (CLRs) (Dectin-1, Dectin-2, Dectin-3, and Mincle) and their downstream effector caspase recruitment domain-containing protein 9 (CARD9), in tumors to provide a reference for further research on intestinal fungi in the diagnosis and treatment of malignant tumors.
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Affiliation(s)
- Lilong Zhang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Dongqi Chai
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Chen Chen
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chunlei Li
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Zhendong Qiu
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Tianrui Kuang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Mungur Parveena
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, China
| | - Keshuai Dong
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jia Yu
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenhong Deng
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Wenhong Deng,
| | - Weixing Wang
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Weixing Wang,
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Kodali P, Schoeder CT, Schmitz S, Crowe JE, Meiler J. RosettaCM for antibodies with very long HCDR3s and low template availability. Proteins 2021; 89:1458-1472. [PMID: 34176159 PMCID: PMC8492515 DOI: 10.1002/prot.26166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 11/07/2022]
Abstract
Antibody-antigen co-crystal structures are a valuable resource for the fundamental understanding of antibody-mediated immunity. Determination of structures with antibodies in complex with their antigens, however, is a laborious task without guarantee of success. Therefore, homology modeling of antibodies and docking to their respective antigens has become a very important technique to drive antibody and vaccine design. The quality of the antibody modeling process is critical for the success of these endeavors. Here, we compare different computational protocols for predicting antibody structure from sequence in the biomolecular modeling software Rosetta-all of which use multiple existing antibody structures to guide modeling. Specifically, we compare protocols developed solely to predict antibody structure (RosettaAntibody, AbPredict) with a universal homology modeling protocol (RosettaCM). Following recent advances in homology modeling with multiple templates simultaneously, we propose that the use of multiple templates over the same antibody regions may improve modeling performance. To evaluate whether multi-template comparative modeling with RosettaCM can improve the modeling accuracy of antibodies over existing methods, this study compares the performance of the three modeling algorithms when modeling human antibodies taken from antibody-antigen co-crystal structures. In these benchmarking experiments, RosettaCM outperformed other methods when modeling antibodies with long HCDR3s and few available templates.
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Affiliation(s)
- Pranav Kodali
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.,Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
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3
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Vallianou N, Kounatidis D, Christodoulatos GS, Panagopoulos F, Karampela I, Dalamaga M. Mycobiome and Cancer: What Is the Evidence? Cancers (Basel) 2021; 13:cancers13133149. [PMID: 34202433 PMCID: PMC8269322 DOI: 10.3390/cancers13133149] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Although comprising a much smaller proportion of the human microbiome, the fungal community has gained much more attention lately due to its multiple and yet undiscovered interactions with the human bacteriome and the host. Head and neck cancer carcinoma, colorectal carcinoma, and pancreatic ductal adenocarcinoma have been associated with dissimilarities in the composition of the mycobiome between cases with cancer and non-cancer subjects. In particular, an abundance of Malassezia has been associated with the onset and progression of colorectal carcinoma and pancreatic adenocarcinoma, while the genera Schizophyllum, a member of the oral mycobiome, is suggested to exhibit anti-cancer potential. The use of multi-omics will further assist in establishing whether alterations in the human mycobiome are causal or a consequence of specific types of cancers. Abstract Background: To date, most researchhas focused on the bacterial composition of the human microbiota. In this review, we synopsize recent data on the human mycobiome and cancer, highlighting specific cancer types based on current available evidence, presenting interesting perspectives and limitations of studies and laboratory methodologies. Recent findings: Head and neck cancer carcinoma (HNCC), colorectal carcinoma (CRC) and pancreatic ductal adenocarcinoma (PDA) have been associated with dissimilarities in the composition of mycobiota between cancer cases and non-cancer participants. Overall, fungal dysbiosis with decreased fungal richness and diversity was common in cancer patients; however, a specific mycobiotic signature in HNSCC or CRC has not emerged. Different strains of Candida albicans have been identified among cases with HNCC, whilst Lichtheimia corymbifera, a member of the Mucoraceae family, has been shown to predominate among patients with oral tongue cancer. Virulence factors of Candida spp. include the formation of biofilm and filamentation, and the secretion of toxins and metabolites. CRC patients present a dysregulated ratio of Basidiomycota/Ascomycota. Abundance of Malassezia has been linked to the occurrence and progression of CRC and PDA, particularly in animal models of PDA. Interestingly, Schizophyllum, a component of the oral mycobiome, may exhibit anti-cancer potential. Conclusion: The human mycobiome, per se, along with its interactions with the human bacteriome and the host, may be implicated in the promotion and progression of carcinogenesis. Fungi may be used as diagnostic and prognostic/predictive tools or treatment targets for cancer in the coming years. More large-scale, prospective, multicentric and longitudinal studies with an integrative multi-omics methodology are required to examine the precise contribution of the mycobiome in the etiopathogenesis of cancer, and to delineate whether changes that occur in the mycobiome are causal or consequent of cancer.
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Affiliation(s)
- Natalia Vallianou
- First Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Str., 10676 Athens, Greece; (D.K.); (F.P.)
- Correspondence: (N.V.); (M.D.)
| | - Dimitris Kounatidis
- First Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Str., 10676 Athens, Greece; (D.K.); (F.P.)
| | - Gerasimos Socrates Christodoulatos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, Goudi, 11527 Athens, Greece;
| | - Fotis Panagopoulos
- First Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Str., 10676 Athens, Greece; (D.K.); (F.P.)
| | - Irene Karampela
- Second Department of Critical Care, Attikon General University Hospital, Medical School, National and Kapodistrian University of Athens, 1 Rimini St, Haidari, 12462 Athens, Greece;
| | - Maria Dalamaga
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias, Goudi, 11527 Athens, Greece;
- Correspondence: (N.V.); (M.D.)
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Niego AG, Rapior S, Thongklang N, Raspé O, Jaidee W, Lumyong S, Hyde KD. Macrofungi as a Nutraceutical Source: Promising Bioactive Compounds and Market Value. J Fungi (Basel) 2021; 7:397. [PMID: 34069721 PMCID: PMC8161071 DOI: 10.3390/jof7050397] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/16/2021] [Accepted: 05/16/2021] [Indexed: 02/06/2023] Open
Abstract
Macrofungi production and economic value have been increasing globally. The demand for macrofungi has expanded rapidly owing to their popularity among consumers, pleasant taste, and unique flavors. The presence of high quality proteins, polysaccharides, unsaturated fatty acids, minerals, triterpene sterols, and secondary metabolites makes macrofungi an important commodity. Macrofungi are well known for their ability to protect from or cure various health problems, such as immunodeficiency, cancer, inflammation, hypertension, hyperlipidemia, hypercholesterolemia, and obesity. Many studies have demonstrated their medicinal properties, supported by both in vivo and in vitro experimental studies, as well as clinical trials. Numerous bioactive compounds isolated from mushrooms, such as polysaccharides, proteins, fats, phenolic compounds, and vitamins, possess strong bioactivities. Consequently, they can be considered as an important source of nutraceuticals. Numerous edible mushrooms have been studied for their bioactivities, but only a few species have made it to the market. Many species remain to be explored. The converging trends and popularity of eastern herbal medicines, natural/organic food product preference, gut-healthy products, and positive outlook towards sports nutrition are supporting the growth in the medicinal mushroom market. The consumption of medicinal mushrooms as functional food or dietary supplement is expected to markedly increase in the future. The global medicinal mushroom market size is projected to increase by USD 13.88 billion from 2018 to 2022. The global market values of promising bioactive compounds, such as lentinan and lovastatin, are also expected to rise. With such a market growth, mushroom nutraceuticals hold to be very promising in the years to come.
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Affiliation(s)
- Allen Grace Niego
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (A.G.N.); (N.T.); (O.R.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Iloilo Science and Technology University, La Paz, Iloilo 5000, Philippines
| | - Sylvie Rapior
- Laboratory of Botany, Phytochemistry and Mycology, Faculty of Pharmacy, CEFE, CNRS, University Montpellier, EPHE, IRD, CS 14491, 15 Avenue Charles Flahault, CEDEX 5, 34093 Montpellier, France;
| | - Naritsada Thongklang
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (A.G.N.); (N.T.); (O.R.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Olivier Raspé
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (A.G.N.); (N.T.); (O.R.)
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Wuttichai Jaidee
- Medicinal Plants Innovation Center, Mae Fah Luang University, Chiang Rai 57100, Thailand;
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; (A.G.N.); (N.T.); (O.R.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
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3D Structural Insights into β-Glucans and Their Binding Proteins. Int J Mol Sci 2021; 22:ijms22041578. [PMID: 33557270 PMCID: PMC7915573 DOI: 10.3390/ijms22041578] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/03/2022] Open
Abstract
β(1,3)-glucans are a component of fungal and plant cell walls. The β-glucan of pathogens is recognized as a non-self-component in the host defense system. Long β-glucan chains are capable of forming a triple helix structure, and the tertiary structure may profoundly affect the interaction with β-glucan-binding proteins. Although the atomic details of β-glucan binding and signaling of cognate receptors remain mostly unclear, X-ray crystallography and NMR analyses have revealed some aspects of β-glucan structure and interaction. Here, we will review three-dimensional (3D) structural characteristics of β-glucans and the modes of interaction with β-glucan-binding proteins.
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Shay E, Sangwan N, Padmanabhan R, Lundy S, Burkey B, Eng C. Bacteriome and mycobiome and bacteriome-mycobiome interactions in head and neck squamous cell carcinoma. Oncotarget 2020; 11:2375-2386. [PMID: 32637029 PMCID: PMC7321695 DOI: 10.18632/oncotarget.27629] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
The etiology of head and neck squamous cell carcinoma (HNSCC) is not fully understood. While risk factors such as positive human papilloma virus (HPV) status, smoking and tobacco use have been identified, they do not account for all cases of the disease. We aimed to characterize the bacteriome, mycobiome and mycobiome-bacteriome interactions of oral wash in HNSCC patients and to determine if they are distinct from those of the oral wash of matched non-HNSCC patients. Oral wash samples were collected from 46 individuals with HNSCC and 46 controls for microbiome analyses. We identified three fungal phyla and eleven bacterial phyla of which Ascomycota (fungi, 72%) and Firmicutes (bacteria, 39%) were the most dominant, respectively. A number of organisms were identified as being differentially abundant between oral wash samples from patients with HNSCC and oral wash samples from those without HNSCC. Of note, strains of Candida albicans and Rothia mucilaginosa were differentially abundant and Schizophyllum commune was depleted in those with HNSCC compared to oral wash from those without HNSCC. Our results suggest that the oral cavity of HNSCC patients harbors unique differences in the mycobiome, bacteriome, and microbiome interactions when compared to those of control patients.
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Affiliation(s)
- Elizabeth Shay
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Naseer Sangwan
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Roshan Padmanabhan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Scott Lundy
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Brian Burkey
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Abdel-Mohsen A, Abdel-Rahman R, Kubena I, Kobera L, Spotz Z, Zboncak M, Prikryl R, Brus J, Jancar J. Chitosan-glucan complex hollow fibers reinforced collagen wound dressing embedded with aloe vera. Part I: Preparation and characterization. Carbohydr Polym 2020; 230:115708. [DOI: 10.1016/j.carbpol.2019.115708] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022]
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