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Garcia-Marquez MA, Thelen M, Bauer E, Maas L, Wennhold K, Lehmann J, Keller D, Nikolić M, George J, Zander T, Schröder W, Müller P, Yazbeck AM, Bruns C, Thomas R, Gathof B, Quaas A, Peifer M, Hillmer AM, von Bergwelt-Baildon M, Schlößer HA. Germline homozygosity and allelic imbalance of HLA-I are common in esophagogastric adenocarcinoma and impair the repertoire of immunogenic peptides. J Immunother Cancer 2024; 12:e007268. [PMID: 38631707 PMCID: PMC11029431 DOI: 10.1136/jitc-2023-007268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The individual HLA-I genotype is associated with cancer, autoimmune diseases and infections. This study elucidates the role of germline homozygosity or allelic imbalance of HLA-I loci in esophago-gastric adenocarcinoma (EGA) and determines the resulting repertoires of potentially immunogenic peptides. METHODS HLA genotypes and sequences of either (1) 10 relevant tumor-associated antigens (TAAs) or (2) patient-specific mutation-associated neoantigens (MANAs) were used to predict good-affinity binders using an in silico approach for MHC-binding (www.iedb.org). Imbalanced or lost expression of HLA-I-A/B/C alleles was analyzed by transcriptome sequencing. FluoroSpot assays and TCR sequencing were used to determine peptide-specific T-cell responses. RESULTS We show that germline homozygosity of HLA-I genes is significantly enriched in EGA patients (n=80) compared with an HLA-matched reference cohort (n=7605). Whereas the overall mutational burden is similar, the repertoire of potentially immunogenic peptides derived from TAAs and MANAs was lower in homozygous patients. Promiscuity of peptides binding to different HLA-I molecules was low for most TAAs and MANAs and in silico modeling of the homozygous to a heterozygous HLA genotype revealed normalized peptide repertoires. Transcriptome sequencing showed imbalanced expression of HLA-I alleles in 75% of heterozygous patients. Out of these, 33% showed complete loss of heterozygosity, whereas 66% had altered expression of only one or two HLA-I molecules. In a FluoroSpot assay, we determined that peptide-specific T-cell responses against NY-ESO-1 are derived from multiple peptides, which often exclusively bind only one HLA-I allele. CONCLUSION The high frequency of germline homozygosity in EGA patients suggests reduced cancer immunosurveillance leading to an increased cancer risk. Therapeutic targeting of allelic imbalance of HLA-I molecules should be considered in EGA.
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Affiliation(s)
- Maria Alejandra Garcia-Marquez
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Martin Thelen
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Eugen Bauer
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Lukas Maas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Kerstin Wennhold
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Jonas Lehmann
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Diandra Keller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Miloš Nikolić
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Julie George
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Cologne, Cologne, Germany
| | - Thomas Zander
- Department I of Internal Medicine and Center for Integrated Oncology (CIO) Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | - Wolfgang Schröder
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Philipp Müller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Ali M Yazbeck
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Roman Thomas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Axel M Hillmer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Michael von Bergwelt-Baildon
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Gene Centre, Ludwig Maximilians University Munich, Munchen, Germany
- Department of Medicine III, Ludwig Maximilians University Munich, Munchen, Germany
| | - Hans Anton Schlößer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
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Etherton BA, Choudhury RA, Alcalá Briseño RI, Mouafo-Tchinda RA, Plex Sulá AI, Choudhary M, Adhikari A, Lei SL, Kraisitudomsook N, Robledo Buritica J, Cerbaro VA, Ogero K, Cox CM, Walsh SP, Andrade-Piedra J, Omondi BA, Navarrete I, McEwan MA, Garrett KA. Disaster plant pathology: Smart solutions for threats to global plant health from natural and human-driven disasters. Phytopathology 2024. [PMID: 38593748 DOI: 10.1094/phyto-03-24-0079-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases, and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, while press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (1) strengthening regional and global cooperation, (2) capacity building for rapid implementation of new technologies, (3) effective clean seed systems that can act quickly to replace seed lost in disasters, (4) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (5) decision support systems that can adapt rapidly to unexpected scenarios.
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Affiliation(s)
- Berea A Etherton
- University of Florida, 3463, Plant Pathology, Gainesville, Florida, United States;
| | - Robin A Choudhury
- University of Texas Rio Grande Valley Department of Biological Sciences, 171779, 1201 W University Dr, Edinburg, Texas, United States, 78539;
| | | | | | - Aaron I Plex Sulá
- University of Florida, 3463, Plant Pathology, Gainesville, Florida, United States;
| | - Manoj Choudhary
- NFREC, University of Florida, Quincy, Florida, United States;
| | - Ashish Adhikari
- University of Florida, 3463, Gainesville, Florida, United States;
| | - Si Lin Lei
- University of Florida, 3463, Gainesville, Florida, United States;
| | - Nattapol Kraisitudomsook
- University of Florida Institute of Food and Agricultural Sciences, 53701, Department of Plant Pathology, Gainesville, Florida, United States;
| | - Jacobo Robledo Buritica
- Citrus Research and Education Center, 57513, Plant Pathology, 700 Experiment Station Rd, Lake Alfred, Florida, United States, 33850;
| | | | - Kwame Ogero
- International Potato Center, Mwanza, Tanzania, United Republic of;
| | - Cindy M Cox
- USAID, 1310, Washington, District of Columbia, United States;
| | - Stephen P Walsh
- USAID, 1310, Washington, District of Columbia, United States;
| | - Jorge Andrade-Piedra
- International Potato Center (CIP) and CGIAR Research Program on Roots Tubers and Bananas (RTB), P.O. Box 1558, Lima , Peru, 12;
| | | | | | | | - Karen A Garrett
- University of Florida, 3463, Plant Pathology Department, Institute for Sustainable Food Systems, Emerging Pathogens Institute, Gainesville, Florida, United States, 32611-7011;
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Mokry RL, Monti CE, Rosas-Rogers S, Schumacher ML, Dash RK, Terhune SS. Replication efficiencies of human cytomegalovirus-infected epithelial cells are dependent on source of virus production. bioRxiv 2024:2024.03.19.585739. [PMID: 38562837 PMCID: PMC10983881 DOI: 10.1101/2024.03.19.585739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Human cytomegalovirus (HCMV) is a prevalent betaherpesvirus, and infection can lead to a range of symptomatology from mononucleosis to sepsis in immunocompromised individuals. HCMV is also the leading viral cause of congenital birth defects. Lytic replication is supported by many cell types with different kinetics and efficiencies leading to a plethora of pathologies. The goal of these studies was to elucidate HCMV replication efficiencies for viruses produced on different cell types upon infection of epithelial cells by combining experimental approaches with data-driven computational modeling. HCMV was generated from a common genetic background of TB40-BAC4, propagated on fibroblasts (TB40Fb) or epithelial cells (TB40Epi), and used to infect epithelial cells. We quantified cell-associated viral genomes (vDNA), protein levels (pUL44, pp28), and cell-free titers over time for each virus at different multiplicities of infection. We combined experimental quantification with data-driven simulations and determined that parameters describing vDNA synthesis were similar between sources. We found that pUL44 accumulation was higher in TB40Fb than TB40Epi. In contrast, pp28 accumulation was higher in TB40Epi which coincided with a significant increase in titer for TB40Epi over TB40Fb. These differences were most evident during live-cell imaging, which revealed syncytia-like formation during infection by TB40Epi. Simulations of the late lytic replication cycle yielded a larger synthesis constant for pp28 in TB40Epi along with increase in virus output despite similar rates of genome synthesis. By combining experimental and computational modeling approaches, our studies demonstrate that the cellular source of propagated virus impacts viral replication efficiency in target cell types.
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Affiliation(s)
- Rebekah L. Mokry
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Christopher E. Monti
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Suzette Rosas-Rogers
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Megan L. Schumacher
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Ranjan K. Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI-53226
| | - Scott S. Terhune
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI-53226
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI-53226
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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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Guo S, Mohan GS, Wang B, Li T, Daver N, Zhao Y, Reville PK, Hao D, Abbas HA. Paired single-B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cells in acute myeloid leukemia. J Immunother Cancer 2024; 12:e008318. [PMID: 38418394 PMCID: PMC10910691 DOI: 10.1136/jitc-2023-008318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is associated with a dismal prognosis. Immune checkpoint blockade (ICB) to induce antitumor activity in AML patients has yielded mixed results. Despite the pivotal role of B cells in antitumor immunity, a comprehensive assessment of B lymphocytes within AML's immunological microenvironment along with their interaction with ICB remains rather constrained. METHODS We performed an extensive analysis that involved paired single-cell RNA and B-cell receptor (BCR) sequencing on 52 bone marrow aspirate samples. These samples included 6 from healthy bone marrow donors (normal), 24 from newly diagnosed AML patients (NewlyDx), and 22 from 8 relapsed or refractory AML patients (RelRef), who underwent assessment both before and after azacitidine/nivolumab treatment. RESULTS We delineated nine distinct subtypes of B cell lineage in the bone marrow. AML patients exhibited reduced nascent B cell subgroups but increased differentiated B cells compared with healthy controls. The limited diversity of BCR profiles and extensive somatic hypermutation indicated antigen-driven affinity maturation within the tumor microenvironment of RelRef patients. We established a strong connection between the activation or stress status of naïve and memory B cells, as indicated by AP-1 activity, and their differentiation state. Remarkably, atypical memory B cells functioned as specialized antigen-presenting cells closely interacting with AML malignant cells, correlating with AML stemness and worse clinical outcomes. In the AML microenvironment, plasma cells demonstrated advanced differentiation and heightened activity. Notably, the clinical response to ICB was associated with B cell clonal expansion and plasma cell function. CONCLUSIONS Our findings establish a comprehensive framework for profiling the phenotypic diversity of the B cell lineage in AML patients, while also assessing the implications of immunotherapy. This will serve as a valuable guide for future inquiries into AML treatment strategies.
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Affiliation(s)
- Shengnan Guo
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Gopi S Mohan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bofei Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tianhao Li
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuting Zhao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Patrick K Reville
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dapeng Hao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Suleman MT, Alturise F, Alkhalifah T, Khan YD. m1A-Ensem: accurate identification of 1-methyladenosine sites through ensemble models. BioData Min 2024; 17:4. [PMID: 38360720 PMCID: PMC10868122 DOI: 10.1186/s13040-023-00353-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/31/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND 1-methyladenosine (m1A) is a variant of methyladenosine that holds a methyl substituent in the 1st position having a prominent role in RNA stability and human metabolites. OBJECTIVE Traditional approaches, such as mass spectrometry and site-directed mutagenesis, proved to be time-consuming and complicated. METHODOLOGY The present research focused on the identification of m1A sites within RNA sequences using novel feature development mechanisms. The obtained features were used to train the ensemble models, including blending, boosting, and bagging. Independent testing and k-fold cross validation were then performed on the trained ensemble models. RESULTS The proposed model outperformed the preexisting predictors and revealed optimized scores based on major accuracy metrics. CONCLUSION For research purpose, a user-friendly webserver of the proposed model can be accessed through https://taseersuleman-m1a-ensem1.streamlit.app/ .
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Affiliation(s)
- Muhammad Taseer Suleman
- Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore, 54770, Pakistan
| | - Fahad Alturise
- Department of Computer, College of Science and Arts in Ar Rass, Qassim University, Ar Rass, Qassim, Saudi Arabia.
| | - Tamim Alkhalifah
- Department of Computer, College of Science and Arts in Ar Rass, Qassim University, Ar Rass, Qassim, Saudi Arabia
| | - Yaser Daanial Khan
- Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore, 54770, Pakistan
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Shibaki R, Fujimoto D, Nozawa T, Sano A, Kitamura Y, Fukuoka J, Sato Y, Kijima T, Matsumoto H, Yokoyama T, Miura S, Hata A, Tamiya M, Taniguchi Y, Sugisaka J, Furuya N, Tanaka H, Yamamoto N, Koh Y, Akamatsu H. Machine learning analysis of pathological images to predict 1-year progression-free survival of immunotherapy in patients with small-cell lung cancer. J Immunother Cancer 2024; 12:e007987. [PMID: 38360040 PMCID: PMC10875545 DOI: 10.1136/jitc-2023-007987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND In small-cell lung cancer (SCLC), the tumor immune microenvironment (TIME) could be a promising biomarker for immunotherapy, but objectively evaluating TIME remains challenging. Hence, we aimed to develop a predictive biomarker of immunotherapy efficacy through a machine learning analysis of the TIME. METHODS We conducted a biomarker analysis in a prospective study of patients with extensive-stage SCLC who received chemoimmunotherapy as the first-line treatment. We trained a model to predict 1-year progression-free survival (PFS) using pathological images (H&E, programmed cell death-ligand 1 (PD-L1), and double immunohistochemical assay (cluster of differentiation 8 (CD8) and forkhead box P3 (FoxP3)) and patient information. The primary outcome was the mean area under the curve (AUC) of machine learning models in predicting the 1-year PFS. RESULTS We analyzed 100,544 patches of pathological images from 78 patients. The mean AUC values of patient information, pathological image, and combined models were 0.789 (range 0.571-0.982), 0.782 (range 0.750-0.911), and 0.868 (range 0.786-0.929), respectively. The PFS was longer in the high efficacy group than in the low efficacy group in all three models (patient information model, HR 0.468, 95% CI 0.287 to 0.762; pathological image model, HR 0.334, 95% CI 0.117 to 0.628; combined model, HR 0.353, 95% CI 0.195 to 0.637). The machine learning analysis of the TIME had better accuracy than the human count evaluations (AUC of human count, CD8-positive lymphocyte: 0.681, FoxP3-positive lymphocytes: 0.626, PD-L1 score: 0.567). CONCLUSIONS The spatial analysis of the TIME using machine learning predicted the immunotherapy efficacy in patients with SCLC, thus supporting its role as an immunotherapy biomarker.
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Affiliation(s)
- Ryota Shibaki
- Internal Medicine Ⅲ, Wakayama Medical University, Wakayama, Japan
| | - Daichi Fujimoto
- Internal Medicine Ⅲ, Wakayama Medical University, Wakayama, Japan
| | | | | | - Yuka Kitamura
- Department of pathology informatics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Junya Fukuoka
- Department of pathology informatics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuki Sato
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Takashi Kijima
- Department of Respiratory Medicine and Hematology, Hyogo Medical University, Hyogo, Japan
| | - Hirotaka Matsumoto
- Department of Respiratory Medicine, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan
| | - Toshihide Yokoyama
- Department of Respiratory Medicine, Kurashiki Central Hospital, Okayama, Japan
| | - Satoru Miura
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Japan
| | - Akito Hata
- Division of Thoracic Oncology, Kobe Minimally Invasive Cancer Center, Hyogo, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yoshihiko Taniguchi
- Department of Internal Medicine, NHO Kinki Chuo Chest Medical Center, Osaka, Japan
| | - Jun Sugisaka
- Department of Pulmonary Medicine, Sendai Kousei Hospital, Miyagi, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Hisashi Tanaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Nobuyuki Yamamoto
- Internal Medicine Ⅲ, Wakayama Medical University, Wakayama, Japan
- Center for Biomedical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Yasuhiro Koh
- Internal Medicine Ⅲ, Wakayama Medical University, Wakayama, Japan
- Center for Biomedical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Hiroaki Akamatsu
- Internal Medicine Ⅲ, Wakayama Medical University, Wakayama, Japan
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Cuevas B, Fraile A, Garcia-Arenal F. An Agent Based Model Shows How Mixed Infections Drive Multi-Year Pathotype Dynamics in a Plant-Virus System. Phytopathology 2024. [PMID: 38330173 DOI: 10.1094/phyto-06-23-0214-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Mathematical models are widely used to understand the evolution and epidemiology of plant pathogens under a variety of scenarios. We use here this approach to analyze the effects of different traits intrinsic and extrinsic to plant-virus interactions on the dynamics of virus pathotypes in genetically heterogeneous plant-virus systems. For this, we propose an agent-based epidemiological model that includes epidemiologically significant pathogen life-history traits related to virulence, transmission, and survival in the environment, and allows to integrate long and short scale transmission, primary and secondary infections, and within-host pathogen competition in mixed infections. The study focusses on the tobamovirus-pepper pathosystem. Model simulations allowed to integrate pleiotropic effects of resistance-breaking mutations on different virus life-history traits into net costs of resistance-breaking, allowing predictions on multi-year pathotype dynamics. We also explored the effects of two control measures, the use of host resistance and roguin of symptomatic plants, that modify epidemiological attributes of the pathogens, to understand how their populations will respond to evolutionary pressures. One major conclusion points to the importance of pathogen competition within mixed-infected hosts as a component of the overall fitness of each pathogen that, thus, drives their multiyear dynamics. .
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Affiliation(s)
- Bruno Cuevas
- Universidad Politécnica de Madrid, 16771, Centro de Biotecnología y Genómica de Plantas UPM-CSIC/INIA, Pozuelo de Alarcón, Madrid, Spain;
| | - Aurora Fraile
- Universidad Politécnica de Madrid, Centro de Biotecnología y Genómica de Plantas UPM-CSIC/INIA, Pozuelo de Alarcón, Madrid, Spain;
| | - Fernando Garcia-Arenal
- Universidad Politécnica de Madrid, 16771, Centro de Biotecnología y Genómica de Plantas UPM-CSIC/INIA, Pozuelo de Alarcón, Madrid, Spain;
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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10
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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11
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Lo EKW, Velazquez JJ, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols. Stem Cell Reports 2023; 18:1721-1742. [PMID: 37478860 PMCID: PMC10444577 DOI: 10.1016/j.stemcr.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
Optimization of cell engineering protocols requires standard, comprehensive quality metrics. We previously developed CellNet, a computational tool to quantitatively assess the transcriptional fidelity of engineered cells compared with their natural counterparts, based on bulk-derived expression profiles. However, this platform and others were limited in their ability to compare data from different sources, and no current tool makes it easy to compare new protocols with existing state-of-the-art protocols in a standardized manner. Here, we utilized our prior application of the top-scoring pair transformation to build a computational platform, platform-agnostic CellNet (PACNet), to address both shortcomings. To demonstrate the utility of PACNet, we applied it to thousands of samples from over 100 studies that describe dozens of protocols designed to produce seven distinct cell types. We performed an in-depth examination of hepatocyte and cardiomyocyte protocols to identify the best-performing methods, characterize the extent of intra-protocol and inter-lab variation, and identify common off-target signatures, including a surprising neural/neuroendocrine signature in primary liver-derived organoids. We have made PACNet available as an easy-to-use web application, allowing users to assess their protocols relative to our database of reference engineered samples, and as open-source, extensible code.
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Affiliation(s)
- Emily K W Lo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeremy J Velazquez
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Peng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
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12
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Omondi C, Chou A, Fond KA, Morioka K, Joseph NR, Sacramento JA, Iorio E, Torres-Espin A, Radabaugh HL, Davis JA, Gumbel JH, Russell Huie J, Ferguson AR. Improving rigor and reproducibility in western blot experiments with the blotRig analysis software. bioRxiv 2023:2023.08.02.551674. [PMID: 37577570 PMCID: PMC10418285 DOI: 10.1101/2023.08.02.551674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Western blot is a popular biomolecular analysis method for measuring the relative quantities of independent proteins in complex biological samples. However, variability in quantitative western blot data analysis poses a challenge in designing reproducible experiments. The lack of rigorous quantitative approaches in current western blot statistical methodology may result in irreproducible inferences. Here we describe best practices for the design and analysis of western blot experiments, with examples and demonstrations of how different analytical approaches can lead to widely varying outcomes. To facilitate best practices, we have developed the blotRig tool for designing and analyzing western blot experiments to improve their rigor and reproducibility. The blotRig application includes functions for counterbalancing experimental design by lane position, batch management across gels, and analytics with covariates and random effects.
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Affiliation(s)
- Cleopa Omondi
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Austin Chou
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kenneth A. Fond
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Kazuhito Morioka
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Nadine R. Joseph
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jeffrey A. Sacramento
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Emma Iorio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Abel Torres-Espin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- School of Public Health Sciences, Faculty of Health Sciences, University of Waterloo, ON, Canada
- Department of Physical Therapy, Faculty of Rehabilitation Medicine, University of Alberta, AB, Canada
| | - Hannah L. Radabaugh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jacob A. Davis
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - Jason H. Gumbel
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
| | - J. Russell Huie
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA USA
| | - Adam R. Ferguson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA USA
- San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA USA
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13
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Abbas Z, Rehman MU, Tayara H, Zou Q, Chong KT. XGBoost framework with feature selection for the prediction of RNA N5-methylcytosine sites. Mol Ther 2023; 31:2543-2551. [PMID: 37271991 PMCID: PMC10422016 DOI: 10.1016/j.ymthe.2023.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/06/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023] Open
Abstract
5-methylcytosine (m5C) is indeed a critical post-transcriptional alteration that is widely present in various kinds of RNAs and is crucial to the fundamental biological processes. By correctly identifying the m5C-methylation sites on RNA, clinicians can more clearly comprehend the precise function of these m5C-sites in different biological processes. Due to their effectiveness and affordability, computational methods have received greater attention over the last few years for the identification of methylation sites in various species. To precisely identify RNA m5C locations in five different species including Homo sapiens, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster, and Danio rerio, we proposed a more effective and accurate model named m5C-pred. To create m5C-pred, five distinct feature encoding techniques were combined to extract features from the RNA sequence, and then we used SHapley Additive exPlanations to choose the best features among them, followed by XGBoost as a classifier. We applied the novel optimization method called Optuna to quickly and efficiently determine the best hyperparameters. Finally, the proposed model was evaluated using independent test datasets, and we compared the results with the previous methods. Our approach, m5C- pred, is anticipated to be useful for accurately identifying m5C sites, outperforming the currently available state-of-the-art techniques.
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Affiliation(s)
- Zeeshan Abbas
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea; Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea.
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Houseini ST, Nemati F, Sattari A, Azadeh M, BishehKolaei R. Design of crRNA to Regulate MicroRNAs Related to Metastasis in Colorectal Cancer Using CRISPR-C2c2 (Cas13a) Technique. Cell J 2023; 25:354-362. [PMID: 37300297 DOI: 10.22074/cellj.2023.1989121.1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Indexed: 06/12/2023]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer with the second-highest mortality rate worldwide. microRNAs (miRNAs) of cancer-derived exosomes have shown promising diagnosis potential. Recent studies have shown the metastatic potential of a specific group of microRNAs called metastasis. Therefore, down-regulation of miRNAs at the transcriptional level can reduce metastasis probability. The aim of this bioinformatics research is targeting of miRNAs precursors using CRISPR-C2c2 (Cas13a) technique. The C2c2 (Cas13a) enzyme structure was downloaded from the RCSB database, the sequence miRNAs and their precursors were collected from miRbase. The crRNAs were designed and evaluated for their specificity by using CRISPR-RT server. The modeling 3D structure of the designed crRNA was performed by RNAComposer server. Finally, HDOCK server was used to perform molecular docking to evaluate docked molecules' energy level and position. The crRNAs designed for miR-1280, miR-206, miR-195, miR- 371a, miR-34a, miR-27a, miR-224, miR-99b, miR-877, miR-495 and miR-384 that showed high structural similarity with the situation observed in normal and appropriate orientation was obtained. Despite high specificity, the correct orientation was not established in the case of crRNAs that designed to target miR-145, miR-378a, miR-199a, miR- 320a and miR-543. The predicted interactions between crRNAs and Cas13a enzyme showed that crRNAs have a strong potential to inhibit metastasis. Therefore, crRNAs may be considered as an effective anticancer agent for further research in drug development.
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Affiliation(s)
- Seyed Taleb Houseini
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
- Young Researchers and Elite Club, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
| | - Farkhondeh Nemati
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran. Emails: ,
| | - Arash Sattari
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Gorgan Brach, Islamic Azad University, Golestan, Iran
| | | | - Roya BishehKolaei
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
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Scotch M, Lauer K, Wieben ED, Cherukuri Y, Cunningham JM, Klee EW, Harrington JJ, Lau JS, McDonough SJ, Mutawe M, O’Horo JC, Rentmeester CE, Schlicher NR, White VT, Schneider SK, Vedell PT, Wang X, Yao JD, Pritt BS, Norgan AP. Genomic epidemiology reveals the dominance of Hennepin County in transmission of SARS-CoV-2 in Minnesota from 2020-2022. medRxiv 2023:2022.07.24.22277978. [PMID: 35923324 PMCID: PMC9347287 DOI: 10.1101/2022.07.24.22277978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020-2022 and use Bayesian phylodynamics to describe county and regional spread in Minnesota. The earliest introduction into Minnesota was to Hennepin County from a domestic source around January 22, 2020; six weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota, and eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International (MSP) airport) totaling 45 (out of 107) over the two-year period. Southern Minnesota counties were most common for domestic introductions with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n=772) over the two-year period. We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases or major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have impact on virus diversity across each individual county.
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Affiliation(s)
- Matthew Scotch
- Research Affiliate, Mayo Clinic Arizona, Phoenix, AZ USA
- Biodesign Center for Environmental Health Engineering, Arizona State University, Tempe, AZ USA
- College of Health Solutions, Arizona State University, Phoenix, Arizona USA
| | - Kimberly Lauer
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
| | - Eric D. Wieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic Rochester, Rochester, MN, USA
| | | | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
- Center for Individualized Medicine, Rochester, MN, USA
| | | | - Julie S Lau
- Center for Individualized Medicine, Rochester, MN, USA
| | | | - Mark Mutawe
- Center for Individualized Medicine, Rochester, MN, USA
| | - John C. O’Horo
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Chad E. Rentmeester
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Saint Mary’s University of Minnesota, Winona, MN, USA
| | - Nicole R Schlicher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Valerie T White
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan K Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter T Vedell
- Department of Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, MN, USA
| | - Xiong Wang
- Minnesota Department of Health, St. Paul, MN, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew P Norgan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Guo X, Sun Z, Chen H, Ling J, Zhao H, Chang A, Zhuo X. SERPINE1 as an Independent Prognostic Marker and Therapeutic Target for Nicotine-Related Oral Carcinoma. Clin Exp Otorhinolaryngol 2023; 16:75-86. [PMID: 36510682 PMCID: PMC9985984 DOI: 10.21053/ceo.2022.01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Nicotine is an ingredient of tobacco, and exposure to nicotine increases the risks of various cancers, including oral cancer. Previous studies have focused on the addictive properties of nicotine, but its carcinogenic mechanism has rarely been studied. We aimed to explore the key genes in the process through which nicotine promotes the occurrence and development of oral cancer via data mining and experimental verification. METHODS This study involved three parts. First, key genes related to nicotine-related oral cancer were screened through data mining; second, the expression and clinical significance of a key gene in oral cancer tissues were verified by bioinformatics. Finally, the expression and clinical significance of the key gene in oral cancer were histologically investigated, and the effects of its expression on cell proliferation, invasion, and drug resistance were cytologically assessed. RESULTS SERPINE1 was identified as the key gene, which was upregulated in nicotine-treated oral cells and may be an independent prognostic factor for oral cancer. SERPINE1 was enriched in various pathways, such as the tumor necrosis factor and apelin pathways, and was related to the infiltration of macrophages, CD4+T cells, and CD8+T cells. Overexpression of SERPINE1 was associated with N staging and may be involved in hypoxia, angiogenesis, and metastasis. Knockdown of SERPINE1 in oral cancer cells resulted in weakened cell proliferation and invasion ability and increased sensitivity to bleomycin and docetaxel. CONCLUSION This study revealed SERPINE1 as a key gene for nicotine-related oral cancer, indicating that SERPINE1 may be a novel prognostic indicator and therapeutic target for oral carcinoma.
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Affiliation(s)
- Xiaopeng Guo
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhen Sun
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Huarong Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Junjun Ling
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Houyu Zhao
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Aoshuang Chang
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xianlu Zhuo
- Department of Otorhinolaryngology-Head and Neck Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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Sarmoko S, Novitasari D, Toriyama M, Fareza MS, Choironi NA, Itoh H, Meiyanto E. Different Modes of Mechanism of Gamma-Mangostin and Alpha-Mangostin to Inhibit Cell Migration of Triple-Negative Breast Cancer Cells Concerning CXCR4 Downregulation and ROS Generation. Iran J Pharm Res 2023; 22:e138856. [PMID: 38655233 PMCID: PMC11036650 DOI: 10.5812/ijpr-138856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 04/26/2024]
Abstract
Background Two mangostin compounds, gamma-mangostin and alpha-mangostin, show anticancer properties through the inhibition of cell proliferation and cell migration. Metastatic triple-negative breast cancer (TNBC) cells, including MDA-MB-231, highly express C-X-C chemokine receptor type 4 (CXCR4) to maintain reactive oxygen species (ROS) and cell migration. Objectives This study was performed to analyze and compare different modes of action of γ-mangostin and α-mangostin as antimigratory effects targeted on CXCR4 in MDA-MB-231 as a model of TNBC cell. Methods This study investigated the effect of γ-mangostin and α-mangostin using a series of assays, including Cell Counting Kit-8 (CCK-8) assay for cytotoxicity, wound healing assay for migration study, quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression analysis, and flow cytometry for ROS measurement, along with in silico study to observe the binding between the compound and CXCR4. Results The findings revealed half maximal inhibitory concentration (IC50) values of 25 and 20 μM for γ-mangostin and α-mangostin in MDA-MB 231 cells, respectively. Moreover, a concentration of 10 μM was used for the migration assay. Both γ-mangostin and α-mangostin significantly suppressed cell migration within 24 hours. The present gene expression studies revealed the downregulation of key migration-associated genes, namely Farp, CXCR4, and LPHN2, upon γ-mangostin treatment but not α-mangostin. Additionally, both γ-mangostin and α-mangostin increased cellular ROS generation, highlighting the same effect of γ-mangostin and α-mangostin ROS elevation to inhibit cancer cell migration. Molecular docking simulations further suggested a potential interaction between γ-mangostin and α-mangostin with CXCR4 in high affinity. Conclusions These findings suggest that both γ-mangostin and α-mangostin inhibit breast cancer cell migration and induce cellular ROS levels in MDA-MB-231 cells; notably, γ-mangostin suppresses CXCR4 mRNA expression that might correlate to its activity to inhibit MDA-MB-231 cell migration.
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Affiliation(s)
- Sarmoko Sarmoko
- Department of Pharmacy, Sumatera Institute of Technology, Lampung, Indonesia
| | - Dhania Novitasari
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Indonesia
- Laboratory of Tumor Cell Biology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Japan
| | - Manami Toriyama
- Laboratory of Molecular Signal Transduction, Nara Institute of Science and Technology, Japan
- Laboratory of Advanced Cosmetic Science, Graduate School of Pharmaceutical Science, Osaka University, Japan
| | | | | | - Hiroshi Itoh
- Laboratory of Molecular Signal Transduction, Nara Institute of Science and Technology, Japan
| | - Edy Meiyanto
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Indonesia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Indonesia
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18
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Zeng Z, Luo M, Li Y, Li J, Huang Z, Zeng Y, Yuan Y, Wang M, Liu Y, Gong Y, Xie C. Prediction of radiosensitivity and radiocurability using a novel supervised artificial neural network. BMC Cancer 2022; 22:1243. [PMID: 36451111 PMCID: PMC9713966 DOI: 10.1186/s12885-022-10339-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Radiotherapy has been widely used to treat various cancers, but its efficacy depends on the individual involved. Traditional gene-based machine-learning models have been widely used to predict radiosensitivity. However, there is still a lack of emerging powerful models, artificial neural networks (ANN), in the practice of gene-based radiosensitivity prediction. In addition, ANN may overfit and learn biologically irrelevant features. METHODS We developed a novel ANN with Selective Connection based on Gene Patterns (namely ANN-SCGP) to predict radiosensitivity and radiocurability. We creatively used gene patterns (gene similarity or gene interaction information) to control the "on-off" of the first layer of weights, enabling the low-dimensional features to learn the gene pattern information. ANN-SCGP was trained and tested in 82 cell lines and 1,101 patients from the 11 pan-cancer cohorts. RESULTS For survival fraction at 2 Gy, the root mean squared errors (RMSE) of prediction in ANN-SCGP was the smallest among all algorithms (mean RMSE: 0.1587-0.1654). For radiocurability, ANN-SCGP achieved the first and second largest C-index in the 12/20 and 4/20 tests, respectively. The low dimensional output of ANN-SCGP reproduced the patterns of gene similarity. Moreover, the pan-cancer analysis indicated that immune signals and DNA damage responses were associated with radiocurability. CONCLUSIONS As a model including gene pattern information, ANN-SCGP had superior prediction abilities than traditional models. Our work provided novel insights into radiosensitivity and radiocurability.
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Affiliation(s)
- Zihang Zeng
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Maoling Luo
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Yangyi Li
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Jiali Li
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Zhengrong Huang
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Department of Biological Repositories, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Yuxin Zeng
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Yu Yuan
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Mengqin Wang
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Yuying Liu
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China
| | - Yan Gong
- grid.413247.70000 0004 1808 0969Department of Biological Repositories, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
| | - Conghua Xie
- grid.413247.70000 0004 1808 0969Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China ,grid.413247.70000 0004 1808 0969Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071 Hubei China
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19
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Hao Y, Wang C, Xu D. Identification and validation of a novel prognostic model based on platinum Resistance-related genes in bladder cancer. Int Braz J Urol 2022; 49:61-88. [PMID: 36512456 PMCID: PMC9881817 DOI: 10.1590/s1677-5538.ibju.2022.0373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/22/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The depth of response to platinum in urothelial neoplasm tissues varies greatly. Biomarkers that have practical value in prognosis stratification are increasingly needed. Our study aimed to select a set of BC (bladder cancer)-related genes involved in both platinum resistance and survival, then use these genes to establish the prognostic model. MATERIALS AND METHODS Platinum resistance-related DEGs (differentially expressed genes) and tumorigenesis-related DEGs were identified. Ten most predictive co-DEGs were acquired followed by building a risk score model. Survival analysis and ROC (receiver operating characteristic) plot were used to evaluate the predictive accuracy. Combined with age and tumor stages, a nomogram was generated to create a graphical representation of survival rates at 1-, 3-, 5-, and 8-year in BC patients. The prognostic performance was validated in three independent BC datasets with platinum-based chemotherapy. The potential mechanism was explored by enrichment analysis. RESULTS PPP2R2B, TSPAN7, ATAD3C, SYT15, SAPCD1, AKR1B1, TCHH, AKAP12, AGLN3, and IGF2 were selected for our prognostic model. Patients in high- and low-risk groups exhibited a significant survival difference with HR (hazard ratio) = 2.7 (p < 0.0001). The prognostic nomogram of predicting 3-year OS (overall survival) for BC patients could yield an AUC (area under the curve) of 0.819. In the external validation dataset, the risk score also has a robust predictive ability. CONCLUSION A prognostic model derived from platinum resistance-related genes was constructed, we confirmed its value in predicting platinum-based chemotherapy benefits and overall survival for BC patients. The model might assist in therapeutic decisions for bladder malignancy.
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Affiliation(s)
- Yining Hao
- Shanghai Jiao Tong University School of MedicineRuijin HospitalDepartment of UrologyShanghaiChinaDepartment of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenghe Wang
- Shanghai Jiao Tong University School of MedicineRuijin HospitalDepartment of UrologyShanghaiChinaDepartment of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Correspondence address: Chenghe Wang, MD, PhD, Department of Urology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, No. 197 Ruijin Second Road, Shanghai, 200025, China. E-mail:
| | - Danfeng Xu
- Shanghai Jiao Tong University School of MedicineRuijin HospitalDepartment of UrologyShanghaiChinaDepartment of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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20
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Dharshika C, Gulbransen BD. Enteric Neuromics: How High-Throughput "Omics" Deepens Our Understanding of Enteric Nervous System Genetic Architecture. Cell Mol Gastroenterol Hepatol 2023; 15:487-504. [PMID: 36368612 DOI: 10.1016/j.jcmgh.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
Recent accessibility to specialized high-throughput "omics" technologies including single cell RNA sequencing allows researchers to capture cell type- and subtype-specific expression signatures. These omics methods are used in the enteric nervous system (ENS) to identify potential subtypes of enteric neurons and glia. ENS omics data support the known gene and/or protein expression of functional neuronal and glial cell subtypes and suggest expression patterns of novel subtypes. Gene and protein expression patterns can be further used to infer cellular function and implications in human disease. In this review we discuss how high-throughput "omics" data add additional depth to the understanding of established functional subtypes of ENS cells and raise new questions by suggesting novel ENS cell subtypes with unique gene and protein expression patterns. Then we investigate the changes in these expression patterns during pathology observed by omics research. Although current ENS omics studies provide a plethora of novel data and therefore answers, they equally create new questions and routes for future study.
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21
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Sové RJ, Verma BK, Wang H, Ho WJ, Yarchoan M, Popel AS. Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model. J Immunother Cancer 2022; 10:e005414. [PMID: 36323435 PMCID: PMC9639136 DOI: 10.1136/jitc-2022-005414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer and is the third-leading cause of cancer-related death worldwide. Most patients with HCC are diagnosed at an advanced stage, and the median survival for patients with advanced HCC treated with modern systemic therapy is less than 2 years. This leaves the advanced stage patients with limited treatment options. Immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) or its ligand, are widely used in the treatment of HCC and are associated with durable responses in a subset of patients. ICIs targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) also have clinical activity in HCC. Combination therapy of nivolumab (anti-PD-1) and ipilimumab (anti-CTLA-4) is the first treatment option for HCC to be approved by Food and Drug Administration that targets more than one immune checkpoints. METHODS In this study, we used the framework of quantitative systems pharmacology (QSP) to perform a virtual clinical trial for nivolumab and ipilimumab in HCC patients. Our model incorporates detailed biological mechanisms of interactions of immune cells and cancer cells leading to antitumor response. To conduct virtual clinical trial, we generate virtual patient from a cohort of 5,000 proposed patients by extending recent algorithms from literature. The model was calibrated using the data of the clinical trial CheckMate 040 (ClinicalTrials.gov number, NCT01658878). RESULTS Retrospective analyses were performed for different immune checkpoint therapies as performed in CheckMate 040. Using machine learning approach, we predict the importance of potential biomarkers for immune blockade therapies. CONCLUSIONS This is the first QSP model for HCC with ICIs and the predictions are consistent with clinically observed outcomes. This study demonstrates that using a mechanistic understanding of the underlying pathophysiology, QSP models can facilitate patient selection and design clinical trials with improved success.
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Affiliation(s)
- Richard J Sové
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Babita K Verma
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Won Jin Ho
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Yarchoan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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22
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Franken A, Van Mol P, Vanmassenhove S, Donders E, Schepers R, Van Brussel T, Dooms C, Yserbyt J, De Crem N, Testelmans D, De Wever W, Nackaerts K, Vansteenkiste J, Vos R, Humblet-Baron S, Lambrechts D, Wauters E. Single-cell transcriptomics identifies pathogenic T-helper 17.1 cells and pro-inflammatory monocytes in immune checkpoint inhibitor-related pneumonitis. J Immunother Cancer 2022; 10:jitc-2022-005323. [PMID: 36171010 PMCID: PMC9528720 DOI: 10.1136/jitc-2022-005323] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Background Immune checkpoint inhibitor (ICI)-related pneumonitis is the most frequent fatal immune-related adverse event associated with programmed cell death protein-1/programmed death ligand-1 blockade. The pathophysiology however remains largely unknown, owing to limited and contradictory findings in existing literature pointing at either T-helper 1 or T-helper 17-mediated autoimmunity. In this study, we aimed to gain novel insights into the mechanisms of ICI-related pneumonitis, thereby identifying potential therapeutic targets. Methods In this prospective observational study, single-cell RNA and T-cell receptor sequencing was performed on bronchoalveolar lavage fluid of 11 patients with ICI-related pneumonitis and 6 demographically-matched patients with cancer without ICI-related pneumonitis. Single-cell transcriptomic immunophenotyping and cell fate mapping coupled to T-cell receptor repertoire analyses were performed. Results We observed enrichment of both CD4+ and CD8+ T cells in ICI-pneumonitis bronchoalveolar lavage fluid. The CD4+ T-cell compartment showed an increase of pathogenic T-helper 17.1 cells, characterized by high co-expression of TBX21 (encoding T-bet) and RORC (ROR-γ), IFN-G (IFN-γ), IL-17A, CSF2 (GM-CSF), and cytotoxicity genes. Type 1 regulatory T cells and naïve-like CD4+ T cells were also enriched. Within the CD8+ T-cell compartment, mainly effector memory T cells were increased. Correspondingly, myeloid cells in ICI-pneumonitis bronchoalveolar lavage fluid were relatively depleted of anti-inflammatory resident alveolar macrophages while pro-inflammatory ‘M1-like’ monocytes (expressing TNF, IL-1B, IL-6, IL-23A, and GM-CSF receptor CSF2RA, CSF2RB) were enriched compared with control samples. Importantly, a feedforward loop, in which GM-CSF production by pathogenic T-helper 17.1 cells promotes tissue inflammation and IL-23 production by pro-inflammatory monocytes and vice versa, has been well characterized in multiple autoimmune disorders but has never been identified in ICI-related pneumonitis. Conclusions Using single-cell transcriptomics, we identified accumulation of pathogenic T-helper 17.1 cells in ICI-pneumonitis bronchoalveolar lavage fluid—a phenotype explaining previous divergent findings on T-helper 1 versus T-helper 17 involvement in ICI-pneumonitis—, putatively engaging in detrimental crosstalk with pro-inflammatory ‘M1-like’ monocytes. This finding yields several novel potential therapeutic targets for the treatment of ICI-pneumonitis. Most notably repurposing anti-IL-23 merits further research as a potential efficacious and safe treatment for ICI-pneumonitis.
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Affiliation(s)
- Amelie Franken
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Pierre Van Mol
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Sam Vanmassenhove
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Elena Donders
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Rogier Schepers
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Thomas Van Brussel
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Christophe Dooms
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Jonas Yserbyt
- Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Nico De Crem
- Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Dries Testelmans
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Walter De Wever
- Department of Imaging & Pathology, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Kristiaan Nackaerts
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Johan Vansteenkiste
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Robin Vos
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Stéphanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Diether Lambrechts
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Els Wauters
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
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23
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Alva A, Brito-Alarcón E, Linares A, Torres-García E, Hernández HO, Pinto-Cámara R, Martínez D, Hernández-Herrera P, D'Antuono R, Wood C, Guerrero A. Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start. J Microsc 2022; 288:218-241. [PMID: 35896096 PMCID: PMC10087389 DOI: 10.1111/jmi.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Abstract
Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of approximately half of the wavelength of visible light, i.e., within the range of 200 to 350 nm. Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) is a term used to encompass a collection of image analysis techniques which rely on the statistical processing of temporal variations of the fluorescence signal. FF-SRM aims to reduce the uncertainty of the location of fluorophores within an image, often improving spatial resolution to several tens of nanometers. FF-SRM is suitable for live-cell imaging due to its compatibility with most fluorescent probes and relatively simple instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are described. Their operational parameters are explained and guidance for its selection is provided. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alma Alva
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Eduardo Brito-Alarcón
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Linares
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Esley Torres-García
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Haydee O Hernández
- Posgrado en Ciencia e Ingeniería de la Computación, Universidad Nacional Autónoma de México, México City, México
| | - Raúl Pinto-Cámara
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Damián Martínez
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Hernández-Herrera
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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24
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Priyamvada P, Debroy R, Anbarasu A, Ramaiah S. A comprehensive review on genomics, systems biology and structural biology approaches for combating antimicrobial resistance in ESKAPE pathogens: computational tools and recent advancements. World J Microbiol Biotechnol 2022; 38:153. [PMID: 35788443 DOI: 10.1007/s11274-022-03343-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 12/11/2022]
Abstract
In recent decades, antimicrobial resistance has been augmented as a global concern to public health owing to the global spread of multidrug-resistant strains from different ESKAPE pathogens. This alarming trend and the lack of new antibiotics with novel modes of action in the pipeline necessitate the development of non-antibiotic ways to treat illnesses caused by these isolates. In molecular biology, computational approaches have become crucial tools, particularly in one of the most challenging areas of multidrug resistance. The rapid advancements in bioinformatics have led to a plethora of computational approaches involving genomics, systems biology, and structural biology currently gaining momentum among molecular biologists since they can be useful and provide valuable information on the complex mechanisms of AMR research in ESKAPE pathogens. These computational approaches would be helpful in elucidating the AMR mechanisms, identifying important hub genes/proteins, and their promising targets together with their interactions with important drug targets, which is a crucial step in drug discovery. Therefore, the present review aims to provide holistic information on currently employed bioinformatic tools and their application in the discovery of multifunctional novel therapeutic drugs to combat the current problem of AMR in ESKAPE pathogens. The review also summarizes the recent advancement in the AMR research in ESKAPE pathogens utilizing the in silico approaches.
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Affiliation(s)
- P Priyamvada
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), 632014, Vellore, India.,Department of Bio-Sciences, SBST, VIT, 632014, Vellore, India
| | - Reetika Debroy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), 632014, Vellore, India.,Department of Bio-Medical Sciences, SBST, VIT, 632014, Vellore, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), 632014, Vellore, India.,Department of Biotechnology, SBST, VIT, 632014, Vellore, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), 632014, Vellore, India. .,Department of Bio-Sciences, SBST, VIT, 632014, Vellore, India. .,School of Biosciences and Technology VIT, 632014, Vellore, Tamil Nadu, India.
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25
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Glendinning N, Hawthorne C, Beck S, Lopez-Campos G. Exploring Molecular Mechanisms Within Biomedical Literature. Stud Health Technol Inform 2022; 290:1094-1095. [PMID: 35673222 DOI: 10.3233/shti220284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Text mining of the biomedical literature enables vast quantities of information to be extracted and summarised. Here we describe an updated and improved version of previous methodology for the analysis of gene and protein biomarkers that enables the use of the newer Pubtator Central annotations, based in full text, improving the performance using a local SQLite database, that reduces the running time and resources required to perform the analyses facilitating its use in any computer, and expands its capabilities to enable the retrieval and analysis of chemical and metabolic biomarkers.
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Affiliation(s)
- Nicole Glendinning
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher Hawthorne
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Stephanie Beck
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Guillermo Lopez-Campos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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26
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Steenson S, Hawthorne C, Lopez-Campos G. A Comparative Analysis of Phenotypes Derived from Genes or Biomedical Literature in COVID-19. Stud Health Technol Inform 2022; 290:1092-1093. [PMID: 35673221 DOI: 10.3233/shti220283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Since the emergence of SARS-CoV-2 in November 2019, there has been an exponential production of literature due to worldwide efforts to understand the interactions between the virus and the human body. Using an "in-house" developed script we retrieved gene annotations and identified phenotype enrichments. Human Phenotype Ontology terms were retrieved from the literature using the Onassis R package. This produced both disease-gene and disease-phenotype data as well as data for gene-phenotype interactions. Overall, we retrieved 181 human phenotypes that were identified by both approaches. Further in-depth analysis of these relationships could provide further insights in the molecular mechanisms related with the observed phenotypes, answers and hypotheses for key concepts within COVID-19 research.
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Affiliation(s)
- Sophie Steenson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher Hawthorne
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Guillermo Lopez-Campos
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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27
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Higgs EF, Bao R, Hatogai K, Gajewski TF. Wilms tumor reveals DNA repair gene hyperexpression is linked to lack of tumor immune infiltration. J Immunother Cancer 2022; 10:jitc-2022-004797. [PMID: 35705315 PMCID: PMC9204399 DOI: 10.1136/jitc-2022-004797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background A T cell-rich tumor microenvironment has been associated with improved clinical outcome and response to immune checkpoint blockade therapies in several adult cancers. Understanding the mechanisms for lack of immune cell infiltration in tumors is critical for expanding immunotherapy efficacy. To gain new insights into the mechanisms of poor tumor immunogenicity, we turned to pediatric cancers, which are generally unresponsive to checkpoint blockade. Methods RNA sequencing and clinical data were obtained for Wilms tumor, rhabdoid tumor, osteosarcoma, and neuroblastoma from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and adult cancers from The Cancer Genome Atlas (TCGA). Using an 18-gene tumor inflammation signature (TIS) representing activated CD8+ T cells, we identified genes inversely correlated with the signature. Based on these results, adult tumors were also analyzed, and immunofluorescence was performed on metastatic melanoma samples to assess the MSH2 relationship to anti-programmed cell death protein-1 (PD-1) efficacy. Results Among the four pediatric cancers, we observed the lowest TIS scores in Wilms tumor. TIS scores were lower in Wilms tumors compared with matched normal kidney tissues, arguing for loss of endogenous T cell infiltration. Pathway analysis of genes upregulated in Wilms tumor and anti-correlated with TIS revealed activated pathways involved DNA repair. The majority of adult tumors in TCGA also showed high DNA repair scores associated with low TIS. Melanoma samples from an independent cohort revealed an inverse correlation between MSH2+ tumor cells and CD8+ T cells. Additionally, melanomas with high MSH2+ tumor cell numbers were largely non-responders to anti-PD-1 therapy. Conclusions Increased tumor expression of DNA repair genes is associated with a less robust immune response in Wilms tumor and the majority of TCGA tumor types. Surprisingly, the negative relationship between DNA repair score and TIS remained strong across TCGA when correcting for mutation count, indicating a potential role for DNA repair genes outside of preventing the accumulation of mutations. While loss of DNA repair machinery has been associated with carcinogenesis and mutational antigen generation, our results suggest that hyperexpression of DNA repair genes might be prohibitive for antitumor immunity, arguing for pharmacologic targeting of DNA repair as a potential therapeutic strategy.
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Affiliation(s)
- Emily F Higgs
- Pathology, University of Chicago Department of Medicine, Chicago, Illinois, USA
| | - Riyue Bao
- Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Ken Hatogai
- Pathology, University of Chicago Department of Medicine, Chicago, Illinois, USA
| | - Thomas F Gajewski
- Pathology, University of Chicago Department of Medicine, Chicago, Illinois, USA
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Zheng J, Zhang B. Correspondence on 'Novel imaging biomarkers predict outcomes in stage III unresectable non-small cell lung cancer treated with chemoradiation and durvalumab' by Jazieh et al. J Immunother Cancer 2022; 10:jitc-2022-004965. [PMID: 35640929 PMCID: PMC9157361 DOI: 10.1136/jitc-2022-004965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Jieling Zheng
- Radiology, Jinan University First Affiliated Hospital, Guangzhou, Guangdong, China
| | - Bin Zhang
- Radiology, Jinan University First Affiliated Hospital, Guangzhou, Guangdong, China
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29
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Kwon J, Lee JH, Lee YH, Lee J, Ahn JH, Kim SH, Kim SH, Kim TI, Yun KH, Park YS, Kim JE, Lee KS, Choi JK, Kim HS. Whole-genome and Transcriptome Sequencing Identified NOTCH2 and HES1 as Potential Markers of Response to Imatinib in Desmoid Tumor (Aggressive Fibromatosis): A Phase II Trial Study. Cancer Res Treat 2022; 54:1240-1255. [PMID: 35038826 PMCID: PMC9582486 DOI: 10.4143/crt.2021.1194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022] Open
Abstract
Purpose Desmoid tumor, also known as aggressive fibromatosis, is well-characterized by abnormal Wnt/β-catenin signaling. Various therapeutic options, including imatinib, are available to treat desmoid tumor. However, molecular mechanism of why imatinib works remains unclear. Here, we describe potential roles of NOTCH2 and HES1 in clinical response to imatinib at genome and transcriptome levels. Materials and Methods We identified somatic mutations in coding and non-coding regions via whole genome sequencing. To validate the genetic interaction with expression level in desmoid-tumor condition, we utilized large-scale whole-genome sequencing and transcriptome datasets from the Pan-Cancer Analysis of Whole Genomes project. RNA-sequencing was performed using prospective and retrospective cohort samples to evaluate the expressional relevance with clinical response. Results Among 20 patients, 4 (20%) had a partial response and 14 (66.7%) had stable disease, 11 of which continued for ≥1 year. With gene-wise functional analyses, we detected significant correlation between recurrent NOTCH2 noncoding mutations and clinical response to imatinib. Based on PCAWG data analyses, NOTCH2 mutations affect expression levels particularly in the presence of CTNNB1 missense mutations. By analyzing RNA-sequencing with additional desmoid tumor samples, we found that NOTCH2 expression was significantly correlated with HES1 expression. Interestingly, NOTCH2 had no statistical power to discriminate responders and non-responders. Instead, HES1 was differentially expressed with statistical significance between responders and non-responders. Conclusion Imatinib was effective and well tolerated for advanced desmoid tumor treatment. Our results show that HES1, regulated by NOTCH2, as an indicator of sensitivity to imatinib, and an important therapeutic consideration for desmoid tumor.
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Affiliation(s)
- Joonha Kwon
- Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Jun Hyeong Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Young Han Lee
- Department of Radiology, Yonsei University College of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jin-Hee Ahn
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Se Hyun Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seung Hyun Kim
- Department of Orthopedic Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Il Kim
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kum-Hee Yun
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Young Suk Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyu Sang Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
| | - Hyo Song Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.,Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
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Ko JM, Mousavi R, Lobo D. Computational Systems Biology of Morphogenesis. Methods Mol Biol 2022; 2399:343-365. [PMID: 35604563 DOI: 10.1007/978-1-0716-1831-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis.
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Affiliation(s)
- Jason M Ko
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Reza Mousavi
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
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31
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Rehman MU, Tayara H, Chong KT. DCNN-4mC: Densely connected neural network based N4-methylcytosine site prediction in multiple species. Comput Struct Biotechnol J 2021; 19:6009-6019. [PMID: 34849205 PMCID: PMC8605313 DOI: 10.1016/j.csbj.2021.10.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/17/2023] Open
Abstract
DNA N4-methylcytosine (4mC) being a significant genetic modification holds a dominant role in controlling different biological functions, i.e., DNA replication, DNA repair, gene regulations and gene expression levels. The identification of 4mC sites is important to get insight information regarding different organics mechanisms. However, getting modification prediction from experimental methods is a challenging task due to high expenses and time-consuming techniques. Therefore, computational tools can be a great option for modification identification. Various computational tools are proposed in literature but their generalization and prediction performance require improvement. For this motive, we have proposed a neural network based tool named DCNN-4mC for identifying 4mC sites. The proposed model involves a set of neural network layers with a skip connection which allows to share the shallow features with dense layers. Skip connection have allowed to gather crucial information regarding 4mC sites. In literature, different models are employed on different species hence in many cases different datasets are available for a single species. In this research, we have combined all available datasets to create a single benchmark dataset for every species. To the best of our knowledge, no model in literature is employed on more than six different species. To ensure the generalizability of DCNN-4mC we have used 12 different species for performance evaluation. The DCNN-4mC tool has attained 2% to 14% higher accuracy than state-of-the-art tools on all available datasets of different species. Furthermore, independent test datasets are also engaged and DCNN-4mC have overall yielded high performance in them as well.
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Affiliation(s)
- Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Department of Avionics Engineering, Air University, Islamabad 44000, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
- Corresponding author at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (Hilal Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea. (Kil To Chong)
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
- Corresponding author at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (Hilal Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea. (Kil To Chong)
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Paz HES, Monteiro MF, Stolf CS, Altabtbaei K, Casati MZ, Casarin RCV, Kumar PS. Predicted functional and taxonomic analysis of subgingival biofilm of grade C periodontitis in young patients under maintenance therapy. J Periodontol 2021; 93:1119-1130. [PMID: 34727386 DOI: 10.1002/jper.21-0411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND In Grade C periodontitis in young patients (PerioC-Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC-Y patients under supportive periodontal therapy (SPT). METHODS Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC-Y patients at two time points: at baseline and after 5.7±1.3 years of SPT. This was compared to 15 patients without a history of periodontitis. The V1-V3 and V4-V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha- and beta-diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2. RESULTS Clinical improvements were seen in PerioC-Y-SPT. Differences in β-diversity between PerioC-Y and Health were observed (Health x PerioC-Y-baseline, p = 0.02; Health x PerioC-Y-SPT, p = 0.05). Moreover, although β-diversity did not statistically change between baseline and SPT in PerioC-Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC-Y. However, compared to healthy individuals, some genes remained more highly abundant in PerioC-Y-SPT, such as quorum sensing and efflux pump transporters. CONCLUSION Despite clinical improvements and a shift in taxonomic composition, the PerioC-Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC-Y regardless of disease control. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hélvis E S Paz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Mabelle F Monteiro
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Camila S Stolf
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Khaled Altabtbaei
- Department of Periodontology, School of Dentistry, University of Alberta, Edmonton, Canada
| | - Márcio Z Casati
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Renato C V Casarin
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Purnima S Kumar
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
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Baseri N, Najar-Peerayeh S, Bakhshi B. Investigating the effect of an identified mutation within a critical site of PAS domain of WalK protein in a vancomycin-intermediate resistant Staphylococcus aureus by computational approaches. BMC Microbiol 2021; 21:240. [PMID: 34474665 PMCID: PMC8414773 DOI: 10.1186/s12866-021-02298-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/23/2021] [Indexed: 11/15/2022] Open
Abstract
Background Vancomycin-intermediate resistant Staphylococcus aureus (VISA) is becoming a common cause of nosocomial infections worldwide. VISA isolates are developed by unclear molecular mechanisms via mutations in several genes, including walKR. Although studies have verified some of these mutations, there are a few studies that pay attention to the importance of molecular modelling of mutations. Method For genomic and transcriptomic comparisons in a laboratory-derived VISA strain and its parental strain, Sanger sequencing and reverse transcriptase quantitative PCR (RT-qPCR) methods were used, respectively. After structural protein mapping of the detected mutation, mutation effects were analyzed using molecular computational approaches and crystal structures of related proteins. Results A mutation WalK-H364R was occurred in a functional zinc ion coordinating residue within the PAS domain in the VISA strain. WalK-H364R was predicted to destabilize protein and decrease WalK interactions with proteins and nucleic acids. The RT-qPCR method showed downregulation of walKR, WalKR-regulated autolysins, and agr locus. Conclusion Overall, WalK-H364R mutation within a critical metal-coordinating site was presumably related to the VISA development. We assume that the WalK-H364R mutation resulted in deleterious effects on protein, which was verified by walKR gene expression changes.. Therefore, molecular modelling provides detailed insight into the molecular mechanism of VISA development, in particular, where allelic replacement experiments are not readily available. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02298-9.
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Affiliation(s)
- Neda Baseri
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahin Najar-Peerayeh
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bita Bakhshi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Monterrubio-López GP, Delgadillo-Gutiérrez K. [Reverse vaccinology: strategy against emerging pathogens]. Rev Med Inst Mex Seguro Soc 2021; 59:233-241. [PMID: 34370422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
New technologies in vaccinology are capable of achieving fast development, as well as large-scale production of effective and safe vaccines. Reverse vaccinology is an in silico methodology, which studies different characteristics of infectious agents, in order to identify antigens that are good vaccine candidates, without the need of traditional culture. This strategy is based on bioinformatics tools, that in a simple, safety and inexpensive way, reduces time and effort significantly in the new vaccine design, against traditional vaccinology. In recent years, the rapid spread of infections by emerging pathogens requires prompt development of new vaccines. Bioinformatic strategies joined with the latest next-generation vaccines allow the selection of vaccine candidates in a short time, which is relevant in the development of new vaccines against pathogens with pandemic potential.
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Affiliation(s)
- Gloria Paulina Monterrubio-López
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas Campus Casco de Santo Tomás, Departamento de Microbiología, Laboratorio de Producción y Control de Biológicos "Dr. Mario González Pacheco". Ciudad de México, México
| | - Karen Delgadillo-Gutiérrez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas Campus Casco de Santo Tomás, Departamento de Microbiología, Laboratorio de Producción y Control de Biológicos "Dr. Mario González Pacheco". Ciudad de México, México
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Lakshmikanth T, Muhammad SA, Olin A, Chen Y, Mikes J, Fagerberg L, Gummesson A, Bergström G, Uhlen M, Brodin P. Human Immune System Variation during 1 Year. Cell Rep 2021; 32:107923. [PMID: 32697987 DOI: 10.1016/j.celrep.2020.107923] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components and the inference of global regulatory principles. Here, we present a longitudinal, systems-level analysis in 99 healthy adults 50 to 65 years of age and sampled every third month for 1 year. We describe the structure of interindividual variation and characterize extreme phenotypes along a principal curve. From coordinated measurement fluctuations, we infer relationships between 115 immune cell populations and 750 plasma proteins constituting the blood immune system. While most individuals have stable immune systems, the degree of longitudinal variability is an individual feature. The most variable individuals, in the absence of overt infections, exhibited differences in markers of metabolic health suggestive of a possible link between metabolic and immunologic homeostatic regulation.
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Affiliation(s)
- Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Sayyed Auwn Muhammad
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Axel Olin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden; Department of Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Karolinska, Sweden; Department of Pediatric Rheumatology, Karolinska University Hospital, Karolinska, Sweden.
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Wu H, Su QX, Zhang ZY, Zhang Z, Gao SL, Lu C, Zuo L, Zhang LF. Exploration of the core genes in ulcerative interstitial cystitis/bladder pain syndrome. Int Braz J Urol 2021; 47:843-855. [PMID: 33848079 PMCID: PMC8321495 DOI: 10.1590/s1677-5538.ibju.2020.1104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Objective: Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a chronic inflammatory disease that can cause bladder pain and accompanying symptoms, such as long-term urinary frequency and urgency. IC/BPS can be ulcerative or non-ulcerative. The aim of this study was to explore the core genes involved in the pathogenesis of ulcerative IC, and thus the potential biomarkers for clinical treatment. Materials and Methods: First, the gene expression dataset GSE11783 was downloaded using the Gene Expression Omnibus (GEO) database and analyzed using the limma package in R to identify differentially expressed genes (DEGs). Then, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for Gene Ontology (GO) functional analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Finally, the protein-protein interaction (PPI) network was constructed, and key modules and hub genes were determined using the STRING and Cytoscape software. The resulting key modules were then analyzed for tissue-specific gene expression using BioGPS. Results: A total of 216 up-regulated DEGs and 267 down-regulated genes were identified, and three key modules and nine hub genes were obtained. Conclusion: The core genes (CXCL8, CXCL1, IL6) obtained in this study may be potential biomarkers of interstitial cystitis with guiding significance for clinical treatment.
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Affiliation(s)
- Hao Wu
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Quan-Xin Su
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Zi-Yi Zhang
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Ze Zhang
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Dalian Medical University, Dalian, China
| | - Sheng-Lin Gao
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Chao Lu
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Li Zuo
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Li-Feng Zhang
- Department of Urology, Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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Zamanian-Azodi M, Arjmand B, Razzaghi M, Rezaei Tavirani M, Ahmadzadeh A, Rostaminejad M. Platelet and Haemostasis are the Main Targets in Severe Cases of COVID-19 Infection; a System Biology Study. Arch Acad Emerg Med 2021; 9:e27. [PMID: 34027422 PMCID: PMC8126352 DOI: 10.22037/aaem.v9i1.1108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introduction: Many proteomics-based and bioinformatics-based efforts are made to detect the molecular mechanism of COVID-19 infection. Identification of the main protein targets and pathways of severe cases of COVID-19 infection is the aim of this study. Methods: Published differentially expressed proteins were screened and the significant proteins were investigated via protein-protein interaction network using Cytoscape software V. 3.7.2 and STRING database. The studied proteins were assessed via action map analysis to determine the relationship between individual proteins using CluePedia. The related biological terms were investigated using ClueGO and the terms were clustered and discussed. Results: Among the 35 queried proteins, six of them (FGA, FGB, FGG, and FGl1 plus TLN1 and THBS1) were identified as critical proteins. A total of 38 biological terms, clustered in 4 groups, were introduced as the affected terms. “Platelet degranulation” and “hereditary factor I deficiency disease” were introduced as the main class of the terms disturbed by COVID-19 virus. Conclusion: It can be concluded that platelet damage and disturbed haemostasis could be the main targets in severe cases of coronavirus infection. It is vital to follow patients’ condition by examining the introduced critical differentially expressed proteins (DEPs).
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Affiliation(s)
- Mona Zamanian-Azodi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahmadzadeh
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostaminejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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He J, Tang J, Feng Q, Li T, Wu K, Yang K, Jia D, Xia Q. Weighted gene co-expression network analysis identifies RHOH and TRAF1 as key candidate genes for psoriatic arthritis. Clin Rheumatol 2021; 40:1381-91. [PMID: 32959187 DOI: 10.1007/s10067-020-05395-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/12/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Psoriatic arthritis (PsA) is inflammatory arthritis associated with psoriasis, which involves the axial joint and the distal interphalangeal joints. Its clinical features are varied, often resulting in delayed diagnosis and treatment. Improved knowledge about disease mechanisms will catalyze the rapid development of effective targeted therapies for this disease. The perturbations in the gene co-expression network may not be detected by the differential expression analysis of the microarray. This study aims to identify key modules and hub genes in psoriatic arthritis-applied WGCNA (weighted gene co-expression network analysis) on a microarray. METHODS This study downloaded the array data of GSE61281 from the gene expression overview (GEO) database, which includes 20 psoriatic arthritis samples and 12 healthy controls. The analysis was performed with the WGCNA package. Gene ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on these key modules. Candidate hub genes were identified using GS and MM measures, Cytoscape, and the online database STRING. RESULTS A total of 10 co-expression modules were constructed. The lightcyan module was identified as the key module. GO and KEGG pathway analyses were mainly enriched in dephosphorylation, regulation of small GTPase-mediated signal transduction, Ras signaling pathway, MAPK signaling pathway, and vascular smooth muscle contraction. Two hub genes, RHOH/TRAF1, were selected. CONCLUSIONS This finding may indicate that RHOH/TRAF1 play a critical role in the pathogenesis of PsA. This is one of the first studies in PsA using WGCNA, which may provide a new research direction for further understanding of the molecular mechanism and clinical application of PsA. Key points • The WGCNA method was applied to the expression profile microarray of psoriatic arthritis and the co-expression module was constructed. • Identify the key modules by combining the onset time of psoriasis in patients with psoriatic arthritis. • Three screening methods are used to identify and verify hub genes of key modules.
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Kim DK, Park YS, Cha KJ, Jang D, Ryu S, Kim KR, Kim SH, Yoon HJ, Cho SH. Cluster Analysis of Inhalant Allergens in South Korea: A Computational Model of Allergic Sensitization. Clin Exp Otorhinolaryngol 2020; 14:93-99. [PMID: 32623852 PMCID: PMC7904440 DOI: 10.21053/ceo.2019.01921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/23/2020] [Indexed: 12/24/2022] Open
Abstract
Objectives. Sensitization to specific inhalant allergens is a major risk factor for the development of atopic diseases, which impose a major socioeconomic burden and significantly diminish quality of life. However, patterns of inhalant allergic sensitization have yet to be precisely described. Therefore, to enhance the understanding of aeroallergens, we performed a cluster analysis of inhalant allergic sensitization using a computational model. Methods. Skin prick data were collected from 7,504 individuals. A positive skin prick response was defined as an allergen-to-histamine wheal ratio ≥1. To identify the clustering of inhalant allergic sensitization, we performed computational analysis using the four-parameter unified-Richards model. Results. Hierarchical cluster analysis grouped inhalant allergens into three clusters based on the Davies-Bouldin index (0.528): cluster 1 (Dermatophagoides pteronyssinus and Dermatophagoides farinae), cluster 2 (mugwort, cockroach, oak, birch, cat, and dog), and cluster 3 (Alternaria tenus, ragweed, Candida albicans, Kentucky grass, and meadow grass). Computational modeling revealed that each allergen cluster had a different trajectory over the lifespan. Cluster 1 showed a high level (>50%) of sensitization at an early age (before 19 years), followed by a sharp decrease in sensitization. Cluster 2 showed a moderate level (10%–20%) of sensitization before 29 years of age, followed by a steady decrease in sensitization. However, cluster 3 revealed a low level (<10%) of sensitization at all ages. Conclusion. Computational modeling suggests that allergic sensitization consists of three clusters with distinct patterns at different ages. The results of this study will be helpful to allergists in managing patients with atopic diseases.
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Affiliation(s)
- Dong-Kyu Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon, Korea
| | - Young-Sun Park
- Department of Mathematics and Institute of Natural Sciences, Hanyang University College of Natural Sciences, Seoul, Korea
| | - Kyung-Joon Cha
- Department of Mathematics and Institute of Natural Sciences, Hanyang University College of Natural Sciences, Seoul, Korea
| | - Daeil Jang
- Department of Mathematics and Institute of Natural Sciences, Hanyang University College of Natural Sciences, Seoul, Korea
| | - Seungho Ryu
- Department of Occupational and Environmental Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung Rae Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Hanyang University College of Medicine, Seoul, Korea
| | - Sang-Heon Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Ho Joo Yoon
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Seok Hyun Cho
- Department of Otorhinolaryngology-Head and Neck Surgery, Hanyang University College of Medicine, Seoul, Korea
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Lin J, Susztak K. Complexities of Understanding Function from CKD-Associated DNA Variants. Clin J Am Soc Nephrol 2020; 15:1028-1040. [PMID: 32513823 PMCID: PMC7341770 DOI: 10.2215/cjn.15771219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genome-wide association studies (GWASs) have facilitated the unbiased discovery of hundreds of genomic loci associated with CKD and kidney function. The vast majority of disease-associated DNA variants are noncoding. Those that are causal in CKD pathogenesis likely modulate transcription of target genes in a cell type-specific manner. To gain novel biological insights into mechanisms driving the development of CKD, the causal variants (which are usually not the most significant variant reported in a GWAS), their target genes, and causal cell types need to be identified. This functional validation requires a large number of new data sets, complex bioinformatics analyses, and experimental cellular and in vivo studies. Here, we review the basic principles and some of the current approaches being leveraged to assign functional significance to a genotype-phenotype association.
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Affiliation(s)
- Jennie Lin
- Division of Nephrology and Hypertension, Feinberg Cardiovascular and Renal Research Institute, Department of Medicine, Northwestern University, Chicago, Illinois
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
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Kim J, Zhang J, Cha Y, Kolitz S, Funt J, Escalante Chong R, Barrett S, Kusko R, Zeskind B, Kaufman H. Advanced bioinformatics rapidly identifies existing therapeutics for patients with coronavirus disease-2019 (COVID-19). J Transl Med 2020. [PMID: 32586380 DOI: 10.26434/chemrxiv.12037416.v1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The recent global pandemic has placed a high priority on identifying drugs to prevent or lessen clinical infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused by Coronavirus disease-2019 (COVID-19). METHODS We applied two computational approaches to identify potential therapeutics. First, we sought to identify existing FDA approved drugs that could block coronaviruses from entering cells by binding to ACE2 or TMPRSS2 using a high-throughput AI-based binding affinity prediction platform. Second, we sought to identify FDA approved drugs that could attenuate the gene expression patterns induced by coronaviruses, using our Disease Cancelling Technology (DCT) platform. RESULTS Top results for ACE2 binding iincluded several ACE inhibitors, a beta-lactam antibiotic, two antiviral agents (Fosamprenavir and Emricasan) and glutathione. The platform also assessed specificity for ACE2 over ACE1, important for avoiding counterregulatory effects. Further studies are needed to weigh the benefit of blocking virus entry against potential counterregulatory effects and possible protective effects of ACE2. However, the data herein suggest readily available drugs that warrant experimental evaluation to assess potential benefit. DCT was run on an animal model of SARS-CoV, and ranked compounds by their ability to induce gene expression signals that counteract disease-associated signals. Top hits included Vitamin E, ruxolitinib, and glutamine. Glutathione and its precursor glutamine were highly ranked by two independent methods, suggesting both warrant further investigation for potential benefit against SARS-CoV-2. CONCLUSIONS While these findings are not yet ready for clinical translation, this report highlights the potential use of two bioinformatics technologies to rapidly discover existing therapeutic agents that warrant further investigation for established and emerging disease processes.
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Affiliation(s)
- Jason Kim
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Jenny Zhang
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Yoonjeong Cha
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Sarah Kolitz
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Jason Funt
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | | | - Scott Barrett
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Rebecca Kusko
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA.
| | - Ben Zeskind
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Howard Kaufman
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
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42
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Kim J, Zhang J, Cha Y, Kolitz S, Funt J, Escalante Chong R, Barrett S, Kusko R, Zeskind B, Kaufman H. Advanced bioinformatics rapidly identifies existing therapeutics for patients with coronavirus disease-2019 (COVID-19). J Transl Med 2020; 18:257. [PMID: 32586380 PMCID: PMC7315012 DOI: 10.1186/s12967-020-02430-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The recent global pandemic has placed a high priority on identifying drugs to prevent or lessen clinical infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused by Coronavirus disease-2019 (COVID-19). METHODS We applied two computational approaches to identify potential therapeutics. First, we sought to identify existing FDA approved drugs that could block coronaviruses from entering cells by binding to ACE2 or TMPRSS2 using a high-throughput AI-based binding affinity prediction platform. Second, we sought to identify FDA approved drugs that could attenuate the gene expression patterns induced by coronaviruses, using our Disease Cancelling Technology (DCT) platform. RESULTS Top results for ACE2 binding iincluded several ACE inhibitors, a beta-lactam antibiotic, two antiviral agents (Fosamprenavir and Emricasan) and glutathione. The platform also assessed specificity for ACE2 over ACE1, important for avoiding counterregulatory effects. Further studies are needed to weigh the benefit of blocking virus entry against potential counterregulatory effects and possible protective effects of ACE2. However, the data herein suggest readily available drugs that warrant experimental evaluation to assess potential benefit. DCT was run on an animal model of SARS-CoV, and ranked compounds by their ability to induce gene expression signals that counteract disease-associated signals. Top hits included Vitamin E, ruxolitinib, and glutamine. Glutathione and its precursor glutamine were highly ranked by two independent methods, suggesting both warrant further investigation for potential benefit against SARS-CoV-2. CONCLUSIONS While these findings are not yet ready for clinical translation, this report highlights the potential use of two bioinformatics technologies to rapidly discover existing therapeutic agents that warrant further investigation for established and emerging disease processes.
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Affiliation(s)
- Jason Kim
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Jenny Zhang
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Yoonjeong Cha
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Sarah Kolitz
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Jason Funt
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | | | - Scott Barrett
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Rebecca Kusko
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA.
| | - Ben Zeskind
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
| | - Howard Kaufman
- Immuneering Corporation, 245 Main Street, Cambridge, MA, 02142, USA
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Mirabzadeh CA, Ytreberg FM. Implementation of adaptive integration method for free energy calculations in molecular systems. PeerJ Comput Sci 2020; 6:e264. [PMID: 33457645 PMCID: PMC7808261 DOI: 10.7717/peerj-cs.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/10/2020] [Indexed: 11/20/2022]
Abstract
Estimating free energy differences by computer simulation is useful for a wide variety of applications such as virtual screening for drug design and for understanding how amino acid mutations modify protein interactions. However, calculating free energy differences remains challenging and often requires extensive trial and error and very long simulation times in order to achieve converged results. Here, we present an implementation of the adaptive integration method (AIM). We tested our implementation on two molecular systems and compared results from AIM to those from a suite of other methods. The model systems tested here include calculating the solvation free energy of methane, and the free energy of mutating the peptide GAG to GVG. We show that AIM is more efficient than other tested methods for these systems, that is, AIM results converge to a higher level of accuracy and precision for a given simulation time.
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Affiliation(s)
| | - F. Marty Ytreberg
- Department of Physics, University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States of America
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44
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Friedrichs M, Shoshi A, Chmura PJ, Ison J, Schwämmle V, Schreiber F, Hofestädt R, Sommer B. JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools. J Integr Bioinform 2020; 16:/j/jib.2019.16.issue-4/jib-2019-0059/jib-2019-0059.xml. [PMID: 31913853 PMCID: PMC7074141 DOI: 10.1515/jib-2019-0059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/30/2019] [Accepted: 12/09/2019] [Indexed: 11/15/2022] Open
Abstract
JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools).
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Affiliation(s)
- Marcel Friedrichs
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Alban Shoshi
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | | | - Jon Ison
- Technical University of Denmark, Department of Bio and Health Informatics, Lyngby, Denmark
| | - Veit Schwämmle
- University of Southern Denmark, Department of Biochemistry and Molecular Biology, Protein Research Group, Odense, Denmark
| | - Falk Schreiber
- Konstanz University, Life Science Informatics, Konstanz, Germany
| | - Ralf Hofestädt
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Bjorn Sommer
- Royal College of Art, School of Design, London, UK
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45
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Shome S, Parra RG, Fatima N, Monzon AM, Cuypers B, Moosa Y, Coimbra NDR, Assis J, Giner-Delgado C, Dönertaş HM, Cuesta-Astroz Y, Saarunya G, Allali I, Gupta S, Srivastava A, Kalsan M, Valdivia C, J Olguin-Orellana G, Papadimitriou S, Parisi D, Kristensen NP, Rib L, Guebila MB, Bauer E, Zaffaroni G, Bekkar A, Ashano E, Paladin L, Necci M, Moreyra NN, Rydén M, Villalobos-Solís J, Papadopoulos N, Rafael C, Karakulak T, Kaya Y, Gladbach Y, Dhanda SK, Šoštarić N, Alex A, DeBlasio D, Rahman F. Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers. F1000Res 2019; 8. [PMID: 31508204 PMCID: PMC6720036 DOI: 10.12688/f1000research.20408.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2019] [Indexed: 11/20/2022] Open
Abstract
Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".
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Affiliation(s)
- Sayane Shome
- Bioinformatics and Computational Biology Program, Iowa State University, Iowa, USA
| | - R Gonzalo Parra
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nazeefa Fatima
- Science for Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Upsala, Sweden
| | | | - Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Yumna Moosa
- KZN Research and Innovation Sequencing Platform, University of KwaZulu Natal, Durban, South Africa
| | - Nilson Da Rocha Coimbra
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Assis
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yesid Cuesta-Astroz
- School of Microbiology, Universidad de Antioquía, Medellín, Colombia.,Colombian Tropical Medicine Institute (ICMT), Universidad CES, Medellín, Colombia
| | - Geetha Saarunya
- Department of Biological Sciences, University of South Carolina, South Caroli a, USA
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.,Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shruti Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ambuj Srivastava
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Manisha Kalsan
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Catalina Valdivia
- Ecosystem's Health Laboratory, Universidad Andres, Bello Santiago, Chile
| | | | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | | | | | - Leonor Rib
- The Bioinformatics Center, Biology and Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Marouen Ben Guebila
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Eugen Bauer
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gaia Zaffaroni
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Amel Bekkar
- Swiss Institute of Bioinformatics (SIB), University of Lausanne, Lausanne, Switzerland
| | - Efejiro Ashano
- Molecular Diagnostics, Laboratory Services, APIN Public Health Initiatives, Abuja, Nigeria
| | - Lisanna Paladin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Marco Necci
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Nicolás N Moreyra
- Genetics and Evolution of Buenos Aires (IEGEBA), CONICET-UBA, Institute of Ecology, Buenos Aires, Argentina
| | - Martin Rydén
- Biomedical Centre, Faculty of Medicine, Lund University, Lund, Sweden
| | - Jordan Villalobos-Solís
- Laboratorio de Biotenología de Plantas, Universidad Nacional de Costa Rica (UNA), Heredia, Costa Rica
| | - Nikolaos Papadopoulos
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Candice Rafael
- Research Unit for Bioinformatics, Rhodes University, Grahamstown, South Africa
| | - Tülay Karakulak
- Izmir Biomedicine and Genome Center, Dokuz Eylül University, Izmir, Turkey
| | - Yasin Kaya
- Hacettepe University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Yvonne Gladbach
- University Medical Center Rostock, University Heidelberg, Heidelberg, Germany
| | - Sandeep Kumar Dhanda
- La Jolla Institute for Allergy and Immunology, La Jolla Institute for Immunology, California, USA
| | | | - Aishwarya Alex
- Roche Diagnostics Automation Solutions GmbH, Roche, Waiblingen, Germany
| | - Dan DeBlasio
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA
| | - Farzana Rahman
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, UK.,School of Human and Life Sciences, Canterbury Christ Church University, Kent, UK
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Lopez-Campos G, Bonner E, McClements L. An Integrative Biomedical Informatics Approach to Elucidate the Similarities Between Pre-Eclampsia and Hypertension. Stud Health Technol Inform 2019; 264:988-992. [PMID: 31438072 DOI: 10.3233/shti190372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Pre-eclampsia is a pregnancy condition affecting 5-10% of pregnancies, and it is the leading cause of death in pregnancy associated with increased risk of cardiovascular disease later in life. Despite research, the pathogenesis of pre-eclampsia is still poorly understood. In this paper, we investigate the overlapping pathogenic mechanisms between pre-eclampsia and adult hypertension using an integrative biomedical informatics strategy that combined text mining techniques to identify genes and proteins, with geneset analyses, generating knowledge on the pathways and mechanisms involved in these conditions. We identified several overlapping pathogenic pathways/systems including metabolic pathways, developmental biology pathways, immune system, haemostasis, tyrosine kinase pathways, extracellular matrix and oxidative stress pathways. This bioinformatics approach could be applied for investigating mechanistic pathways of other disorders.
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Affiliation(s)
- Guillermo Lopez-Campos
- Centre for Experimental Medicine, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Emma Bonner
- Centre for Experimental Medicine, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom
| | - Lana McClements
- Centre for Experimental Medicine, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom.,School of Life Sciences, University of Technology Sydney, PO Box 123 Broadway, New South Wales, Australia
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Christodoulou D, Kuehne A, Estermann A, Fuhrer T, Lang P, Sauer U. Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms. iScience 2019; 19:1133-1144. [PMID: 31536961 PMCID: PMC6831883 DOI: 10.1016/j.isci.2019.08.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 07/13/2019] [Accepted: 08/24/2019] [Indexed: 02/03/2023] Open
Abstract
All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress. Characterization of immediate metabolic response to oxidative stress The metabolic response in glycolysis and PP pathway depends on stress severity Identification of NADPH feedback inhibition on G6PDH as key regulatory interaction The identified oxidative stress regulatory interaction is conserved across kingdoms
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Affiliation(s)
- Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | - Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paul Lang
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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48
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Easterly CW, Sajulga R, Mehta S, Johnson J, Kumar P, Hubler S, Mesuere B, Rudney J, Griffin TJ, Jagtap PD. metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. Mol Cell Proteomics 2019; 18:S82-S91. [PMID: 31235611 PMCID: PMC6692774 DOI: 10.1074/mcp.ra118.001240] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/21/2019] [Indexed: 01/15/2023] Open
Abstract
Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, the study of microbial proteins at the community level, integrates genomic, transcriptomic, and proteomic data to determine the taxonomic and functional state of a microbiome. However, standard metaproteomics software is subject to several limitations, commonly supporting only spectral counts, emphasizing exploratory analysis rather than hypothesis testing and rarely offering the ability to analyze the interaction of function and taxonomy - that is, which taxa are responsible for different processes.Here we present metaQuantome, a novel, multifaceted software suite that analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information, emphasizing label-free intensity-based methods. For experiments with multiple experimental conditions, metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. We benchmark metaQuantome analysis against standard methods, using two previously published datasets: (1) an artificially assembled microbial community dataset (taxonomy benchmarking) and (2) a dataset with a range of recombinant human proteins spiked into an Escherichia coli background (functional benchmarking). Furthermore, we demonstrate the use of metaQuantome on a previously published human oral microbiome dataset.In both the taxonomic and functional benchmarking analyses, metaQuantome quantified taxonomic and functional terms more accurately than standard summarization-based methods. We use the oral microbiome dataset to demonstrate metaQuantome's ability to produce publication-quality figures and elucidate biological processes of the oral microbiome. metaQuantome enables advanced investigation of metaproteomic datasets, which should be broadly applicable to microbiome-related research. In the interest of accessible, flexible, and reproducible analysis, metaQuantome is open source and available on the command line and in Galaxy.
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Affiliation(s)
- Caleb W Easterly
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Ray Sajulga
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Subina Mehta
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
| | - Praveen Kumar
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN; Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN
| | - Shane Hubler
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Joel Rudney
- ‡School of Dentistry, University of Minnesota, Minneapolis, MN
| | - Timothy J Griffin
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Pratik D Jagtap
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN.
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Abstract
The reproducibility of bioinformatics analyses can be elevated to equal status with biological discovery. To achieve this, reproducibility must become part of the process, not an afterthought.
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Affiliation(s)
| | - Laurent Gatto
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
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50
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Savage SR, Shi Z, Liao Y, Zhang B. Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. Mol Cell Proteomics 2019; 18:S141-S152. [PMID: 31142576 PMCID: PMC6692773 DOI: 10.1074/mcp.tir118.001263] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/22/2019] [Indexed: 01/04/2023] Open
Abstract
Gene set analysis plays a critical role in the functional interpretation of omics data. Although this is typically done for one omics experiment at a time, there is an increasing need to combine gene set analysis results from multiple experiments performed on the same or different omics platforms, such as in multi-omics studies. Integrating results from multiple experiments is challenging, and annotation redundancy between gene sets further obscures clear conclusions. We propose to use a weighted set cover algorithm to reduce redundancy of gene sets identified in a single experiment. Next, we use affinity propagation to consolidate similar gene sets identified from multiple experiments into clusters and to automatically determine the most representative gene set for each cluster. Using three examples from over representation analysis and gene set enrichment analysis, we showed that weighted set cover outperformed a previously published set cover method and reduced the number of gene sets by 52-77%. Focusing on overlapping genes between the list of input genes and the enriched gene sets in over-representation analysis and leading-edge genes in gene set enrichment analysis further reduced the number of gene sets. A use case combining enrichment analysis results from RNA-Seq and proteomics data comparing basal and luminal A breast cancer samples highlighted the known difference in proliferation and DNA damage response. Finally, we used these algorithms for a pan-cancer survival analysis. Our analysis clearly revealed prognosis-related pathways common to multiple cancer types or specific to individual cancer types, as well as pathways associated with prognosis in different directions in different cancer types. We implemented these two algorithms in an R package, Sumer, which generates tables and static and interactive plots for exploration and publication. Sumer is publicly available at https://github.com/bzhanglab/sumer.
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Affiliation(s)
- Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
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