Review
Biochemistry & Molecular Biology
Nicole Hartwig Trier, Gunnar Houen, Giuseppe Murdaca
Summary: Autoimmunity is characterized by the presence of antibodies and/or T cells targeting self-components. It is often associated with infections, which may increase the risk of autoimmune diseases. Molecular mimicry, referring to cross-reactivity between foreign pathogens and self-antigens, can cause tissue damage and contribute to autoimmunity. This review aims to explore the nature of potential cross-reactive immune reactions between infectious non-self and self-tissue antigens associated with autoimmunity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Vinay Kumar Pathak, Itu Singh, Shoor Vir Singh, Utpal Sengupta
Summary: This study aimed to identify cross-reactive proteins in clinical samples of leprosy patients and use them as prognostic biomarkers for Type 1 Reaction (T1R) in leprosy. The results showed the presence of cross-reactive proteins in saliva and slit skin scrapings (SSS) of leprosy patients, and predicted B cell epitopes of these proteins. These cross-reactive protein epitopes could be further studied for predicting leprosy reactions and potentially utilized as early diagnostic biomarkers for T1R in leprosy.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Immunology
Dagmar J. M. van Mourik, Dorien M. Salet, Saskia Middeldorp, Max Nieuwdorp, Thijs E. van Mens
Summary: There is a relationship between the gut microbiome and antiphospholipid syndrome (APS). Studies on systemic lupus erythematosus, which overlaps with APS, have shown changes in the gut microbiome composition and altered intestinal IgA response in patients. Molecular mimicry has been identified as a potential mechanism for APS and other autoimmune diseases. The gut microbiome can also affect key drivers of thrombosis and may impact the severity of APS through non-immunological mechanisms.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Maedeh Vahabi, Tooba Ghazanfari, Saeed Sepehrnia
Summary: SARS-CoV-2 infection can lead to various clinical manifestations, either directly related to viral tissue damage or indirectly induced by the immune response. The virus's molecular mimicry can undermine the host's immune system and trigger autoimmunity. Autoimmune diseases like lupus and autoimmune thyroid disease have been linked to COVID-19, and monitoring for autoimmunity is important. Autoimmune drugs may be effective in treating COVID-19.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Immunology
Manuel Rojas, Maria Herran, Carolina Ramirez-Santana, Patrick S. C. Leung, Juan-Manuel Anaya, William M. Ridgway, M. Eric Gershwin
Summary: Infectious diseases are known to contribute to the development of autoimmune diseases in susceptible individuals, and molecular mimicry is believed to be one of the mechanisms involved. Other factors such as defects in central tolerance and constant antigenic stimuli may also contribute to the breach of tolerance and the development of autoimmune diseases. The use of peptide modeling and molecular docking analyses are emerging as critical strategies to study the links between molecular mimicry and autoimmunity.
JOURNAL OF AUTOIMMUNITY
(2023)
Article
Gastroenterology & Hepatology
Hasan Ali, Taqi Rizvi, Mumtaz Niazi, Mark Galan, Nikolaos Pyrsopoulos
Summary: This case study presents a potential link between syphilitic hepatitis and autoimmune hepatitis, suggesting that treatment for syphilis may trigger an autoimmune response. Autoimmune hepatitis is a chronic liver disease that is believed to result from a combination of genetic and environmental factors.
JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY
(2022)
Article
Medicine, General & Internal
Michael Kasperkiewicz, Marta Bednarek, Stefan Tukaj
Summary: This study investigated 24 individuals who recovered from COVID-19 and received the Pfizer-BioNTech COVID-19 vaccine, and found that none of them showed antibody reactivity to any tested autoantigens. Therefore, the study suggests that there is no relationship between SARS-CoV-2 infection/vaccines and AIBDs in terms of disease-triggering antibody cross-reactivity.
FRONTIERS IN MEDICINE
(2021)
Review
Rheumatology
Yu Liu, Amr H. Sawalha, Qianjin Lu
Summary: This study evaluates the association between SARS-CoV-2 infection and autoimmunity, highlighting similarities between COVID-19 and autoimmune diseases in immune responses and potential development of autoimmune conditions. Patients with COVID-19 may develop autoimmune diseases post-infection, emphasizing the importance of medication adherence in preventing disease flares.
CURRENT OPINION IN RHEUMATOLOGY
(2021)
Review
Allergy
Yekbun Adiguzel, Naim Mahroum, Sylviane Muller, Miri Blank, Gilad Halpert, Yehuda Shoenfeld
Summary: Epstein-Barr virus (EBV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have the ability to activate autoimmunity and induce various autoimmune diseases. Molecular mimicry may be a common mechanism for autoimmunity induction in individuals susceptible to SARS-CoV-2 infection. The presence of molecular mimicry between SARS-CoV-2 and human proteins, as well as EBV and human proteins, supports this notion. Carriers of certain HLA serotypes may be at higher risk of autoimmune response upon infection with these viruses.
CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aaron Lerner, Carina Benzvi, Aristo Vojdani
Summary: This study aims to explore the sequence similarity between SARS-CoV-2 viral antigens and human gut antigens, and their potential role in gut autoimmune diseases. Sequence alignment revealed similarity and cross-reactivity between 10 pairs of immunoreactive epitopes. Antibodies against viral proteins that interact with human gut antigens are involved in several essential cellular functions.
Article
Cell Biology
Mahasish Shome, Yunro Chung, Ramani Chavan, Jin G. Park, Ji Qiu, Joshua LaBaer
Summary: Autoantibodies are found in both autoimmune disease and cancer, as well as in healthy individuals. Through a meta-analysis of multiple datasets, we identified 77 common autoantibodies in healthy individuals. These autoantibodies are not affected by gender, but increase in number with age and plateau around adolescence. Bioinformatics analysis revealed potential molecular mimicry peptides that may contribute to the development of these autoantibodies. Common autoantigens are enriched in intrinsic properties of proteins and have specific subcellular localization and tissue expression patterns.
Review
Gastroenterology & Hepatology
Albert J. Czaja
Summary: Molecular mimicry is suggested to be a cause of autoimmune hepatitis, with cross-reacting antibodies found in patients. This review discusses the evidence for molecular mimicry in experimental models and clinical cases, as well as the limitations and uncertainties associated with this theory. It calls for further investigations into diverse environmental antigens as potential sources of disease-relevant molecular mimics. The occurrence of immune-mediated hepatitis after vaccination suggests that vaccine-induced peptides may mimic tissue antigens relevant to the disease. The intestinal microbiome and chaperone molecules are also suggested to play a role in molecular mimicry.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Article
Immunology
Aristo Vojdani, Elroy Vojdani, Datis Kharrazian
Summary: The study found immune reactivity between SARS-CoV-2 antibodies and various human tissue antigens, as well as similarities between COVID-19 viral proteins and human tissue antigens. This extensive immune cross-reactivity may impact the disease progression of COVID-19, affecting disease severity, triggering autoimmunity, and exacerbating pre-existing autoimmune diseases. The results highlight potential risks for autoimmunity and multi-system disorders with COVID-19, emphasizing the importance of ensuring the safety of vaccines and treatments against this disease.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Mutaib M. Mashraqi, Ahmad Alzamami, Norah A. Alturki, Saleh Alshamrani, Mousa M. Alshahrani, Hassan H. Almasoudi, Zarrin Basharat
Summary: This study reveals the potential of Streptococcus pneumoniae to induce autoimmunity through molecular mimicry. By identifying proteins with sequence similarity to human proteins, the study suggests a possible link between S. pneumoniae infections and autoimmune disorders. The use of mimic-based vaccine designs shows promise in triggering an immune response against S. pneumoniae infections.
Article
Biochemical Research Methods
Dan Wang, Dong Yang, Liuhui Yang, Lihong Diao, Yuqi Zhang, Yang Li, Hongye Wang, Jing Ren, Linlin Cheng, Qiaoyun Tan, Ran Zhang, Xiaohong Han, Xiaohan Zhang, Bingwei Wang, Dong Li, Meng Chen, Henning Hermjakob, Yongzhe Li, Joshua LaBaer, Zhou Zhou, Xiaobo Yu
Summary: Understanding autoimmunity to endogenous proteins is crucial in diagnosing and treating autoimmune diseases. A user-friendly AAgAtlas portal was developed, which provides information on autoantigens (AAgs) and post-translationally modified AAgs associated with human diseases. The portal allows for a systematic investigation of the immunogenic properties of AAgs, including their genetic, biophysical, cytological, expression profile, and evolutionary characteristics. This information can aid in understanding humoral autoimmunity and identifying biomarkers for human diseases.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Peter Zhang, Alida Palmisano, Ravindra Kumar, Ming-Chung Li, James H. Doroshow, Yingdong Zhao
Summary: The NCI TPW is a compilation of transcriptional responses to anti-cancer agents in the NCI-60 cancer cell lines, with data accessible through a web interface. TPWshiny is a standalone R application developed to provide an intuitive and comprehensive graphical interface for interactive data exploration, allowing researchers to understand how tumor cell lines respond to therapeutic agents.
Article
Biochemical Research Methods
Neelja Singhal, Anjali Garg, Nirpendra Singh, Manish Kumar, Manisha Goel
Summary: Through gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, with most being multifunctional and involved in microbial metabolism activities. In comparison with gel-based LC-MS analysis, gel-free method proved to be better in identifying a greater number of proteins, including those with higher/lower molecular weights.
CURRENT PROTEOMICS
(2022)
Article
Biochemistry & Molecular Biology
Shilpa Mohanty, Govinda Rao Dabburu, Manish Kumar, Yogender Pal Khasa, Yogender Pal Babbal
Summary: This study identified and characterized two novel SUMO proteases, SpUlp1 and SpUlp2, from Schizosaccharomyces pombe. The catalytic domains of these proteases were able to efficiently cleave the SUMO fusion tag from proteins, making them potential candidates for large scale protein production.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Multidisciplinary Sciences
Anjali Garg, Govinda Rao Dabburu, Neelja Singhal, Manish Kumar
Summary: Microbial mimicry of host proteins/peptides can lead to autoimmune diseases. This study revealed that many bacterial and viral host mimicry proteins have structural disorder, but only a few overlap with host's intrinsically disordered protein regions. Most pathogens mimic host proteins involved in ion binding and signaling pathways.
Article
Biotechnology & Applied Microbiology
Kanchan Bhardwaj, Anjali Garg, Abhay Deep Pandey, Himani Sharma, Manish Kumar, Sudhanshu Vrati
Summary: This study investigated the gut DNA-virome of an unexplored ethnic population in Northern India and found that most of the identified virome belongs to bacteriophages, with a smaller fraction consisting of viruses that infect animals, archaea, protists, multiple domains or plants. The study also discovered a previously undetected virus family in the human gut. Additionally, the research revealed that the dominant lifestyle of gut phages in this population is lysogenic, which contradicts some earlier studies.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Govinda Rao Dabburu, Aakriti Jain, Naidu Subbarao, Manish Kumar
Summary: Malaria is a major global concern, particularly in Africa. The resistance to current antimalarial drugs is a growing problem. In this study, potential dual inhibitors of two important enzymes involved in the haemoglobin degradation pathway of Plasmodium falciparum were identified using in-silico molecular docking and simulation techniques. These novel dual inhibitors may have better efficacy than existing antimalarial drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Microbiology
Sahar Zaidi, Manisha Aswal, Manish Kumar, Faraz Rashid, Asad U. Khan
Summary: This study aimed to explore the general stress response of S. mutans at the proteome level under cell wall stress. Through high-throughput proteomics analysis, 41 significantly overexpressed proteins and 30 significantly underexpressed proteins were identified. The upregulated proteins mainly involved sortases and proteins in the EPS biosynthesis pathway, while the downregulated proteins were primarily related to glycolysis. Sortase family of proteins are potential targets for inhibiting multiple virulence pathways simultaneously.
JOURNAL OF MEDICAL MICROBIOLOGY
(2022)
Article
Microbiology
Deeksha Pandey, Neelja Singhal, Manish Kumar
Summary: Beta-lactams, a widely used class of antimicrobial agents, have led to the extensive spread of beta-lactamase enzymes. To counteract this effect, newer generations of beta-lactams have been developed, resulting in a highly diverse family of beta-lactamases. Traditional methods for determining the hydrolytic profile and classification of beta-lactamases are time-consuming and resource-intensive. Therefore, a machine-learning-based in silico method called beta-LacFamPred was developed for the prediction and annotation of beta-lactamases. This method showed high accuracy and outperformed other prediction tools in benchmarking tests.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Microbiology
Anjali Garg, Neelja Singhal, Manish Kumar
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nikita Ray, Rahul Kumar Vishwakarma, Aakriti Jain, Manish Kumar, Manisha Goel
Summary: In the early 1990s, it was discovered that certain proteins relied on additional polypeptide regions, known as prosequences/prodomains, for proper folding. While numerous examples of such proteins have been documented in literature, there has been no study investigating their evolutionary differences and similarities. The ProSeqA-ProDb database was created to comprehensively study these proteins and their prosequences. It contains a curated dataset of 2140 prosequence assisted proteins from various organisms, which will contribute to a better understanding of protein folding processes.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Manisha Aswal, Neelja Singhal, Manish Kumar
Summary: In this study, genome sequences of three strains of Escherichia coli from the Yamuna river in India were assembled, annotated, and analyzed. The strains showed different antibiotic susceptibilities and resistances. The bioinformatics assembly approach used in this study could be applied to study other bacterial genomes.
Article
Biochemical Research Methods
Aakriti Jain, Neelja Singhal, Manish Kumar
Summary: This study describes a database of all the mutations responsible for antifungal resistance, named as antifungal resistance database (AFRbase), which provides better information and visualization options compared to existing databases of antifungal resistance. AFRbase is an open access database that can be useful for genotypic susceptibility testing of fungi and studying the course of evolution of antifungal resistance. The current version of AFRbase contains 3691 unique mutations in 29 proteins of 32 fungal species along with information on the drugs causing resistance.
Article
Public, Environmental & Occupational Health
Nambram Somendro Singh, Neelja Singhal, Manish Kumar, Jugsharan Singh Virdi
Summary: This study investigates the presence of antimicrobial resistance genes in Escherichia coli isolated from a major river in northern India. The results show that most strains are susceptible to fluoroquinolones and some aminoglycosides, but a significant portion exhibit resistance to streptomycin, kanamycin, and gentamicin. Plasmid-mediated quinolone resistance (PMQR) genes and aminoglycoside resistance genes are identified, implying their potential transferability through plasmids.
EPIDEMIOLOGY AND INFECTION
(2022)
Article
Biochemical Research Methods
Deeksha Pandey, Bandana Kumari, Neelja Singhal, Manish Kumar
Summary: Antibiotic resistance is a major public health issue, and regular surveillance of antibiotic resistance genes is crucial. Whole-genome sequencing can expedite monitoring and analysis of ARGs, but the fragmentation of genome databases poses a challenge for annotation.
BIOLOGY METHODS & PROTOCOLS
(2022)