Article
Immunology
Huyan Wang, Xiaowei Shi, Huanhuan Yang, Yan Du, Jing Xue
Summary: This study compared the diagnostic value of metagenomic next-generation sequencing (mNGS) shotgun and conventional microbiological tests in determining infections in patients with connective tissue diseases (CTDs). The results showed that mNGS had a high sensitivity in identifying infectious pathogens and performed well in detecting mixed infections. Additionally, mNGS was effective in detecting Pneumocystis jirovecii infections, which are closely associated with low CD4+ T-cell counts. Therefore, mNGS is an important tool for diagnosing infections and guiding treatment in CTDs patients.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Rui Su, Huanhuan Yan, Na Li, Tingting Ding, Baochen Li, Yuhuan Xie, Chong Gao, Xiaofeng Li, Caihong Wang
Summary: This study found that mNGS has incremental application value in patients with connective tissue diseases suspected of co-infection, showing high sensitivity in detecting pathogens, particularly with high positive detection rates in virus infections. Attention should be paid to rare pathogen infections and bacterial-virus coinfections.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Clinical Neurology
Nelson Astur, Brenno Ferreira Bento Maciel, Andre Mario Doi, Marines Dalla Valle Martino, Marcela Souza Basqueira, Marcelo Wajchenberg, Mario Lenza, Delio Eulalio Martins
Summary: This study analyzed the microbiome of the intervertebral disc using next-generation sequencing (NGS) molecular test and validated it with tissue culture and clinical data. The results showed the presence of bacteria or remnant DNA in herniated discs, indicating that the disc is not sterile. However, the study did not find any evidence of infection-related Cutibacterium acnes in patients with lumbar disc herniation.
Article
Biochemistry & Molecular Biology
Anna Junkiert-Czarnecka, Maria Pilarska-Deltow, Aneta Bak, Marta Heise, Anna Latos-Bielenska, Jacek Zaremba, Alicja Bartoszewska-Kubiak, Olga Haus
Summary: This study utilized NGS technology to detect variants in multiple genes, revealing the association between variants in COL5A1, COL5A2, COL1A1, and COL1A2 genes and cEDS patients. The results demonstrate the potential of next-generation sequencing in aiding the diagnosis of EDS and other connective tissue disorders, and highlight the yet undiscovered causative genes.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)
Review
Immunology
Ilaria Mormile, Francesca Mosella, Piergiorgio Turco, Filomena Napolitano, Amato de Paulis, Francesca Wanda Rossi
Summary: Calcinosis is a severe complication of autoimmune disorders, including types like calcinosis cutis and calciphylaxis. Calcification of damaged tissues in the presence of normal calcium and phosphate levels is commonly associated with autoimmune diseases. Calciphylaxis, characterized by vascular calcifications and thrombosis, is also related to autoimmune conditions. It is important for physicians to be aware of the clinical presentation and management of calcinosis in order to choose appropriate treatment and prevent long-term complications.
Article
Microbiology
Bao-Zhu Li, Hua Wang, Xian-Bao Li, Qian-Ru Zhang, Rong-Gui Huang, Hong Wu, Yi-Yu Wang, Kai-Di Li, Xiu-Jie Chu, Nv-Wei Cao, Hao-Yue Zhou, Xin-Yu Fang, Rui-Xue Leng, Yin-Guang Fan, Jin-Hui Tao, Zong-Wen Shuai, Dong-Qing Ye
Summary: This study presents a pilot analysis of fungal microbiota in patients with systemic lupus erythematosus (SLE), showing significant differences in diversity and composition compared to other diseases and healthy controls. The composition of fungal and bacterial microbiota is imbalanced in SLE patients, and there is a complex relationship network between them.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Review
Infectious Diseases
Koay Chun Giok, Rohit Kunnath Menon
Summary: It is beneficial to use mechanical debridement augmented with antibiotics for the treatment of peri-implantitis. The microbial profile plays a key role in selecting the appropriate antibiotics. Further studies with standardization and universal clinical parameters are needed for a better understanding of peri-implantitis.
Article
Respiratory System
Vincent Cottin, Luca Richeldi, Ivan Rosas, Maria Otaola, Jin Woo Song, Sara Tomassetti, Marlies Wijsenbeek, Manuela Schmitz, Carl Coeck, Susanne Stowasser, Rozsa Schlenker-Herceg, Martin Kolb
Summary: In patients with progressive fibrosing ILDs, the effect of nintedanib in reducing FVC decline was not affected by the use of immunomodulatory therapies, allowing for combination use of nintedanib with these therapies.
RESPIRATORY RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Respiratory System
Franck F. Rahaghi, Vivien M. Hsu, Robert J. Kaner, Maureen D. Mayes, Ivan O. Rosas, Rajan Saggar, Virginia D. Steen, Mary E. Strek, Elana J. Bernstein, Nitin Bhatt, Flavia V. Castelino, Lorinda Chung, Robyn T. Domsic, Kevin R. Flaherty, Nishant Gupta, Bashar Kahaleh, Fernando J. Martinez, Lee E. Morrow, Teng Moua, Nina Patel, Oksana A. Shlobin, Brian D. Southern, Elizabeth R. Volkmann, Dinesh Khanna
Summary: This study aimed to develop consensus recommendations on the management of patients with SSc-ILD based on expert physician insights. A modified Delphi process was completed by pulmonologists and rheumatologists, resulting in the generation of a management algorithm that addresses the current gaps in management approaches.
RESPIRATORY RESEARCH
(2023)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Article
Immunology
Jielin Wang, Xuan You, Yanmin He, Xiaozhen Hong, Ji He, Sudan Tao, Faming Zhu
Summary: In this study, a high-throughput method was developed for simultaneous genotyping of HLA-A and HLA-B loci, as well as HPA genotyping. The method was found to be accurate and successfully genotyped 204 blood specimens for all 34 HPA systems as well as HLA-A and HLA-B loci. This method provides important genetic information for the treatment of alloimmunization platelet transfusion refractoriness.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Genetics & Heredity
Anna Wajda, Ewa Walczuk, Barbara Stypinska, Jakub Lach, Danat Yermakovich, Larysa Sivitskaya, Katarzyna Romanowska-Prochnicka, Tomasz Wysocki, Malgorzata Jaronczyk, Agnieszka Paradowska-Gorycka
Summary: The study analyzed gene expression associated with MTX metabolism in rheumatoid arthritis patients, suggesting that genetic variations in AHRR may impact treatment response. IL-6 inhibitor treatment may improve the effectiveness of low-dose MTX in patients with poor response.
PHARMACOGENOMICS JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Tomasz Wysocki, Agnieszka Paradowska-Gorycka
Summary: Rheumatoid arthritis is a common inflammatory arthritis in which tumor necrosis factor plays a key role. However, there is variation in response to TNF-targeting drugs, which may be influenced by genetic factors. The field of pharmacogenomics offers potential for developing novel prognostic tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Tomasz Kmiolek, Agnieszka Paradowska-Gorycka
Summary: In recent years, there has been increasing attention on the epigenetic dysregulation in autoimmune rheumatic diseases. MicroRNAs (miRNA) have been identified as key regulators of immune cell development and function, and could potentially serve as biomarkers for RA diagnosis, prognosis, and treatment.
Review
Oncology
Daryush Purrahman, Arshid Yousefi Avarvand, Agnieszka Paradowska-Gorycka, Najmaldin Saki, Hossein Karimpourian, Hossein Jodat, Mohammad-Reza Mahmoudian-Sani
Summary: Breast cancer is a common cancer among women, and its exact cause is still unknown. The association between human papillomavirus (HPV) and breast cancer has been explored in numerous studies, but contradictory results have been obtained. This review examines the existing evidence and hypotheses about the association between HPV infection and breast cancer, as well as the potential mechanisms involved.
Article
Biochemistry & Molecular Biology
Agnieszka Paradowska-Gorycka, Anna Wajda, Ewa Rzeszotarska, Tomasz Kmiolek, Barbara Stypinska, Ewa Dudek, Katarzyna Romanowska-Prochnicka, Piotr Syrowka
Summary: Circulating free-cell miRNAs have become increasingly important as potential non-invasive biomarkers, particularly in the field of oncology. This research aimed to investigate the association between selected miRNAs in serum and the expression of Th17/Treg transcription factors, as well as clinical features, in rheumatoid arthritis (RA) patients. The study found that miR-10 was only detected in RA patients and its expression was correlated with IL-35 serum concentration and STAT5a mRNA level. Additionally, miR-326 was significantly upregulated in RA patients with rheumatoid factor presence. The differential association of transcription factor expression with serum miRNA levels may have implications for the diagnosis and progression of RA and osteoarthritis (OA).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anna Wajda, Marcela Walczyk, Ewa Dudek, Barbara Stypinska, Aleksandra Lewandowska, Katarzyna Romanowska-Prochnicka, Marek Chojnowski, Marzena Olesinska, Agnieszka Paradowska-Gorycka
Summary: Systemic sclerosis (SSc) is a rare multisystem chronic disease with autoimmune features. In this study, the expression profile of selected microRNAs, including miR-126, -132, -143, -145, -155, -181a, -29a and -3148, was investigated in SSc patients compared to healthy controls. The results showed that the expression of these microRNAs was significantly altered in SSc patients, with miR-181a downregulated and miR-132, miR-143, miR-145 and miR-155 overexpressed. These findings suggest that these microRNAs may serve as potential biomarkers for SSc diagnosis and disease progression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Pharmacology & Pharmacy
Anna Wajda, Carlo Perricone, Anniruddh Kashyap, Mahmud Yerima Iliyasu
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Pharmacology & Pharmacy
Ewa Kuca-Warnawin, Weronika Kurowska, Magdalena Plebanczyk, Anna Wajda, Anna Kornatka, Tomasz Burakowski, Iwona Janicka, Piotr Syrowka, Urszula Skalska
Summary: Rheumatoid arthritis (RA) and osteoarthritis (OA) are joint diseases associated with expansion of pathogenic T lymphocytes. Mesenchymal stem cells provide a potential therapeutic option due to their regenerative and immunomodulatory abilities. This study evaluates the phenotype, regenerative potential and effects of adipose-derived stem cells (ASCs) from the infrapatellar fat pad (IFP) of RA and OA patients on CD4+ T cell proliferation.
Article
Biochemistry & Molecular Biology
Gabriela Filipowicz, Anna Wajda, Barbara Stypinska, Tomasz Kmiolek, Anna Felis-Giemza, Sandra Stanczyk, Zenobia Czuszynska, Marcela Walczyk, Marzena Olesinska, Agnieszka Paradowska-Gorycka
Summary: Mixed connective tissue disease (MCTD) is a rare disorder with unclear pathogenesis. This study analyzed whole blood samples from MCTD, SSc, SLE patients, and healthy donors, and found that hypomethylation distinguishes MCTD patients from SSc and SLE patients. However, global DNA methylation may not be a good diagnostic marker to distinguish MCTD from other ACTDs patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anna Wajda, Diana Bogucka, Barbara Stypinska, Marcin Jerzy Radkowski, Tomasz Targowski, Ewa Dudek, Tomasz Kmiolek, Ewa Modzelewska, Agnieszka Paradowska-Gorycka
Summary: The present study analyzed the association between selected prostaglandin pathway genes and clinical parameters in patients with sarcopenia and frailty syndrome. The results showed a significant effect of age on PTGER4 gene expression and a negative correlation between PTGER4 expression and appendicular skeletal muscle mass. PTGES2 and PTGS2 expressions were negatively correlated with creatine phosphokinase and positively correlated with the functional mobility test timed up and go scale. In the older control group, a negative association between iron levels and the expression of PTGS2 was observed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Adam Ejma-Multanski, Anna Wajda, Agnieszka Paradowska-Gorycka
Summary: Cell cultures play a significant role in the research and treatment of autoimmune connective tissue diseases (ACTDs). Culturing different cell types involved in ACTDs helps broaden knowledge of these diseases, potentially leading to finding cures. By analyzing gene expression patterns, surface proteins, and cytokine profiles in cell cultures, potential biomarkers can be identified for diagnosing, monitoring disease activity, and predicting treatment response. Moreover, cell culturing allows evaluation of the effects of therapies on patient-specific cell populations, aiding in personalized medicine.
Article
Rheumatology
Magdalena Chmielinska, Marzena Olesinska, Anna Felis-Giemza, Agnieszka Paradowska-Gorycka, Karolina Palej, Julita Rejmer-Szczesniak, Dariusz Szukiewicz
Summary: Based on the ASAS-EULAR recommendations, patients with axial spondyloarthritis who have failed to respond to at least two courses of NSAID therapy may be considered for modified NSAID treatment. This study aimed to identify risk factors for treatment failure and found that higher zonulin levels, ankylosing spondylitis, X-ray sacroiliitis, magnetic resonance imaging sacroiliitis, long duration of symptoms, high BASDAI score, and high spinal pain intensity were associated with treatment failure. Additionally, positive correlations were observed between haptoglobin concentration with C-reactive protein and erythrocyte sedimentation rate, and between zonulin levels and white blood count.
RHEUMATOLOGY INTERNATIONAL
(2023)
Article
Rheumatology
Anna Felis-Giemza, Agata Matusiewicz, Anna Wajda, Marzena Olesinska
Summary: This study evaluated the safety of esthetic medicine procedures in patients with AIRD and found that most patients underwent these procedures during remission or low disease activity. Adverse events were mostly mild and transient site reactions, and most patients expressed satisfaction with the results.
RHEUMATOLOGY INTERNATIONAL
(2023)
