Article
Genetics & Heredity
Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Berenice Batut, Subina Mehta, James E. Johnson, Bjoern Gruening, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin, Magnus O. Arntzen
Summary: This study presents three integrative meta-omics workflows developed in Galaxy for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with a newly developed web-application ViMO to analyze metabolisms in complex microbial communities. The workflows were applied on a cellulose-degrading consortium to analyze the roles of uncultured microorganisms in biomass degradation processes. The workflows allowed for reconstruction of metagenome-assembled genomes (MAGs) and analysis of the functional potential of the microbiome using metatranscriptomics and metaproteomics.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Genetics & Heredity
Bo Li, Xu Zhao, Wanrun Xie, Zhenzhen Hong, Yi Zhang
Summary: Diabetic nephropathy (DN) is a common complication of diabetes and a major cause of kidney disease. Although significant progress has been made in understanding the etiopathogenesis of DN, the genetic mechanisms underlying these effects remain unknown.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Karla Cervantes-Gracia, Richard Chahwan, Holger Husi
Summary: The wealth of high-throughput data has provided new opportunities for analyzing and describing biological processes. Meta-analysis methods have become a popular approach to correlate large-scale datasets from different research groups, leading to results with greater statistical power. This has helped identify gene signatures, biomarkers, and pathways that offer insights into specific phenotypes. However, there is still a lack of standardized regulations for reporting large-scale data and identifying molecular targets and signaling networks.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Stavroula L. Kastora, Georgios Kounidas, Valerie Speirs, Yazan A. Masannat
Summary: Breast cancer is the most frequently diagnosed cancer in women globally. This study aimed to identify novel secreted biomarkers that may indicate progression to high-grade breast cancer and predict metastatic potential. Through comprehensive systematic review and bioinformatic analysis, potential predictors of breast cancer progression and their association with patient mortality outcomes were identified.
Review
Pharmacology & Pharmacy
Lance M. O'Connor, Blake A. O'Connor, Su Bin Lim, Jialiu Zeng, Chih Hung Lo
Summary: Bioinformatic analysis of omics datasets has become increasingly important in neuroscience, enabling improved diagnostic and therapeutic targeting of neurodegenerative diseases. This review summarizes data mining studies in different omics layers and discusses integration approaches to analyze complex biological data. The review also emphasizes the need for combining bioinformatics analysis with experimental validation to achieve precision phenotyping of neurodegenerative diseases.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Psychiatry
Yang Du, Wen-Long Tan, Lei Chen, Zi-Meng Yang, Xue-Song Li, Xiong Xue, Yan-Shan Cai, Yong Cheng
Summary: Transplantation of serum exosomes from schizophrenia patients into mice caused behavioral abnormalities, possibly related to neuro-related genes and epigenetic regulation. This study may provide a potential animal model and new therapeutic targets for schizophrenia.
SCHIZOPHRENIA BULLETIN
(2021)
Article
Critical Care Medicine
Mulong Du, Joe G. N. Garcia, Jason D. Christie, Junyi Xin, Guoshuai Cai, Nuala J. Meyer, Zhaozhong Zhu, Qianyu Yuan, Zhengdong Zhang, Li Su, Sipeng Shen, Xuesi Dong, Hui Li, John N. Hutchinson, Paula Tejera, Xihong Lin, Meilin Wang, Feng Chen, David C. Christiani
Summary: The study identified genetic diversity in ARDS between Europeans and African Americans, with rs7967111 at 12p13.2 being functionally associated with ARDS susceptibility in Europeans. The results suggest that comorbidity of inflammatory bowel disease, elevated levels of C-reactive protein and interleukin-10 increase ARDS risk, while vitamin D supplementation and vasodilator use ameliorate risk.
INTENSIVE CARE MEDICINE
(2021)
Article
Biochemical Research Methods
Kai Shi, Wei Lin, Xing-Ming Zhao
Summary: Molecular biomarkers are specific molecules that can aid in diagnosing or predicting diseases. Advances in high-throughput technologies have allowed for the accumulation of large omics data for screening biomarkers. Research involves various machine learning approaches to identify biomarkers and address potential challenges in biomedical data for future biomarker identification.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Review
Cell Biology
Maxim N. Shokhirev, Adiv A. Johnson
Summary: Alzheimer's disease, an incurable age-related brain disorder, was studied through the analysis of genes, proteins, and microRNAs. The results showed that factors such as cell death, cellular senescence, energy metabolism, genomic integrity, and glia were associated with the disease. These factors exhibited unique characteristics in different age groups.
AGEING RESEARCH REVIEWS
(2022)
Article
Cell Biology
Guihua Jin, Qingqing Ruan, Fugen Shangguan, Linhua Lan
Summary: The study identified RUNX2 and LAMC2 as promising targets for early diagnosis and therapy of pancreatic carcinoma, based on integrative analysis of multiple datasets.
Review
Biology
Pandiyan Muthuramalingam, Rajendran Jeyasri, Kasinathan Rakkammal, Lakkakula Satish, Sasanala Shamili, Adhimoolam Karthikeyan, Alaguvel Valliammai, Arumugam Priya, Anthonymuthu Selvaraj, Pandiyan Gowri, Qiang-Sheng Wu, Shunmugiah Karutha Pandian, Hyunsuk Shin, Jen-Tsung Chen, Venkidasamy Baskar, Muthu Thiruvengadam, Manoharan Akilan, Manikandan Ramesh
Summary: Rice is an important food crop in Asian countries, but its growth and yield are affected by salinity stress. Understanding the mechanisms of salinity stress and developing salinity-tolerant rice varieties are crucial for future food security. This review discusses the use of high-throughput technologies and multi-omics approaches to study salinity stress in rice and highlights the potential ways to enhance salt tolerance and develop salt-tolerant varieties. The review also emphasizes the importance of incorporating the latest advancements and knowledge in plant stress biology to further understand the mechanisms of salinity stress in rice.
Article
Medicine, Research & Experimental
Bincy Varghese, Sreeranjini Babu, Aishwarya Jala, Panchanan Das, Rajesh Raju, Roshan M. Borkar, Ramu Adela
Summary: Through integrating next-generation sequencing and metabolomics multi-omics analysis of placenta, this study identified differentially expressed miRNAs, their target genes, altered metabolites, and metabolic pathways in gestational hypertension (GH) patients. The findings obtained from this study may contribute to further understanding of the molecular pathways associated with GH and the evaluation of prognostic markers.
ARCHIVES OF MEDICAL RESEARCH
(2024)
Article
Clinical Neurology
Christopher Clark, Loiec Dayon, Mojgan Masoodi, Gene L. Bowman, Julius Popp
Summary: By integrating multi-omics approaches, this study identified novel molecular and pathway alterations associated with Alzheimer's disease pathology. The findings revealed multiple interactions between single 'omics modalities and distinct multi-omics molecular signatures related to amyloid pathology, neuronal injury, and tau hyperphosphorylation. Pathway enrichment analysis highlighted overrepresentation of hemostasis, immune response, and extracellular matrix signaling pathways in association with AD, while combinations of specific molecules improved prediction of AD pathology and cognitive decline.
ALZHEIMERS RESEARCH & THERAPY
(2021)
Article
Pharmacology & Pharmacy
W-C Dan, X-Y Guo, G-Z Zhang, S-L Wang, M. Deng, J-L Liu
Summary: This study identified radiation-associated genes in breast cancer through analysis of gene expression data. Five hub genes and 11 candidate genes were identified as potential diagnostic markers for breast cancer. The findings provide novel insights into the functional characteristics of breast cancer and suggest potential therapeutic targets.
EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES
(2023)
Article
Cell Biology
Shifu Li, Qian Zhang, Zheng Huang, Fenghua Chen
Summary: Through bioinformatics analysis, key biomarkers associated with intracranial aneurysm formation were identified. The study revealed enhanced immune response and suppressed extracellular matrix organization during aneurysm progression. A three-gene model (CXCR4, S100B, and OSM) was constructed and showed favorable diagnostic value for aneurysms.
INFLAMMATION RESEARCH
(2023)
Article
Biochemical Research Methods
Anastasiya Kostyusheva, Sergey Brezgin, Yurii Babin, Irina Vasilyeva, Dieter Glebe, Dmitry Kostyushev, Vladimir Chulanov
Summary: This review focuses on the potential of CRISPR-based technologies to become platforms for point-of-care nucleic acid detection methods and deployable diagnostic platforms. Many Cas proteins have been utilized in the development of highly accurate and sensitive diagnostic tools, enabling fast, affordable, and user-friendly diagnostics.
Article
Medicine, Research & Experimental
Sergey Batskikh, Sergey Morozov, Elena Vinnitskaya, Evgeniya Sbikina, Zanna Borunova, Alexey Dorofeev, Yulia Sandler, Kirill Saliev, Dmitry Kostyushev, Sergey Brezgin, Anastasiya Kostyusheva, Vladimir Chulanov
Summary: The study found that a significant proportion of patients with autoimmune liver diseases are positive for anti-HBc, with some also having occult HBV infection. Among patients with AILDs, anti-HBc positivity is most common in the PBC group and in those with advanced liver fibrosis. These findings suggest a potential role of previous HBV infection in the etiology and pathogenesis of AILDs, specifically PBC.
ADVANCES IN THERAPY
(2022)
Article
Biochemistry & Molecular Biology
Dmitry Kostyushev, Anastasiya Kostyusheva, Natalia Ponomareva, Sergey Brezgin, Vladimir Chulanov
Summary: After almost a decade of research, CRISPR/Cas9 technology is moving towards clinical trials for treating hepatitis B virus infections. Early studies show promising antiviral effects, but key challenges still need to be addressed to make CRISPR/Cas9 a viable therapy against HBV.
NUCLEIC ACID THERAPEUTICS
(2022)
Editorial Material
Endocrinology & Metabolism
Silvia Pieralice, Luca D'Onofrio, Paolo Pozzilli, Raffaella Buzzetti
DIABETES-METABOLISM RESEARCH AND REVIEWS
(2022)
Article
Endocrinology & Metabolism
Francesca De Ridder, Kristien J. Ledeganck, Benedicte De Winter, Rie Braspenning, Danae Delbeke, Eric Renard, Paolo Pozzilli, Silvia Pieralice, Dirk Vissers, Christophe De Block
Summary: This study assessed trends in glucose, lactate, and ketones during anaerobic and aerobic exercise in individuals with type 1 diabetes (T1D) and compared the differences between the two types of exercise. It was found that omitting pre-meal insulin and basal insulin could prevent hypoglycemia but resulted in hyperglycemia due to excessive carbohydrate intake. No ketosis was observed during or after the exercises.
DIABETES-METABOLISM RESEARCH AND REVIEWS
(2022)
Review
Endocrinology & Metabolism
Ernesto Maddaloni, Geremia B. Bolli, Brian M. Frier, Randie R. Little, Richard D. Leslie, Paolo Pozzilli, Raffaela Buzzetti
Summary: C-peptide measurement is valuable in autoimmune diabetes but limited in type 2 diabetes due to confounding factors like insulin resistance. Standardization issues exist that may affect comparability between different laboratories.
DIABETES OBESITY & METABOLISM
(2022)
Article
Cardiac & Cardiovascular Systems
D. Bruttomesso, C. Irace, P. Pozzilli
Summary: This study reported on glycemic control in Italian participants with type 1 diabetes and found that younger patients had better glycemic control compared to older patients. Factors such as body mass index and adherence to diet were associated with glycemic control.
NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES
(2023)
Article
Medicine, Research & Experimental
Dmitry Kostyushev, Anastasiya Kostyusheva, Sergey Brezgin, Natalia Ponomareva, Natalia F. Zakirova, Aleksandra Egorshina, Dmitry V. Yanvarev, Ekaterina Bayurova, Anna Sudina, Irina Goptar, Anastasiya Nikiforova, Elena Dunaeva, Tatiana Lisitsa, Ivan Abramov, Anastasiia Frolova, Alexander Lukashev, Ilya Gordeychuk, Andrey A. Zamyatnin Jr, Alexander Ivanov, Vladimir Chulanov
Summary: CRISPR-Cas9 systems show remarkable anti-HBV activity by targeting the hepatitis B virus major genomic form, cccDNA. However, inactivating cccDNA alone is not enough to cure the infection, as HBV replication rebounds due to the de novo formation of cccDNA from its precursor, rcDNA. Depleting rcDNA before delivering CRISPR-Cas9 RNPs can prevent viral rebound and promote resolution of HBV infection. These findings lay the groundwork for developing a virological cure of HBV infection using a single dose of short-lived CRISPR-Cas9 RNPs, with the help of widely used reverse transcriptase inhibitors to block cccDNA replenishment.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Computer Science, Information Systems
Federico D'Antoni, Lorenzo Petrosino, Alessandro Marchetti, Luca Bacco, Silvia Pieralice, Luca Vollero, Paolo Pozzilli, Vincenzo Piemonte, Mario Merone
Summary: This study proposes a layered meta-learning approach based on multi-expert systems to predict adverse events in patients with type 1 diabetes. Three deep neural networks are used to specialize in predicting hypoglycemia, hyperglycemia, or euglycemia. The outputs of the experts are then passed to a meta-learner to provide the final classification. The approach is able to predict hypoglycemia events with an average time gain of 22.8 minutes and hyperglycemia events with an average advance of 24.0 minutes.
Article
Pharmacology & Pharmacy
Sergey Brezgin, Anastasiya Kostyusheva, Natalia Ponomareva, Ekaterina Bayurova, Alla Kondrashova, Anastasia Frolova, Olga Slatinskaya, Landysh Fatkhutdinova, Georgy Maksimov, Mikhail Zyuzin, Ilya Gordeychuk, Alexander Lukashev, Sergey Makarov, Alexander Ivanov, Andrey A. Zamyatnin Jr, Vladimir Chulanov, Alessandro Parodi, Dmitry Kostyushev
Summary: Biological nanoparticles, such as extracellular vesicles (EVs) and extracellular vesicle-mimetic nanovesicles (EMNVs), have been extensively studied as drug delivery vehicles in medical applications. This study investigated the properties and drug delivery abilities of EVs and EMNVs, and analyzed their use for delivering the chemotherapeutic drug doxorubicin. EMNVs were found to be more effectively internalized, while EVs showed higher intracellular release of doxorubicin.
Review
Endocrinology & Metabolism
Felecia D'Souza, Raffaella Buzzetti, Paolo Pozzilli
Summary: Recent evidence suggests that diabetes is associated with increased risk and adverse outcomes from COVID-19 infection. The mechanisms include dysregulation of specific enzymes and impaired immune responses, exacerbated by hyperglycemia. Limited studies on COVID-19 vaccination in people with diabetes show that vaccination is protective against adverse outcomes. People with diabetes should be prioritized in vaccination efforts and blood sugar optimization is essential in reducing their COVID-19-associated risk.
DIABETES-METABOLISM RESEARCH AND REVIEWS
(2023)
Editorial Material
Endocrinology & Metabolism
Pozzilli Paolo
DIABETES-METABOLISM RESEARCH AND REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Ekaterina P. Kolesova, Vera S. Egorova, Anastasiia O. Syrocheva, Anastasiia S. Frolova, Dmitry Kostyushev, Anastasiia Kostyusheva, Sergey Brezgin, Daria B. Trushina, Landysh Fatkhutdinova, Mikhail Zyuzin, Polina A. Demina, Evgeny V. Khaydukov, Andrey A. Zamyatnin, Alessandro Parodi
Summary: Proteolytic activity plays a crucial role in cell homeostasis and function, with implications in cancer progression and treatment response. Endosomes, which are often the final destination of internalized nanoparticles, are major sites of cellular proteolytic activity. However, little is known about the impact of nanoparticles on endosomal biology. In this study, we generated albumin nanoparticles with varying resistance to proteolysis and demonstrated a relationship between their sensitivity to proteases and drug delivery properties, irrespective of the degree of proteolytic degradation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Dmitry Kostyushev, Sergey Brezgin, Anastasiya Kostyusheva, Natalia Ponomareva, Ekaterina Bayurova, Natalia Zakirova, Alla Kondrashova, Irina Goptar, Anastasiya Nikiforova, Anna Sudina, Yurii Babin, Ilya Gordeychuk, Alexander Lukashev, Andrey A. Zamyatnin Jr, Alexander Ivanov, Vladimir Chulanov
Summary: APOBEC/AID cytidine deaminases play an important role in innate immunity and antiviral defenses. Researchers developed a CRISPR-activation-based approach to induce APOBEC/AID overexpression and control its effects on HBV replication and cellular toxicity. The study highlights the potential for precise control of APOBEC/AID activation as a strategy for suppressing HBV replication without toxicity.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Review
Cell Biology
Ekaterina Bayurova, Alla Zhitkevich, Daria Avdoshina, Natalya Kupriyanova, Yuliya Kolyako, Dmitry Kostyushev, Ilya Gordeychuk
Summary: Common marmosets (CMs) are small primates widely used in biomedical research, but the number of available standardized and well-defined CM cell lines derived from different tissues is still small. The main applications of CM stem cells include regenerative medicine, stem cell research, generation of transgenic CMs, transplantology, cell therapy, reproductive physiology, oncology, and neurodegenerative diseases.