Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Article
Biochemistry & Molecular Biology
Ravita Kumari, Shikha Tiwari, Mahendra Atlani, Athira Anirudhan, Sudhir K. Goel, Ashok Kumar
Summary: The prevalence of chronic kidney disease of unknown etiology (CKDu) is increasing globally, including in the Indian population. This study analyzed the association between single nucleotide polymorphisms (SNPs) in three genes and the susceptibility to CKDu. The results showed that certain genetic variants in KCNA10 and SLC13A3 genes were significantly associated with CKDu susceptibility. These findings suggest that genetic factors play a role in the predisposition to CKDu.
BIOCHEMICAL GENETICS
(2023)
Article
Medicine, General & Internal
Imaniar Noor Faridah, Haafizah Dania, Rita Maliza, Wan-Hsuan Chou, Wen-Hung Wang, Yen-Hsu Chen, Dyah Aryani Perwitasari, Wei-Chiao Chang
Summary: Dengue is a global arboviral disease that has become a major public health concern. This study investigated the associations of variations in the MICB and PLCE1 genes with dengue severity and thrombocytopenia in Indonesian and Taiwanese populations. The results showed associations between MICB rs3132468 and dengue shock syndrome (DSS), as well as between PLCE1 rs3740360 and secondary dengue hemorrhagic fever (DHF) in Indonesian patients.
Review
Agriculture, Dairy & Animal Science
Roman Wenne
Summary: In recent decades, the importance of considering genetic changes in aquatic populations for effective management and protection of aquatic ecosystems has been recognized. Single nucleotide polymorphism (SNP) is a high-resolution molecular marker suitable for studying the genetic diversity of populations. This review highlights the benefits of using SNPs to identify natural populations of aquatic animals and detect threats to them from released farm animals, fishery, and climate changes.
Article
Pediatrics
Yanqing Liu, Wen Fu, Kai Fu, Xiaoyu Zuo, Wei Jia, Ning Wang, Yan Zhang, Guochang Liu, Fuming Deng
Summary: This study investigated the association between HAAO gene polymorphism rs3816183 T>C and hypospadias in a cohort of Chinese children. The results showed that the rs3816183[T] polymorphism is associated with increased risk of anterior/middle hypospadias. However, the overall risk of hypospadias could not be confirmed.
FRONTIERS IN PEDIATRICS
(2022)
Article
Genetics & Heredity
Puneet Talwar, Suman Kushwaha, Chitra Rawat, Harpreet Kaur, Ankit Srivastava, Rachna Agarwal, Puneet Chandna, Paolo Tucci, Luciano Saso, Ritushree Kukreti
Summary: This study validated the reliability of the genomic convergence and network analysis approach in identifying candidate genes associated with Alzheimer's disease by studying the association of genetic variants from three critical genes, APOE, EGFR, and ACTB. The results showed significant associations between certain SNPs in these genes and AD, further supporting the utility of this approach in identifying potential AD-related genes.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Dorte Wittenburg, Michael Doschoris, Jan Klosa
Summary: This study constructs different groups based on dependencies between genomic regions and develops a new function package to account for the impact of family structure on genome-based evaluations. The research demonstrates that considering family structure can more accurately identify dependencies in the genome and improve the accuracy of genome-based association studies.
BMC BIOINFORMATICS
(2021)
Article
Immunology
Ata Abbasi, Chixiang Chen, Chintan K. Gandhi, Rongling Wu, Annie Pardo, Moises Selman, Joanna Floros
Summary: This study compared the genetic variants of surfactant proteins (SPs) in patients with idiopathic pulmonary fibrosis (IPF) and hypersensitivity pneumonitis (HP). The research findings suggest that SNPs of SP genes may play an important role in the genetic susceptibility to IPF and HP, and can be used as markers to distinguish between these two diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Tamara Perez-Jeldres, Fabien Magne, Gabriel Ascui, Danilo Alvares, Matias Orellana, Manuel Alvarez-Lobos, Cristian Hernandez-Rocha, Lorena Azocar, Nataly Aguilar, Alberto Espino, Ricardo Estela, Sergio Escobar, Alejandra Zazueta, Pablo Baez, Veronica Silva, Andres de la Vega, Elizabeth Arriagada, Carolina Pavez-Ovalle, Alejandro Diaz-Asencio, Dante Travisany, Juan Francisco Miquel, Eduardo J. Villablanca, Mitchell Kronenberg, Maria Leonor Bustamante
Summary: This study investigated the genetic risk variants of IBD in a Chilean cohort, finding an association between Native American ancestry and IBD risk. Variants associated with IBD risk in this Andean region were related to myeloid cells and the innate immune response.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Maha Daghestani, Nashwa Othman, Mohammed A. Omair, Fahidah Alenzi, Maha A. Omair, Eman Alqurtas, Shireen Amin, Arjumand Warsy
Summary: This study conducted an investigation on the Saudi population and found that 6 single nucleotide polymorphisms (SNPs) were significantly associated with rheumatoid arthritis (RA), with 4 of them having a protective effect. Two SNPs showed significantly higher heterozygote frequencies in the control group compared to the patients. This indicates considerable heterogeneity in the genetics of RA in different populations.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Health Care Sciences & Services
Yu-Ting Hsiao, Feng-Chih Shen, Shao-Wen Weng, Pei-Wen Wang, Yung-Jen Chen, Jong-Jer Lee
Summary: This study identified genetic determinants of increased risk of diabetic retinopathy (DR) in individuals with type 2 diabetes mellitus (T2DM), focusing on FTO (rs8050136) and PSMD6 (rs831571) genetic variations. By combining genetic and nongenetic risk factors, the predictive model showed improved accuracy in predicting DR risk, especially in patients with poor glycemic control or severe microalbuminuria.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Helene Muranty, Caroline Denance, Luca Bianco, John Tillman, Eric van de Weg
Summary: This study assessed the concordance and accuracy of Illumina Infinium and Affymetrix Axiom SNP array data in apple genomes. The majority of the data was found to be compatible, although intense data filtering and curation were required for data integration. This in-depth analysis may provide valuable insights for future work on SNP array data integration and interpretation, as well as for probe/platform development.
Article
Microbiology
Jelmer B. Jukema, Bernice M. Hoenderboom, Birgit H. B. van Benthem, Marianne A. B. Van der Sande, Henry J. C. de Vries, Christian J. P. A. Hoebe, Nicole H. T. M. Dukers-Muijrers, Caroline J. Bax, Servaas A. Morre, Sander Ouburg
Summary: Clear inter-individual differences in response to C. trachomatis infections exist, with certain genes' SNPs potentially influencing susceptibility and severity. NOD1 and IL10 gene SNPs may increase the risk of infection and late complications such as ectopic pregnancy or infertility. Further confirmatory studies on a larger scale are needed to explore the role of SNPs in CT infections.
Review
Biotechnology & Applied Microbiology
Luiz Alexandre Chisini, Rodrigo Varella de Carvalho, Francine dos Santos Costa, Luana Carla Salvi, Flavio Fernando Demarco, Marcos Britto Correa
Summary: The aim of this systematic review and meta-analysis was to investigate the influence of single nucleotide polymorphisms (SNPs), related to genes in salivary composition and flow, on dental caries experience. Sixteen studies were included in the systematic review and ten in the meta-analysis. Forty-four SNPS, covering four genes (CA6, AQP2, AQP5, and MUC5B) were identified. Most of the SNPs were not associated with caries in meta-analysis. Homozygous TT genotype of the SNP CA6 rs17032907(C/T) was associated with caries [OR = 3.23(1.39-7.49)]. The pool effect of the SNPs assessed in AQP5 was associated with a reduction in the likelihood of caries [OR = 0.75(0.59-0.95)]. Considering all SNPs of salivary composition and flow, the effect allele was associated with a 75% increase in the likelihood of caries [OR = 1.75(1.06-2.89)] in the homozygous genotype. The present findings showed that the genes in salivary composition and flow can play an important role in dental caries experience.
Article
Microbiology
Kazunari Kamachi, Kentaro Koide, Nao Otsuka, Masataka Goto, Tsuyoshi Kenri
Summary: Bordetella pertussis is a highly infectious bacterium that easily causes pertussis outbreaks in humans, especially in school-aged children. In detection and investigation of outbreaks, excluding non-outbreak isolates is important for understanding the bacterial transmission routes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Physiology
Anil Kumar Jaiswal, Jyoti Yadav, Sangeet Makhija, Maninder Sandey, Amol Suryawanshi, Amit Kumar Mitra, Amarjit Mishra
Summary: The study found that aged mice exhibit increased airway hyperresponsiveness, mixed granulomatous airway inflammation, and changes in immune response, suggesting that the development of airway inflammation may be age-related. Additionally, the age-dependent decline in SPLUNC1 levels may be involved in developing steroid-resistant airway inflammation and asthma heterogeneity.
AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY
(2022)
Article
Oncology
Chameera Ekanayake Weeramange, Danhua Shu, Kai Dun Tang, Jyotsna Batra, Rahul Ladwa, Lizbeth Kenny, Sarju Vasani, Ian H. Frazer, Riccardo Dolcetti, Jonathan J. Ellis, Richard A. Sturm, Paul Leo, Chamindie Punyadeera
Summary: The risk of human papillomavirus (HPV)-positive head and neck cancer (HNC) is associated with distinct human leukocyte antigen (HLA) variants, some of which are shared by both cervical cancer and HPV-positive HNC. Several previous genome-wide association studies were replicated in this study, but the associations were limited to the HPV-positive HNC group.
Article
Oncology
Abdelrahman H. Elsayed, Xueyuan Cao, Amit K. Mitra, Huiyun Wu, Susana Raimondi, Christopher Cogle, Zeina Al-Mansour, Raul C. Ribeiro, Alan Gamis, Edward Anders Kolb, Richard Aplenc, Todd A. Alonzo, Soheil Meshinchi, Jeffrey Rubnitz, Stanley Pounds, Jatinder K. Lamba
Summary: A patient-specific polygenic score was established to personalize acute myeloid leukemia (AML) treatment. Patients with low ACS10 score had significantly worse outcomes with standard therapy, but showed improvement with augmented therapy. The polygenic ACS10 score can identify patients with unfavorable pharmacogenetic characteristics and offer potential for elective augmented therapy.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Immunology
Anil Kumar Jaiswal, Jyoti Yadav, Sangeet Makhija, Suman Mazumder, Amit Kumar Mitra, Amol Suryawanshi, Maninder Sandey, Amarjit Mishra
Summary: The study revealed a direct regulatory role of the Irg1/itaconate pathway in dendritic cells for the development of airway inflammation, suggesting a possible therapeutic target in modulating allergic asthma.
MUCOSAL IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Harsh Sharma, Trishna Pani, Ujjaini Dasgupta, Jyotsna Batra, Ravi Datta Sharma
Summary: Alternative splicing (AS) is a key post-transcriptional modification that increases protein diversity. Many protein-coding genes in humans undergo AS and code for different transcripts, some of which are associated with diseases. A pipeline called FASE has been developed to determine the structure and concentration of transcripts, and it can efficiently predict novel transcripts for the identification of biomarkers and therapeutics.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Hannu Koistinen, Ruusu-Maaria Kovanen, Morley D. Hollenberg, Antoine Dufour, Evette S. Radisky, Ulf-Hakan Stenman, Jyotsna Batra, Judith Clements, John D. Hooper, Eleftherios Diamandis, Oliver Schilling, Antti Rannikko, Tuomas Mirtti
Summary: Since the proposition of the pro-invasive activity of proteolytic enzymes over 70 years ago, several roles for proteases in cancer progression have been established. About half of the 473 active human proteases are expressed in the prostate and many of the most well-characterized members of this enzyme family are regulated by androgens, hormones essential for development of prostate cancer. Most notably, several kallikrein-related peptidases, including KLK3 (prostate-specific antigen, PSA), the most well-known prostate cancer marker, and type II transmembrane serine proteases, such as TMPRSS2 and matriptase, have been extensively studied and found to promote prostate cancer progression. Recent findings also suggest a critical role for proteases in the development of advanced and aggressive castration-resistant prostate cancer (CRPC). Perhaps the most intriguing evidence for this role comes from studies showing that the protease-activated transmembrane proteins, Notch and CDCP1, are associated with the development of CRPC.
Article
Orthopedics
X. Wu, C. Liyanage, M. Plan, T. Stark, T. McCubbin, R. A. Barrero, J. Batra, R. Crawford, Y. Xiao, I. Prasadam
Summary: This study aims to identify the changes in energy metabolism in osteoarthritis (OA) cartilage. Metabolomics, proteomics, and transcriptomics analyses were conducted to investigate the global alterations in OA metabolism. The results showed increased lactate production and decreased mitochondrial respiratory rates in OA chondrocytes. This study provides a basis for targeting metabolism as a therapeutic approach for OA.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Genetics & Heredity
Leire Moya, Samaneh Farashi, Prashanth Suravajhala, Panchadsaram Janaththani, Jyotsna Batra
Summary: COVID-19 has caused significant impacts globally, infecting over 112 million people and causing more than 2.5 million deaths. In Europe, Spain and Italy had a high number of COVID-19 related deaths, while many infected individuals did not develop severe illness. Researchers speculated that unique genomic characteristics in these populations could contribute to a poorer prognosis.
Article
Oncology
Suman Mazumder, Taraswi Mitra Ghosh, Ujjal K. Mukherjee, Sayak Chakravarti, Farshad Amiri, Razan S. Waliagha, Farnaz Hemmati, Panagiotis Mistriotis, Salsabil Ahmed, Isra Elhussin, Ahmad-Bin Salam, Windy Dean-Colomb, Clayton Yates, Robert D. Arnold, Amit K. Mitra
Summary: Prostate cancer (PCa) is a major cause of cancer deaths in US men. Drug resistance and specific cancer subtypes, such as epithelial-to-mesenchymal transdifferentiation (EMT) and neuroendocrine PCa (NEPC), pose significant challenges in PCa treatment. In this study, a computational prediction algorithm called secDrug identified potential secondary drugs for advanced-stage PCa. The proof-of-concept drug FK866, which targets NAMPT, showed promise in inhibiting drug resistance and stemness in PCa. The study also demonstrated the effects of FK866 on tumor metastasis, cell migration, and invasion, as well as regulation of genes associated with cancer stemness. The development pipeline introduced in this study has the potential to improve the management of lethal PCa.
Article
Biochemistry & Molecular Biology
Ikhlak Ahmed, Mubarak Ziab, Sahar Da'as, Waseem Hasan, Sujitha P. Jeya, Elbay Aliyev, Sabah Nisar, Ajaz A. Bhat, Khalid Adnan Fakhro, Ammira S. Alshabeeb Akil
Summary: Diabetic nephropathy (DN) is a common microvascular complication of diabetes that leads to end-stage renal disease. This study aimed to identify key transcription factors (TFs) associated with DN progression by performing a meta-analysis on gene expression profiles from multiple datasets. The analysis revealed distinct clusters of dysregulated susceptibility genes in different renal compartments, with a subset of these genes encoding critical TFs involved in DN development and podocyte function. The role of these TFs was validated in a hyperglycemic zebrafish model, showing that altered expression of these genes leads to morphological abnormalities in various kidney structures. This study provides insights into the molecular drivers, essential genes, and pathways involved in DN initiation and development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Oncology
Leire Moya, Carina Walpole, Fiona Rae, Srilakshmi Srinivasan, Inge Seim, John Lai, David Nicol, Elizabeth D. Williams, Judith A. Clements, Jyotsna Batra
Summary: This study successfully established four cell lines derived from localized prostate cancer, including two benign and two malignant cell lines. The characteristics and molecular events of these cell lines could help in understanding the development and progression of cancer.
PROSTATE CANCER AND PROSTATIC DISEASES
(2023)
Article
Multidisciplinary Sciences
Dulari K. Jayarathna, Miguel E. Renteria, Jyotsna Batra, Neha S. Gandhi
Summary: This study identified stage-specific competing endogenous RNAs (ceRNAs) in breast cancer using cancer genome atlas data and investigated their molecular functions and prognostic ability. Five genes and one long non-coding RNA were found to be unique to the stage IV ceRNA network, and these genes have been described in previous breast cancer studies. Survival analysis identified prognostic microRNAs in stages I, II, and III. These findings reveal a set of unique ceRNAs in metastatic breast cancer, and further experimental work is needed to evaluate their role in metastasis. Identifying stage-specific ceRNAs will also contribute to the understanding of personalized therapeutics in breast cancer.
SCIENTIFIC REPORTS
(2023)
Review
Oncology
Fatemeh Davoudi, Afshin Moradi, Therese M. M. Becker, John G. G. Lock, Brian Abbey, Davide Fontanarosa, Annette Haworth, Judith Clements, Rupert C. C. Ecker, Jyotsna Batra
Summary: Prostate cancer is a commonly diagnosed malignant neoplasm and a leading cause of cancer-related death in men worldwide. Personalized therapeutic strategies for this disease remain limited, but emerging biomarkers based on individual patient profiles and computer-assisted diagnostics have the potential to guide precision medicine. This review discusses screening methods, genetic aberrations, and phenotypic biomarkers for advanced prostate cancer, exploring their clinical implications in diagnosis, prognosis, and treatment prediction. Prognostic and treatment predictive biomarker discovery can improve patient management and personalized treatment regimens.
CURRENT TREATMENT OPTIONS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Adil Malik, Dulari K. Jayarathna, Mark Fisher, Tabassum Khair Barbhuiya, Neha S. Gandhi, Jyotsna Batra
Summary: In this study, the researchers investigated the mechanism of IRX4 homeodomain-DNA recognition and the impact of somatic mutations on these interactions using sequence analysis, homology modeling, and molecular dynamics simulations. They also identified the gene expression and protein expression of IRX4 in various tissues and highlighted the importance of conserved residues in DNA binding and the role of somatic mutations in destabilizing the protein-DNA complex. Additionally, they predicted that the C-terminal sequence of the IRX4 homeodomain could act as a potential cell-penetrating peptide.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Review
Oncology
Srilakshmi Srinivasan, Thomas Kryza, Jyotsna Batra, Judith Clements
Summary: This review discusses the complex biology of kallikrein-related peptidases and their role in cancer and the tumor microenvironment. It also explores their involvement in tumor immune suppression and resistance to cancer therapy. Understanding the functions of these peptidases can provide insights into tumor development and help in developing new therapeutic strategies.
NATURE REVIEWS CANCER
(2022)
