Article
Chemistry, Multidisciplinary
Paul Le Floch, Qiang Li, Zuwan Lin, Siyuan Zhao, Ren Liu, Kazi Tasnim, Han Jiang, Jia Liu
Summary: This study reports a cyborg brain organoid platform that utilizes stretchable electrode arrays to establish long-term stable electrical contacts with brain organoids, enabling continuous recording and analysis of the electrical properties during the development of brain organoids.
ADVANCED MATERIALS
(2022)
Article
Multidisciplinary Sciences
Minshi Peng, Yue Li, Brie Wamsley, Yuting Wei, Kathryn Roeder
Summary: A method named cFIT is proposed for integrating and transferring single-cell RNA sequencing datasets across different conditions, allowing for synchronized integration and precise transfer of knowledge. The study demonstrates the effectiveness of cFIT in capturing batch effects and preserving biological variations in diverse datasets, providing insights into cellular identity and functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Hongru Shen, Jilei Liu, Jiani Hu, Xilin Shen, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, Xiangchun Li
Summary: tGPT is a method for learning feature representation of transcriptomes, which efficiently handles the exponential growth of single-cell transcriptome data. It shows good performance on tasks such as single-cell analysis and tumor tissue analysis.
Article
Biology
Galina Popova, Hanna Retallack, Chang N. Kim, Albert Wang, David Shin, Joseph L. DeRisi, Tomasz Nowakowski
Summary: This study reveals that rubella virus predominantly infects microglia in developing brain, and the infection leads to a profound interferon response in non-microglial cells, affecting fetal neurodevelopment.
Article
Biotechnology & Applied Microbiology
Teng Gao, Ruslan Soldatov, Hirak Sarkar, Adam Kurkiewicz, Evan Biederstedt, Po-Ru Loh, Peter Kharchenko
Summary: Numbat is a computational method that integrates expression, allele, and haplotype information to detect copy number variations in single-cell RNA sequencing (scRNA-seq). It can reconstruct the tumor copy number profile and accurately identify malignant cells, facilitating the understanding of tumor heterogeneity and therapy resistance.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei, Min Hu, Alastair Thompson, Ken Chen, Savitri Krishnamurthy, Nicholas E. Navin
Summary: CellTrek is a computational method that combines single-cell RNA sequencing and spatial transcriptomics to achieve single-cell spatial mapping. It has demonstrated accuracy and robustness through simulation and experimental validation, and has been successfully applied to tumor tissues.
NATURE BIOTECHNOLOGY
(2022)
Article
Entomology
Xiaojing Liu, Zhongjie Zhang, Bo Hu, Kai Chen, Ye Yu, Hui Xiang, Anjiang Tan
Summary: In this study, we characterized the brain cell repertoire of larval and adult silkworm using single-cell transcriptomics. We identified different cell types and their proportions in the brain, and found a significant increase in glial cells during the transition from larva to adult. Interestingly, silkworms have a lower proportion of mushroom body kenyon cells compared to flies and ants.
Review
Neurosciences
Ethan J. Armand, Junhao Li, Fangming Xie, Chongyuan Luo, Eran A. Mukamel
Summary: Single-cell sequencing technologies provide insights into the diversity and developmental relationships of brain cell types, aiding in the design of tools for targeted functional studies of brain circuit components.
Article
Genetics & Heredity
Qiuyan Huo, Yu Yin, Fangfang Liu, Yuying Ma, Liming Wang, Guimin Qin
Summary: Using single-cell sequencing, this study identified eight cell types in melanoma, with two key cell types closely related to MHC activities, one associated with mitosis, and the other with pathways related to multiple diseases. The candidate cell markers for these key cell types may serve as potential therapeutic targets for melanoma.
BMC MEDICAL GENOMICS
(2021)
Article
Oncology
Yibin Dai, Ziyu Wang, Yingchao Xia, Jin Li, Yaping Wu, Yanling Wang, Hongbing Jiang, Jie Cheng
Summary: This study defines the intrinsic epithelial subtypes for head and neck squamous cell carcinoma (HNSCC) through integrative analyses of single-cell and bulk RNA sequencing datasets, providing a more effective molecular subtyping approach for this malignancy.
CLINICAL CANCER RESEARCH
(2023)
Article
Biochemical Research Methods
Qiaoming Liu, Ximei Luo, Jie Li, Guohua Wang
Summary: In this study, the authors propose an evolutionary sparse imputation (ESI) algorithm for single-cell transcriptomes to address the dropout problem and reduce data noise in gene expression profiles. The ESI algorithm constructs a sparse representation model based on gene regulation relationships between cells and uses an optimization framework based on nondominated sorting genetics to iteratively search for the global optimal solution. The results show that scESI outperforms benchmark methods in simulated datasets and real scRNA-seq datasets, improving cell classification, trajectory reconstruction, and identification of differentially expressed genes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Ruli Gao, Shanshan Bai, Ying C. Henderson, Yiyun Lin, Aislyn Schalck, Yun Yan, Tapsi Kumar, Min Hu, Emi Sei, Alexander Davis, Fang Wang, Simona F. Shaitelman, Jennifer Rui Wang, Ken Chen, Stacy Moulder, Stephen Y. Lai, Nicholas E. Navin
Summary: CopyKAT is a method for estimating genomic copy number profiles from high-throughput single-cell RNA sequencing data, which can accurately distinguish cancer cells from normal cell types in tumors and resolve clonal subpopulations within tumors.
NATURE BIOTECHNOLOGY
(2021)
Article
Cell Biology
Xin Ding, Tao Pan, Qiuyan Tian, Wenxi Huang, Lauren S. Hayashi, Qin Liu, Fuyong Li, Li-Xiao Xu, Po Miao, Xiaofeng Yang, Bin Sun, Chen-Xi Feng, Xing Feng, Mei Li, Jian Huang
Summary: This study identified the transcriptome changes in different cell types of the pineal gland following neonatal HIBD using single cell RNA sequencing. It revealed the responses of pineal cells to HIBD and the pyroptosis pathway in pineal microglia cells, providing potential therapeutic targets for improving circadian rhythm dysfunction in neonates with HIBD.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Mi K. Trinh, Clarissa N. Pacyna, Gerda Kildisiute, Christine Thevanesan, Alice Piapi, Kirsty Ambridge, Nathaniel D. Anderson, Eleonora Khabirova, Elena Prigmore, Karin Straathof, Sam Behjati, Matthew D. Young
Summary: This study reveals that the common approach of using shifts in average expression to separate cancer and non-cancer cells can lead to erroneous conclusions. Instead, allelic imbalances representing copy number changes provide a more accurate method to detect and separate cancer cells. This finding offers a definitive approach to identifying cancer cells in single cell mRNA sequencing data.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Martin Philpott, Jonathan Watson, Anjan Thakurta, Tom Brown, Tom Brown, Udo Oppermann, Adam P. Cribbs
Summary: scCOLOR-seq is a method for single-cell corrected long-read sequencing, allowing standalone cDNA nanopore sequencing of single cells. It corrects errors in barcode and unique molecular identifier sequences, and is used for evaluating the transcriptomic features of different cell lines.
NATURE BIOTECHNOLOGY
(2021)
Article
Rehabilitation
Murat Kara, Oezguer Kara, Yasin Ceran, Bayram Kaymak, Tugce Cansu Kaya, Beyza Nur citir, Mahmut Esad Durmus, Esra Durmusoglu, Sarah Razaq, Yahya Dogan, Dia Shehab, Salem A. Alkandari, Ahmad J. Abdulsalam, Ayse Merve Ata, Esra Gizem Koyuncu, Evrim Coskun, Goekhan Turan, Banu Dilek, Mehmet Ali Culha, Pelin Yildirim, Kamal Mezian, Beril Dogu, Gamze Kilic, Zeliha uenlue, Jorge Barbosa, Sergio Pinho, Pelin Analay, Deniz Palamar, Orhan Guevener, Hasan Ocak, Fevziye uensal Malas, Murat Baday, Banu cakir, Levent oezcakar
Summary: The objective of this study was to investigate the relationship between sarcopenia and renin-angiotensin system-related disorders and explore the effects of angiotensin-converting enzyme inhibitors and angiotensin II receptor blockers on muscle mass/function and physical performance. The results showed a strong association between hypertension and sarcopenia, and different antihypertensive drugs had different effects on muscle mass and function.
AMERICAN JOURNAL OF PHYSICAL MEDICINE & REHABILITATION
(2023)
Article
Cardiac & Cardiovascular Systems
Murat Gok, Alparslan Kurtul, Gokay Taylan, Cihan Ozturk, Burcu Cakir, Efe Yilmaz, Servet Altay, Kenan Yalta
Summary: Co-existing non-IRA CTO has an independent association with the evolution of CAN in STEMI patients managed with P-PCI.
Article
Ophthalmology
Sedat Ozmen, Nilgun Ozkan Aksoy, Burcin Cakir, Gursoy Alagoz
Summary: This report describes three cases of acute angle-closure glaucoma due to hyponatremia from COVID-19 infection. All cases had tested positive for COVID-19 and had low serum sodium levels. It is important to consider the possibility of angle-closure glaucoma in COVID-19 patients with hyponatremia.
EUROPEAN JOURNAL OF OPHTHALMOLOGY
(2023)
Review
Medicine, General & Internal
Fatma Dilek Dellal, Gulsum Karaahmetli, Serdar Can Guven, Cevdet Aydin, Oya Topaloglu, Reyhan Ersoy, Bekir Cakir
Summary: This article reports a rare case of SIADH secondary to EGPA. Effective treatment of EGPA resulted in the resolution of SIADH, suggesting a causality between the two conditions.
IRISH JOURNAL OF MEDICAL SCIENCE
(2023)
Article
Food Science & Technology
Ayse Gulden Goksu, Bilal Cakir, Ibrahim Gulseren
Summary: In this study, antidiabetic hazelnut peptides were obtained through enzymatic hydrolysis and fractionation. In vitro assays showed that these peptides had antidiabetic activities, and digestion trials and in silico analyses indicated that food processing and peptide degradation could affect their bioactivity.
JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
(2023)
Article
Endocrinology & Metabolism
Muhammet Cuneyt Bilginer, Abbas Ali Tam, Sevgul Faki, Nagihan Bestepe, Fatma Dilek Dellal, Didem Ozdemir, Oya Topaloglu, Reyhan Ersoy, Bekir Cakir
Summary: Patients with DTC receiving TSH suppression therapy may be at risk for adrenal insufficiency, especially with longer duration or more severe suppression. Dynamic testing with synthetic ACTH can be used to reveal insufficient cortisol response in case of clinical suspicion.
ENDOCRINE RESEARCH
(2023)
Review
Physiology
Giacomo Roman, Benedicte Stavik, Knut H. Lauritzen, Per Morten Sandset, Sean P. Harrison, Gareth J. Sullivan, Maria Eugenia Chollet
Summary: The low or undetectable activity of proteins involved in hemostasis due to genetic alterations causes bleeding phenotype in hereditary coagulation disorders. Current in vitro models using human or animal cells do not fully represent hepatocellular biology and genetic background of patients, limiting the study of these disorders. However, Induced Pluripotent Stem Cell technology combined with CRISPR/Cas9 allows for the generation of autologous and gene-corrected liver cells in the form of three-dimensional organoids, providing a more physiological model to study coagulation proteins and model hereditary coagulation disorders.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Neurosciences
Yu Hong, Cecilie Katrin Kristiansen, Anbin Chen, Gonzalo Sanchez Nido, Lena Elise Hoyland, Mathias Ziegler, Gareth John Sullivan, Laurence A. Bindoff, Kristina Xiao Liang
Summary: Diseases caused by POLG mutations are the most common form of mitochondrial diseases, but the molecular mechanisms behind the lower survival rate in patients with compound heterozygous mutations are unknown. This study used an iPSC model to investigate the differences between homozygous and compound heterozygous genotypes in different cell types. The results showed that compound heterozygous NSCs exhibited more severe functional defects and downregulation of mitochondrial and metabolic pathways compared to homozygous NSCs.
EXPERIMENTAL NEUROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cecilie Katrin Kristiansen, Jessica Furriol, Anbin Chen, Gareth John Sullivan, Laurence A. Bindoff, Kristina Xiao Liang
Summary: In this study, POLG patient-induced pluripotent stem cell (iPSC)-derived neural stem cells (iNSCs) were investigated to understand the impact of POLG mutations on mtDNA maintenance. It was found that iNSCs carrying compound heterozygous POLG mutations had delayed mtDNA level restoration, while iNSCs with homozygous POLG mutation recovered at a similar rate to controls. Moreover, supplementation of deoxyribonucleosides (dNs) reduced mtDNA depletion and increased repopulation rates in patient iNSCs. These findings suggest that POLG mutations impair mtDNA repopulation and dNs supplementation may offer a new therapeutic approach for mitochondrial diseases caused by disturbed mtDNA homeostasis.
Article
Microbiology
Caglayan Merve Ayaz, Nesrin Damla Karakaplan, Ahmet Cagkan Inkaya, Banu Cakir, Serhat Unal, Pinar Zarakolu
Summary: The aim of this study was to investigate the frequency of Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis and Mycoplasma genitalium in men living with HIV. The study found that young age, having multiple partners, drug use, and exchanging sex for money/drugs were associated with STI infection.
MIKROBIYOLOJI BULTENI
(2023)
Article
Multidisciplinary Sciences
Benjamin Patterson, Bing Yang, Yoshiaki Tanaka, Kun-Yong Kim, Bilal Cakir, Yangfei Xiang, Jonghun Kim, Siyuan Wang, In-Hyun Park
Summary: Using chromatin tracing, researchers characterized the 3D state of the X chromosome in naive and primed human pluripotent stem cells (hPSCs) and found that X chromosomes in naive hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. This study provides insight into the unique epigenetic regulation in early embryonic cells.
Article
Biochemistry & Molecular Biology
Sean P. Harrison, Richard Siller, Yoshiaki Tanaka, Maria Eugenia Chollet, Maria Eugenia de la Morena-barrio, Yangfei Xiang, Benjamin Patterson, Elisabeth Andersen, Carlos Bravo-Perez, Henning Kempf, Kathrine S. Asrud, Oleg Lunov, Alexandr Dejneka, Marie-Christine Mowinckel, Benedicte Stavik, Per Morten Sandset, Espen Melum, Saphira Baumgarten, Flavio Bonanini, Dorota Kurek, Santosh Mathapati, Runar Almaas, Kulbhushan Sharma, Steven R. Wilson, Froydis S. Skottvoll, Ida C. Boger, Inger Lise Bogen, Tuula A. Nyman, Jun Jie Wu, Ales Bezrouk, Dana Cizkova, Javier Corral, Jaroslav Mokry, Robert Zweigerdt, In-Hyun Park, Gareth J. Sullivan
Summary: The lack of physiological parity between 2D cell culture and in vivo culture has led to the development of more organotypic models, such as organoids. Organoids are characterized by a reliance on extracellular matrices (ECMs), 2D culture patterning, costly growth factors, and a lack of cellular diversity, structure, and organization. However, a new approach has been developed that overcomes these limitations and produces liver-like organoids with high cellular complexity and functionality. These organoids exhibit key liver functions and can be transplanted and maintained long-term. This approach has significant potential in various applications such as cellular therapy, tissue engineering, drug toxicity assessment, and disease modeling.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
