Article
Biochemical Research Methods
Dailin Gan, Jun Li
Summary: SCIBER is a new batch-effect-removal method that can remove batch effects before integrating multiple single-cell RNA-sequencing datasets to avoid misleading interpretations. It has better scalability and tunability compared to existing methods, and it can output expression data of individual genes for downstream analyses.
Article
Biology
Bas Molenaar, Louk T. Timmer, Marjolein Droog, Ilaria Perini, Danielle Versteeg, Lieneke Kooijman, Jantine Monshouwer-Kloots, Hesther de Ruiter, Monika M. Gladka, Eva van Rooij
Summary: Molenaar et al. used single-cell RNA sequencing to study gene expression changes in cardiac cells following ischemic injury, revealing that cardiomyocytes secrete B2M to promote scar formation. This data may offer insights for identifying therapeutic targets for cardiac repair.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daniele Mercatelli, Nicola Balboni, Alessandro Palma, Emanuela Aleo, Pietro Paolo Sanna, Giovanni Perini, Federico Manuel Giorgi
Summary: The study investigated two cell lines, BE2C and Kelly, of neuroblastoma, showing distinct transcriptional network activities with BE2C having more mesenchymal characteristics compared to Kelly. Single-cell data revealed that MYCN is not constantly active in these cells, and highlighted higher variance in metallothionein transcripts in Kelly cells.
Review
Plant Sciences
Tom Denyer, Marja C. P. Timmermans
Summary: Droplet-based single-cell RNA sequencing has rapidly evolved from a technology with great potential to a widely used method for studying cell responses. However, to maximize its potential, various practical considerations such as optimizing cell-isolation procedures and determining the number of cells and sequencing reads needed should be taken into account.
TRENDS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Valeria Garcia-Flores, Yi Xu, Errile Pusod, Roberto Romero, Roger Pique-Regi, Nardhy Gomez-Lopez
Summary: Single-cell RNA-sequencing (scRNA-seq) is a powerful tool to study cellular composition and interactions in complex tissues. This study presents a protocol for preparing high-quality single-cell suspensions from human placental tissues, including the basal plate, placental villi, and chorioamniotic membranes. The protocol includes tissue collection, tailored dissociation procedures, and cryopreservation of single-cell suspensions. The resulting suspensions are compatible with droplet-based scRNA-seq technology and exhibit high yield and viability. The entire process takes approximately 6 hours, with an additional 2 hours for thawing of cryopreserved single cells.
Article
Multidisciplinary Sciences
Clara Leung, Shaina Robbins, Alison Moss, Maci Heal, Mahyar Osanlouy, Richard Christie, Navid Farahani, Corey Monteith, Jin Chen, Peter Hunter, Susan Tappan, Rajanikanth Vadigepalli, Zixi (Jack) Cheng, James S. Schwaber
Summary: The study developed and analyzed a single-cell scale anatomical map of the rat intrinsic cardiac nervous system (ICNS) across male and female hearts, revealing a reliable structural organization plan and providing a foundation for further analysis in cardiac function and disease. The distribution and clustering of ICNS neurons were highly conserved across all male and female rat hearts with distinct clusters consistently localized, though female hearts had fewer neurons and slightly reduced distribution. The anatomical data from each heart were registered to a geometric scaffold for standardization of common anatomical planes, allowing integration and comparison of multiple experimental results and data types.
Article
Biochemical Research Methods
Micha Sam Brickman Raredon, Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason, Yuval Kluger
Summary: NICHES is a tool that explores extracellular signaling at the truly single-cell level by embedding ligand-receptor signal proxies to visualize heterogeneous signaling archetypes within and between cell clusters as well as across experimental conditions. It can be applied to spatial transcriptomic data to reflect local cellular microenvironment, is compatible with existing single-cell packages, and allows rapid, flexible analysis of cell-cell signaling at single-cell resolution.
Review
Cardiac & Cardiovascular Systems
Wei Chen, Chuling Li, Yijin Chen, Jianping Bin, Yanmei Chen
Summary: Single-cell transcriptomics plays a crucial role in cardiac repair research. This technique allows us to understand the heterogeneity of cardiac cells and the changes in different cell types and molecular signatures during myocardial repair. These studies contribute to the development of new therapeutic approaches for preventing heart failure.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Article
Genetics & Heredity
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
Summary: Spatial transcriptomics is a method to reveal spatially resolved gene expression of diverse cells in complex tissues. SpiceMix, an interpretable method based on probabilistic, latent variable modeling, improves on the inference of cell types and their spatial patterns. By analyzing spatial transcriptome data of brain regions in human and mouse, SpiceMix enhances the inference of complex cell identities, reveals interpretable spatial metagenes, and uncovers differentiation trajectories. SpiceMix is a generalizable analysis framework for spatial transcriptome data to investigate cell-type composition and spatial organization of cells in complex tissues.
Article
Biology
Sachin Sharma, Russell Littman, John D. Tompkins, Douglas Arneson, Jaime Contreras, Al-Hassan Dajani, Kaitlyn Ang, Amit Tsanhani, Xin Sun, Patrick Y. Jay, Herbert Herzog, Xia Yang, Olujimi A. Ajijola
Summary: The study reveals the diversity and distinction of sympathetic neurons innervating the heart in the stellate ganglion. Three subtypes of these neurons primarily innervate the heart, with high and low neuropeptide-Y expression cells exhibiting distinct morphological, neurochemical, and electrophysiological characteristics. Modulating NPY signaling differentially controls cardiac responses by these subpopulations.
Article
Medicine, Research & Experimental
Zhang Chen, Heng Xu, Yuan Li, Xi Zhang, Jikai Cui, Yanqiang Zou, Jizhang Yu, Jie Wu, Jiahong Xia
Summary: This study investigated the immune cell dynamics and local intercellular communication of acute cardiac allograft rejection using single-cell RNA sequencing. The results revealed the functional characteristics and differentiation trajectory of various alloreactive cell subpopulations, and suggested that the CXCR3 pathway may serve as a potential therapeutic target for transplant rejection.
Article
Plant Sciences
Sandra Thibivilliers, Marc Libault
Summary: Plants are made up of cells that interact and adapt to their environment, with single-cell omics technologies allowing researchers to study the unique molecular properties of individual plant cells and their dynamic regulation during differentiation and response to the environment. By collecting and analyzing plant single-cell biological datasets, a better understanding of cellular interactions can be achieved.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Pharmacology & Pharmacy
Domenico Ribatti, Giovanni Ligresti, Roberto F. Nicosia
Summary: The blood microvascular endothelium is composed of various cells with different morphologies and transcriptional signatures in different tissues and organs. Endothelial cells not only provide an anti-thrombogenic surface for blood flow, but also perform multiple regulatory tasks including organogenesis, metabolism, angiogenesis, inflammation, repair, and organ homeostasis. In order to communicate and carry out their functions, endothelial cells secrete angiocrine factors, while nonendothelial cells regulate endothelial growth, differentiation, and survival through paracrine mechanisms. Recent advancements in molecular biology, animal genetics, single cell transcriptomics, and microscopic imaging have greatly expanded our knowledge of organotypic vasculatures, with the kidney vasculature being a primary focus. This paper reviews the morphology, function, and development of the kidney vasculature, emphasizing on endothelial heterogeneity, and provides examples of factors critical for kidney development, growth, injury response, and homeostasis derived from both endothelial and nonendothelial cells.
VASCULAR PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jules Duruz, Cyrielle Kaltenrieder, Peter Ladurner, Remy Bruggmann, Pedro Martinez, Simon G. Sprecher
Summary: By utilizing whole-body single-cell transcriptomics on the acoel Isodiametra pulchra, researchers identified ten major cell type categories contributing to main biological functions, as well as a large number of clade-specific marker genes, indicating the emergence of clade-specific common molecular machineries functioning in distinct cell types. These results offer novel insights into the evolution of bilaterian cell types.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Michael W. Dorrity, Cristina M. Alexandre, Morgan O. Hamm, Anna-Lena Vigil, Stanley Fields, Christine Queitsch, Josh T. Cuperus
Summary: The study reports the regulatory landscape of Arabidopsis thaliana roots at single-cell resolution and identifies thousands of differentially accessible sites. It finds that a cell's regulatory landscape and transcriptome independently capture cell type identity, and leveraging this information to integrate data helps characterize developmental progression and cell division. The approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
NATURE COMMUNICATIONS
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Michelle Gee, Eden Hornung, Alison Moss, Lakshmi Kuttippurathu, James S. Schwaber, Babatunde Ogunnaike, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Eden Hornung, Shaina Robbins, Sirisha Achanta, Ankita Srivastava, Alison Moss, James Schwaber, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Suranjana Gupta, Jessica M. Feldman, Adam J. H. Newton, Lakshmi Kuttippurathu, Alison Moss, James S. Schwaber, Rajanikanth Vadigepalli, William W. Lytton
Meeting Abstract
Biochemistry & Molecular Biology
Sirisha Achanta, Eden Hornung, Alison Moss, James Schwaber, Rajanikanth Vadigepalli
Meeting Abstract
Biochemistry & Molecular Biology
Ankita Srivastava, Shaina Robbins, Sirisha Achanta, James S. Schwaber, Rajanikanth Vadigepalli
Article
Engineering, Chemical
Michelle M. Gee, Abraham M. Lenhoff, James S. Schwaber, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Summary: This paper developed a computational model that incorporates the intrinsic cardiac nervous system into the computational model of blood pressure regulation. The central and local contributions to the control of heart rate, ventricular functions, and respiratory sinus arrhythmia were studied. The simulations matched the experimental observations and predicted the relative contributions of sensory and motor neuron pathways to heart rate changes. This closed-loop cardiovascular control model is important for evaluating bioelectronic interventions to treat heart failure and renormalize cardiovascular physiology.
Article
Neurosciences
Anas Mistareehi, Kohlton T. Bendowski, Ariege Bizanti, Jazune Madas, Yuanyuan Zhang, Andrew M. Kwiat, Duyen Nguyen, Nicole Kogut, Jichao Ma, Jin Chen, Zixi (Jack) Cheng
Summary: This study examined the distribution and morphology of Substance-P immunoreactive (SP-IR) axons in different layers of the mouse stomach. It revealed that SP-IR axons densely innervated the muscular, submucosal, and mucosal layers, forming various structures. This data provides important insights into the detailed network of SP-IR axons in the stomach.
AUTONOMIC NEUROSCIENCE-BASIC & CLINICAL
(2023)
Article
Engineering, Chemical
Daniel Cook, Alexandra Manchel, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Summary: Recent experiments on liver homeostatic renewal have found that hepatocyte populations with high replication capacity are primarily responsible for maintaining liver mass. However, the processes controlling liver homeostatic renewal are still unknown. To address this, a mathematical model was developed that describes the interactions of cellular networks underlying liver homeostatic renewal. Simulation results showed that without feedback control, basic homeostatic renewal is not robust and can lead to tissue loss under persistent/repetitive injury. Incorporating putative regulatory interactions in the model improved its robustness, but simulations indicated that repeated injury can still destabilize liver homeostasis over several months, contrasting with the slower decay of liver function observed in epidemiological studies. Further extending the model to include feedback control by liver nonparenchymal cells suggested that achieving robust liver homeostatic renewal requires intrinsic stability in hepatocellular networks combined with feedback control by nonparenchymal cells.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Neurosciences
Ariege Bizanti, Yuanyuan Zhang, Scott W. W. Harden, Jin Chen, Donald B. B. Hoover, David Gozal, Kalyanam Shivkumar, Zixi Jack Cheng
Summary: In this study, the distribution and morphology of sympathetic efferent axons in the heart were characterized using immunohistochemical labeling. Dense terminal networks of sympathetic nerves were found in the atria and ventricles, with close contact to cardiomyocytes, vessels, and adipocytes. This research provides a foundation for future quantification of the cardiac sympathetic innervation in different pathological conditions.
JOURNAL OF COMPARATIVE NEUROLOGY
(2023)
Article
Neurosciences
Jichao Ma, Anas Mistareehi, Jazune Madas, Andrew M. M. Kwiat, Kohlton Bendowski, Duyen Nguyen, Jin Chen, De-Pei Li, John B. Furness, Terry L. Powley, Zixi (Jack) Cheng
Summary: The study reveals the distribution and morphology of SP-IR axons and terminals in the whole stomach, providing an anatomical foundation for functional mapping of SP-IR axon innervation in the stomach and its pathological remodeling in gastrointestinal diseases.
JOURNAL OF COMPARATIVE NEUROLOGY
(2023)
Review
Physiology
Michelle M. Gee, Eden Hornung, Suranjana Gupta, Adam J. H. Newton, Zixi Jack Cheng, WilliamW. Lytton, Abraham M. Lenhoff, James S. Schwaber, Rajanikanth Vadigepalli
Summary: The vagus nerve plays an important role in brain-heart signaling and is crucial for cardiovascular health. Studying the neural regulation of cardiac function has been challenging due to the complexity of the data and its distribution across different systems. Computational modeling based on molecular-scale and physiological data can provide insights into the fast and slow regulation of the vagus nerve in the cardiovascular system. These insights can guide future experimental research on neuromodulation and cardiovascular health.
EXPERIMENTAL PHYSIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yuanyuan Zhang, Ariege Bizanti, Scott W. Harden, Jin Chen, Kohlton Bendowski, Donald B. Hoover, David Gozal, Kalyanam Shivkumar, Maci Heal, Susan Tappan, Zixi Jack Cheng
Summary: This study provides a detailed neuroanatomical map of the sympathetic innervation of the heart in mice, showing that the sympathetic nerves enter the atria through multiple pathways and have different densities in different regions. The study also finds that sympathetic nerves innervate blood vessels and adipocytes.
SCIENTIFIC REPORTS
(2023)
Article
Neurosciences
Jichao Ma, Duyen Nguyen, Jazune Madas, Ariege Bizanti, Anas Mistareehi, Andrew M. Kwiat, Jin Chen, Mabelle Lin, Richard Christie, Peter Hunter, Maci Heal, Shane Baldwin, Susan Tappan, John B. Furness, Terry L. Powley, Zixi (Jack) Cheng
Summary: By using immunohistochemistry labeling and imaging techniques, the distribution and morphology of CGRP-IR axon innervation in the whole mouse stomach muscular layers were characterized. CGRP-IR axons were found to densely interact with blood vessels and run parallel with the longitudinal and circular muscles, forming contacts with myenteric ganglion neurons. This study provides important information for understanding the role of CGRP-IR axons in gastric function regulation.
JOURNAL OF COMPARATIVE NEUROLOGY
(2023)
Article
Physiology
Jacqueline M. Chivers, Shannon A. Whiles, Conor B. Miles, Brianna E. Biederman, Megan F. Ellison, Connor W. Lovingood, Marie H. Wright, Donald B. Hoover, Muhammad A. Raafey, George A. Youngberg, Manjeri A. Venkatachalam, Nadezhda N. Zheleznova, Chun Yang, Pengyuan Liu, Alison J. Kriegel, Allen W. Cowley, Paul M. O'Connor, Maria M. Picken, Aaron J. Polichnowski
Summary: Chronic kidney disease (CKD) has a strong genetic component, and rats are commonly used to study the genetic determinants of CKD. In this study, it was found that SS/JrHsdMcwi rats develop age-related CKD, while SS.BN1 rats do not. Additionally, structural abnormalities and activation of inflammatory pathways were observed in the renal tubules of SS/JrHsdMcwi rats before the development of CKD, providing new insights into the pathogenesis of kidney disease in this model.
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2023)