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Benjamin N. Ostendorf, Mira A. Patel, Jana Bilanovic, H.-Heinrich Hoffmann, Sebastian E. Carrasco, Charles M. Rice, and Sohail. F. Tavazoie
Lung tissue from knock-in mice expressing common variants of human APOE (APOE2, APOE3 and APO4) showed differences in gene expression that causally impacted the outcome of COVID-19 infection. APOE2 and APOE4 knock-in mice had increased disease progression and mortality relative to APOE3 knock-in mice. Human data from the UK Biobank supports the finding that genetic variation in APOE partially explains the variation in severity of COVID-19 disease outcomes.
Pin Shie Quah, Bang M. Tran, Vincent D.A. Corbin, Jessie J.-Y. Chang, Chinn Yi Wong, Andrés Diaz-Méndez, Carol A. Hartley, Weiguang Zeng, Eric Hanssen, Zlatan Trifunovic, Patrick C. Reading, David C. Jackson, Elizabeth Vincan, Lachlan J.M. Coin, Georgia Deliyannis
To enhance research into BHV-1, authors developed a 3-D matrix system for bovine tracheal organoid culture. scRNA-seq data showed vulnerability to BHV-1 virus and robust immune response to stimulation by Pam2Cys, demonstrating the utility of the 3-D model system in studying viral infections.
Maneesh Dave, Atul Dev, Rodrigo A Somoza, Nan Zhao, Satish Viswanath, Pooja Rani Mina, Prathyush Chirra, Verena Carola Obmann, Ganapati H Mahabeleshwar, Paola Menghini, Blythe Durbin Johnson, Jan A Nolta, Christopher Soto, Abdullah Osme, Lam T Khuat, William Murphy, Arnold I Caplan, Fabio Cominelli
Human Mesenchymal Stem Cells (hMSC) modulate T cells and macrophages when administered into a Chron’s disease model. scRNA-seq showed long-term anti-inflammatory macrophage reprogramming, providing evidence of prolonged therapeutic effects of hMSC.
Yuan Guan, Zhuoqing Fang, Angelina Hu, Sarah Roberts, Patrik K. Johansson, Sarah C. Heilshorn, Annika Enejder, Gary Peltz
In a hepatic organoid model, scRNA-seq identified the liver fibrosis-inducing ligand. TGFβ1 exposure transformed mesenchymal cells into myofibroblast-like cells, upregulating proteases, anti-proteases, and extracellular matrix genes, thereby promoting liver fibrosis development.
Mikaela Koutrouli, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen
Introduces FAVA, a novel analysis method to handle large-scale scRNA-seq and proteomic data, predict high-confidence functional associations, and provide good coverage for understudied proteins. Performance was evaluated using freely available proteomic and PBMC scRNA-Seq datasets.
Anthony Flamier, Punam Bisht, Alexsia Richards, Danielle Tomasello, Rudolf Jaenisch
In COVID-19-infected human sensory neurons, scRNA-seq was critical in revealing that sensory neurons can be infected by SARS-CoV-2 but are unable to produce new viruses. This may have implications for understanding the infection’s long-term impact on the peripheral nervous system.
Joseph Fogerty, Ping Song, Patrick Boyd, Sarah E. Grabinski, Thanh Hoang, Adrian Reich, Lauren T. Cianciolo, Seth Blackshaw, Jeff S. Mumm, David R. Hyde, and Brian D. Perkins
In a zebrafish model of progressive retinal degeneration, inflammation alone was not sufficient to trigger Müller glia reprogramming into multipotent retinal progenitors. Single cell RNA-seq showed that notch signaling remained active with progressive degeneration in contrast to what has been seen previously with acute injury.
Vuong Tran, Efthymia Papalexi, Sarah Schroeder, Grace Kim, Ajay Sapre, Joey Pangallo, Alex Sova, Peter Matulich, Lauren Kenyon, Zeynep Sayar, Ryan Koehler, Daniel Diaz, Archita Gadkari, Kamy Howitz, Maria Nigos, Charles M. Roco, and Alexander B. Rosenberg
A detailed performance evaluation of Evercode™ WT v2 that highlights improved gene and transcript detection, robustness across samples, and no bias in gene expression data. Multiple sample types were assessed, including cells and nuclei.
Samuel Morabito, Fairlie Reese, Negin Rahimzadeh, Emily Miyoshi, and Vivek Swarup
Athanasios Dimitriadis, Fuquan Zhang, Thomas Murphy, Thomas Trainer, Zane Jaunmuktane, Christian Schmidt, Tamsin Nazari, Jacqueline Linehan, Sebastian Brandner, John Collinge, Simon Mead, and Emmanuelle Viré
Transcriptomic studies on prion-infected mouse brains revealed gene signatures similar to human prion disease, shedding light on underlying molecular mechanisms. By introducing a protein denaturation step, samples could be transferred from a BSL-3 to a BSL-2 lab for library preparation and sequencing.
Merrick Pierson Smela, Christian Kramme, Patrick Fortuna, Jessica Adams, Edward Dong, Mutsumi Kobayashi, Garyk Brixi, Emma Tysinger, Richie. E. Kohman, Toshi Shioda, Pranam Chatterjee, and George M. Church
Two transcription factors required for developing ovarian granulosa cells – previously lacking components of human ovary organoids – were identified. Human iPSCs were induced to differentiate into human ovary organoids, whose identities were confirmed based on differential gene expression.
