Publications and Posters

Spotlight

Common human genetic variants of APOE impact murine COVID-19 mortality

Benjamin N. Ostendorf, Mira A. Patel, Jana Bilanovic, H.-Heinrich Hoffmann, Sebastian E. Carrasco, Charles M. Rice, and Sohail. F. Tavazoie
WT Mouse Lung
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.

Publications

C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model

Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea Tenner
WT Mouse Brain
Inhibition of the C5aR1 receptor with PMX205 reduces plaque load and gliosis while improving short-term memory in Alzheimer's Disease (AD) mouse models. Using scRNA-Seq and snRNA-Seq, the authors found that PMX205 treatment enhanced cell growth and repair and decreased the inflammatory gene expression in microglia despite little alteration of the protein levels in reactive cells. The results highlight the attractiveness of a C5aR1 inhibition-based strategy.

Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer’s Disease

Emily Miyoshi, Samuel Morabito, Caden M. Henningfield, Negin Rahimzadeh, Sepideh Kiani Shabestari, Sudeshna Das, Neethu Michael, Fairlie Reese, Zechuan Shi, Zhenkun Cao, Vanessa Scarfone, Miguel A. Arreola, Jackie Lu, Sierra Wright, Justine Silva, Kelsey Leavy, Ira T. Lott, Eric Doran, William H. Yong, Saba Shahin, Mari Perez-Rosendahl, Elizabeth Head, Kim N. Green, Vivek Swarup
WT Mouse Brain Nuclei
Researchers used snRNA-Seq to compare gene expression in early and late-stage Alzheimer's Disease (AD) and AD in Down Syndrome (DS), bridging the gap between genetic mouse models and sporadic AD. The study revealed a complex interaction between the extra chr21 and the genome, identified shared and unique pathways between late-stage AD and AD in DS, and discovered sex-related expression differences in AD in DS, enhancing our understanding of factors influencing AD progression.

Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture

Madison R Glass, Elisa A. Waxman, Satoshi Yamashita, Michael Lafferty, Alvaro Beltran, Tala Farah, Niyanta K Patel, Nana Matoba, Sara Ahmed, Mary Srivastava, Emma Drake, Liam T. Davis, Meghana Yeturi, Kexin Sun, Michael I. Love, Kazue Hashimoto-Torii, Deborah L. French, Jason L. Stein
WT Organoids
In a multisite study to test the reproducibility of human cortical organoids (hCO) differentiation protocols, scRNA-Seq was used to characterize cross-site similarities and differences. The results showed reproducible key features, such as cell type proportions and structure, including neuroepithelial budding and cortical wall-like organization, as well as some differences that limit the utility of hCO models. Understanding how stem cell states influence early hCO cell types could lead to more reliable hCO protocols for studying neurodevelopmental disorders.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology

Jared A Tangeman, Sofia M Rebull, Erika Grajales-Esquivel, Jacob M Weaver, Stacy Bendezu-Sayas, Michael L Robinson, Salil A Lachke, Katia Del Rio-Tsonis
WT Chicken Embryo
Using snRNA-Seq on chicken embryos, researchers profiled gene expression and chromatin accessibility associated with the chicken ocular lens development. They found three distinct populations representing major cell states (epithelial, intermediate, and fiber cell) and established a continuous trajectory from epithelial to fiber cell differentiation. The study confirmed known pathways and cataract-linked genes while uncovering new factors involved in lens development, homeostasis, and pathology.

A Risk-reward Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq

Daniel V. Brown, Casey J.A. Anttila, Ling Ling, Patrick Grave, Tracey M. Baldwin, Ryan Munnings, Anthony J. Farchione, Vanessa L. Bryant, Amelia Dunstone, Christine Biben, Samir Taoudi, Tom S. Weber, Shalin H. Naik, Anthony Hadla, Holly E. Barker, Cassandra J. Vandenberg, Genevieve Dall, Clare L. Scott, Zachery Moore, James R. Whittle, Saskia Freytag, Sarah A. Best, Anthony T. Papenfuss, Sam W.Z. Olechnowicz, Sarah E. MacRaild, Stephen Wilcox, Peter F. Hickey, Daniela Amann-Zalcenstein, Rory Bowden
WT Mini Ovarian PDX
The authors compared various scRNA-Seq reagents. Parse WT v2 and 10x Flex were tested on fixed tumor nuclei. 10x Flex failed due to clogging. Parse data had more reads, genes, and fewer doublets than 10x fresh nuclei data. 10X data had high mitochondrial and ribosomal transcripts, but gene expression was concordant with Parse data. Parse WT v2 captured more biological variation and outperformed other assays.

Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing

Yi Xie, Huimei Chen, Vasuki Ranjani Chellamuthu, Ahmad bin Mohamed Lajam, Salvatore Albani, Andrea Hsiu Ling Low, Enrico Petretto, Jacques Behmoaras
WT PBMCs
Parse and 10X were compared using scRNA-seq on PBMC from 2 healthy donors. Parse demonstrated better data quality with lower multiplets rates but had lower cell recovery. Parse detected 1.2-fold more genes, had better clustering performance, and greater power in distinguishing cell types with specific gene signatures. Parse also excelled in detecting longer transcripts and rare cell types.

Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury

Gianluca T. DiGiovanni, Wei Han, Taylor Sherrill, Chase J. Taylor, David S. Nichols, Natalie M. Geis, Ujjal K. Singha, Carla L. Calvi, A. Scott McCall, Molly M. Dixon, Yang Lui, Ji-Hoon Jang, Sergey S. Gutor, Vasiliy V. Polosukhin, Timothy S. Blackwell, Jonathan A. Kropski, Jason J. Gokey
WT Mega Lung
Alveolar epithelium regeneration and repair following injury is not completely understood. Evidence suggests that the Hippo-YAP/TAZ pathway is vital for AT2 to AT1 development and dysregulation of this pathway is a key feature of idiopathic pulmonary fibrosis. In a mouse model, AT2 cells lacking YAP/TAZ were injured with bleomycin. scRNA-Seq showed upregulated fibroblast activation markers, increased fibrillar collagen expression, and prolonged inflammation 28 days post-injury, ultimately resulting in lung fibrosis.

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

Carina Shiau, Jingyi Cao, Mark T Gregory, Dennis Gong, Xunqin Yin, Jae-Won Cho, Peter L Wang, Jennifer Su, Steven Wang, Jason W Reeves, Tae Kyung Kim, Youngmi Kim, Jimmy A Guo, Nicole A Lester, Nathan Schurman, Jamie L Barth, Ralph Weissleder, Tyler Jacks, Motaz Qadan, Theodore S Hong, Jennifer Y Wo, Hannah Roberts, Joseph M Beechem, Carlos Fernandez-del Castillo, Mari Mino-Kenudson, David T Ting, Martin Hemberg, William L Hwang
WT Mini Mouse Nuclei
Spatial molecular imaging is combined with single-cell sequencing to characterize the tumor microenvironment of human pancreatic cancer. These multi-modal data lead to the generation of the SCOTIA model to better explain the emergence of treatment resistance.

Preventing recurrence in Sonic Hedgehog Subgroup Medulloblastoma using OLIG2 inhibitor CT-179

Yuchen Li, Chaemin Lim, Taylor Dismuke, Daniel Malawsky, Sho Oasa, Zara Bruce, Carolin Offenhäuser, Ulrich Baumgartner, Rochele D'Souza, Stacey Edwards, Juliet French, Lucy Ock, Sneha Nair, Haran Sivakumaran, Lachlan Harris, Andrey Tikunov, Duhyeong Hwang, Coral Del Mar Alicea Pauneto, Mellissa Maybury, Timothy Hassall, Brandon Wainwright, Santosh Kesari, Gregory Stein, Michael Piper, Terrance Johns, Marina Sokolsky-Papkov, Lars Terenius, Vladana Vukojevic, Bryan Day, Timothy Gershon
WT MB Organoids
Using an organoid and mouse model of SHH medulloblastoma (MB), scRNA-seq data shows tumor cells expressing the reoccurrence driver OLIG2, are disrupted by CT-179 with minimal off-target toxicity. Post-treatment, tumors up-regulate CDK4 mediating CT-179 resistance. However, combined therapy with a CDK4/6 inhibitor delayed cancer recurrence compared to either single agent.

Generating human neural diversity with a multiplexed morphogen screen in organoids

Neal D. Amin, Kevin W. Kelley, Jin Hao, Yuki Miura, Genta Narazaki, Tommy Li, Patrick McQueen, Shravanti Kulkarni, Sergey Pavlov, Sergiu P. Paşca
WT Human Organoids
Using scRNA-seq, researchers developed a scalable screening platform to establish a morphogen atlas of human neural cell fate. By applying 14 morphogen modulators to neural organoids, they identified distinct cellular and structural characteristics of brain regions and critical timing windows.

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

Yoshiaki Yasumizu, Daiki Takeuchi, Reo Morimoto, Yusuke Takeshima, Tatsusada Okuno, Makoto Kinoshita, Takayoshi Morita, Yasuhiro Kato, Min Wang, Daisuke Motooka, Daisuke Okuzaki, Yamami Nakamura, Norihisa Mikami, Masaya Arai, Xuan Zhang, Atsushi Kumanogoh, Hideki Mochizuki, Naganari Ohkura, Shimon Sakaguchi
WT Mega Human PBMCs
Using scRNA-seq data of CD4+ T cells from healthy individuals and autoimmune disease patients, clustering was performed through non-negative matrix factorization (NMF). Analysis of publicly available scRNA-seq datasets identified 12 transcriptional gene programs that characterized each autoimmune disease and predicted clinical status accurately.

Development of Matrix-Embedded Bovine Tracheal Organoids to Study the Innate Immune Response against Bovine Respiratory Disease

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
WT Mini Bovine Tracheal Organoids
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.

Mesenchymal stem cells ameliorate inflammation in an experimental model of Crohn's disease via the mesentery

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
WT Human MSCs
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.

Characterization of Pro-Fibrotic Signaling Pathways using Human Hepatic Organoids

Yuan Guan, Zhuoqing Fang, Angelina Hu, Sarah Roberts, Patrik K. Johansson, Sarah C. Heilshorn, Annika Enejder, Gary Peltz
WT Mini Human Liver
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.

High-quality functional association networks inferred from scRNA-seq and proteomics data

Mikaela Koutrouli, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen
WT PBMCs
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.

Human iPS cell-derived sensory neurons can be infected by SARS-CoV-2 strain WA1/2020 as well as variants delta and omicron

Anthony Flamier, Punam Bisht, Alexsia Richards, Danielle Tomasello, Rudolf Jaenisch
WT Mini Human iPS
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.

Notch Inhibition Promotes Regeneration and Immunosuppression Supports Cone Survival in a Zebrafish Model of Inherited Retinal Dystrophy

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
WT Zebrafish Retina
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.

High sensitivity single cell RNA sequencing with split pool barcoding

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
WT Mouse Brain Mouse Liver Human PBMCs Cell Lines
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.

High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

Samuel Morabito, Fairlie Reese, Negin Rahimzadeh, Emily Miyoshi, and Vivek Swarup
WT Mega Human PBMCs
Introduces hdWGCNA, an analysis framework supporting system-level analysis of data from complex biological systems. Data was integrated from the 1M Evercode WT Mega v1 Type-1 Diabetes dataset from human PBMCs to demonstrate utility and scalability.

Single-nuclei transcriptomics of mammalian prion diseases identifies dynamic gene signatures shared between species

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
WT Mouse Brain
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.

Directed Differentiation of Human iPSCs to Functional Ovarian Granulosa-Like Cells via Transcription Factor Overexpression

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
WT Mega Human iPSCs
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.

Absence of microglia promotes diverse pathologies and early lethality in Alzheimer’s disease mice

Sepideh Kiani Shabestari, Samuel Morabito, Emma Pascal Danhash, Amanda McQuade, Jessica Ramirez Sanchez, Emily Miyoshi, Jean Paul Chadarevian, Christel Claes, Morgan Alexandra Coburn, Jonathan Hasselmann, Jorge Hidalgo, Kayla Nhi Tran, Alessandra C. Martini, Winston Chang Rothermich, Jesse Pascual, Elizabeth Head, David A. Hume, Clare Pridans, Hayk Davtyan, Vivek Swarup, and Mathew Blurton-Jones
WT Mouse Brain
Microglia are brain cells with a role in Alzheimer’s Disease development and progression. A knock-out mouse model revealed a role for microglia in protecting brains by removing calcium deposits.

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara J. Wold, and Ali Mortazavi
WT Cell Lines
Full length transcript isoforms were identified using long-read sequencing on the PacBio platform with a protocol modification described as LR-Split-Seq. Applying this approach in mouse muscle cell lines, previously known and novel alternatively spliced transcript isoforms were detected.

Posters