Publications | UCSF CoLabs

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells

Authors: Adamik Juraj, Munson Paul V., Hartmann Felix J., Combes Alexis J., Pierre Philippe, Krummel Matthew F., Bendall Sean C., Argüello Rafael J., Butterfield Lisa H.

September 2022

Tumor-Associated Macrophage Heterogeneity is Driven by Tissue Territories in Breast Cancer

Authors: Laviron Marie, Petit Maxime, Weber-Delacroix Eléonore, Combes Alexis J., Arkal Arjun Rao, Barthélémy Sandrine, Courau Tristan, Hume David A., Combadière Christophe, Krummel Matthew F., Boissonnas Alexandre

September 2022

T Cells Use Distinct Topographical and Membrane Receptor Scanning Strategies that Individually Coalesce During Receptor Recognition

Authors: Cai En, Beppler Casey, Eichorst John, Marchuk Kyle, Eastman Scott W., Krummel Matthew F.

August 2022

A Functional Circuit Formed by the Autonomic Nerves and Myofibroblasts Controls Mammalian Alveolar Formation for Gas Exchange

Authors: Zhang Kuan, Yao Erica, Wang Shao-An, Chuang Ethan, Wong Julia, Minichiello Liliana, Schroeder Andrew, Eckalbar Walter, Wolters Paul J., Chuang Pao-Tien

July 2022

Spatiotemporal Co-Dependency Between Macrophages and Exhausted CD8+ T Cells in Cancer

Authors: Kersten Kelly, Hu Kenneth H., Combes Alexis J., Samad Bushra, Harwin Tory, Ray Arja, Rao Arjun Arkal, Cai En, Marchuk Kyle, Artichoker Jordan, Courau Tristan, Shi Quanming, Belk Julia, Satpathy Ansuman T., Krummel Matthew F.

June 2022

Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis

Authors: Elvira Mennillo, Yang Joon Kim, Iulia Rusu, Gyehyun Lee, Leah C Dorman, Faviola Bernard-Vazquez, Jared L Bain, Ravi Patel, Christopher Andersen, Arjun Rao, Stanley Tamaki, Jessica Tsui, Alan Shen, Mohammad Naser, Walter Eckalbar,&... See more

June 2022

Deep Immunophenotyping Reveals Endometriosis is Marked by Dysregulation of the Mononuclear Phagocytic System in Endometrium and Peripheral Blood

Authors: Vallvé-Juanico Júlia, George Ashley F, Sen Sushmita, Thomas Reuben, Shin Min-Gyoung, Kushnoor Divyashree, Vásquez Joshua J, Vo Kim Chi, Irwin Juan C, Roan Nadia R, Combes Alexis J, Giudice Linda C. 

April 2022

Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

Authors: Mujal Adriana M, Combes Alexis J, Rao Arjun A, Binnewies Mikhail, Samad Bushra, Tsui Jessica, Boissonnas Alexandre, Pollack Joshua L,  Argüello Rafael J, Meng Maxwell V, Porten Sima P, Ruhland Megan K, Barry Kevin C, Chan Vincent, Krummel Matthew F. 

April 2022

Obesity alters pathology and treatment response in inflammatory disease

Authors: Bapat Sagar P., Whitty Caroline, Mowery Cody T., Liang Yuqiong, Yoo Arum, Jiang Zewen, Peters Michael C., Zhang Ling-juan, Vogel Ian, Zhou Carmen, Nguyen Vinh Q., Li Zhongmei, Chang Christina, Zhu Wandi S., Hastie Annette T., He Helen, Ren Xin, Qiu Wenli, Gayer Sarah G., Liu Chang, Choi Eun Jung, Fa... See more

March 2022

Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types

Authors: Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC and Nolan GP

March 2022

A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates

Authors: Bjornson-Hooper Zachary B., Fragiadakis Gabriela K., Spitzer Matthew H., Chen Han, Madhireddy Deepthi, Hu Kevin, Lundsten Kelly, McIlwain David R., Nolan Garry P.

March 2022

Bile Acid–Sensitive Tuft Cells Regulate Biliary Neutrophil Influx

Authors: O’Leary Claire E., Sbierski-Kind Julia, Kotas Maya E., Wagner Johanna C., Liang Hong-Erh, Schroeder Andrew W., de Tenorio Jeshua C., von Moltke Jakob, Ricardo-Gonzalez Roberto R., Eckalbar Walter L., Molofsky Ari B., Schneider Christoph, Locksley Richard M.

March 2022

CRISPR activation and interference screens decode stimulation responses in primary human T cells

Authors: Schmidt Ralf, Steinhart Zachary, Layeghi Madeline, Freimer Jacob W., Bueno Raymund, Nguyen Vinh Q., Blaeschke Franziska, Ye Chun Jimmie, Marson Alexander

February 2022

Discovering dominant tumor immune archetypes in a pan-cancer census

Authors: Combes Alexis J., Samad Bushra, Tsui Jessica, Chew Nayvin W., Yan Peter, Reeder Gabriella C., Kushnoor Divyashree, Shen Alan, Davidson Brittany, Barczak Andrea J., Adkisson Michael, Edwards Austin, Naser Mohammad, Barry Kevin C., Courau Tristan, Hammoudi Taymour, Argüello Rafael J., Rao Arjun Arkal,... See more

January 2022

IL-6 and TNFα Drive Extensive Proliferation of Human Tregs Without Compromising Their Lineage Stability or Function

Authors: Skartsis Nikolaos, Peng Yani, Ferreira Leonardo M. R., Nguyen Vinh, Ronin Emilie, Muller Yannick D., Vincenti Flavio, Tang Qizhi

December 2021

The intersection of COVID-19 and autoimmunity

Authors: Knight Jason S., Caricchio Roberto, Casanova Jean-Laurent, Combes Alexis J., Diamond Betty, Fox Sharon E., Hanauer David A., James Judith A., Kanthi Yogendra, Ladd Virginia, Mehta Puja, Ring Aaron M., Sanz Ignacio, Selmi Carlo, Tracy Russell P., Utz Paul J., Wagner Catriona A., Wang Julia Y., McCune... See more

December 2021

Genetic and Immunologic Features of Recurrent Stage I Lung Adenocarcinoma

Authors: Kratz Johannes R., Li Jack Z., Tsui Jessica, Lee Jen C., Ding Vivianne W., Rao Arjun A., Mann Michael J., Chan Vincent, Combes Alexis J., Krummel Matthew F., Jablons David M.

December 2021

Polyclonal Regulatory T Cell Manufacturing Under cGMP: A Decade of Experience

Authors: Balcerek Joanna, Shy Brian R., Putnam Amy L., Masiello Lisa M., Lares Angela, Dekovic Florinna, Acevedo Luis, Lee Michael R., Nguyen Vinh, Liu Weihong, Paruthiyil Sreenivasan, Xu Jingying, Leinbach Ashley S., Bluestone Jeffrey A., Tang Qizhi, Esensten Jonathan H.

November 2021

Molecular Programs of Fibrotic Change in Aging Human Lung

Authors: Lee Seoyeon, Islam Mohammad Naimul, Boostanpour Kaveh, Aran Dvir, Jin Guangchun, Christenson Stephanie, Matthay Michael A., Eckalbar Walter L., DePianto Daryle J., Arron Joseph R., Magee Liam, Bhattacharya Sunita, Matsumoto Rei, Kubota Masaru, Farber Donna L., Bhattacharya Jahar, Wolters Paul J., Bh... See more

November 2021

Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer’s Disease Across Two Brain Regions

Authors: Belonwu Stella A., Li Yaqiao, Bunis Daniel, Rao Arjun Arkal, Solsberg Caroline Warly, Tang Alice, Fragiadakis Gabriela K., Dubal Dena B., Oskotsky Tomiko, Sirota Marina

October 2021