Publications | UCSF CoLabs

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants

Authors: Hysenaj Lisiena, Little Samantha, Kulhanek Kayla, Magnen Melia, Bahl Kriti, Gbenedio Oghenekevwe M., Prinz Morgan, Rodriguez Lauren, Andersen Christopher, Rao Arjun Arkal, Shen Alan, Lone Jean-Christophe, Lupin-Jimenez Leonard C., Bonser Luke R., Serwas Nina K., Mick Eran, Khalid Mir M., Taha Taha Y... See more

Journal:

Stem Cell Reports

February 2023

Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet

Authors: Wastyk Hannah C., Perelman Dalia, Topf Madeline, Fragiadakis Gabriela K., Robinson Jennifer L., Sonnenburg Justin L., Gardner Christopher D., Sonnenburg Erica D.

Journal:

Gut Microbes

January 2023

Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma

Authors: Koh Kyung Duk, Bonser Luke R., Eckalbar Walter L., Yizhar-Barnea Ofer, Shen Jiangshan, Zeng Xiaoning, Hargett Kirsten L., Sun Dingyuan I., Zlock Lorna T., Finkbeiner Walter E., Ahituv Nadav, Erle David J.

Journal:

Cell Genomics

December 2022

Selective decrease of donor-reactive T after liver transplantation limits T therapy for promoting allograft tolerance in humans

Authors: Tang Qizhi, Leung Joey, Peng Yani, Sanchez-Fueyo Alberto, Lozano Juan-Jose, Lam Alice, Lee Karim, Greenland John R., Hellerstein Marc, Fitch Mark, Li Kelvin W., Esensten Jonathan H., Putnam Amy L., Lares Angela, Nguyen Vinh, Liu Weihong, Bridges Nancy D., Odim Jonah, Demetris Anthony J., Levitsky Jo... See more

Journal:

Science Translational Medicine

November 2022

Archetypes of checkpoint-responsive immunity

Authors: Im Kwok, Combes Alexis J., Spitzer Matthew H., Satpathy Ansuman T., Krummel Matthew F.

Journal:

Trends in Immunology

October 2022

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.

Journal:

Nature Communications

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

Journal:

Cell Reports

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.

Journal:

Proceedings of the National Academy of Sciences

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

Journal:

Developmental Cell

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.

Journal:

Cancer Cell

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. 

Journal:

BMC Medicine

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. 

Journal:

Cancer Immunology Research

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

Journal:

Nature

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

Journal:

Frontiers in Immunology

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.

Journal:

Frontiers in Immunology

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.

Journal:

Science Immunology

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

Journal:

Science

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

Journal:

Cell

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

Journal:

Frontiers in Immunology

December 2021