Publications | UCSF CoLabs

Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19

Authors: Maguire Cole, Chen Jing, Rouphael Nadine, Pickering Harry, Phan Hoang Van, Glascock Abigail, Chu Victoria, Dandekar Ravi, Corry David, Kheradmand Farrah, Baden Lindsey R., Selaky Rafick, McComsey Grace A., Haddad Elias K., Cairns Charles B., Pulendran Bali, Sesma Ana Fernandez-, Simon Viviana, Metca... See more

November 2024

Phosphatidylserine phospholipase A1 enables GPR34-dependent immune cell accumulation in the peritoneal cavity

Authors: Tam Hanson, Xu Ying, An Jinping, Schöneberg Torsten, Schulz Angela, Muppidi Jagan R., Cyster Jason G.

Journal:

Journal of Experimental Medicine

November 2024

Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia

Authors: Spottiswoode Natasha, Tsitsiklis Alexandra, Chu Victoria T., Phan Hoang Van, DeVoe Catherine, Love Christina, Ghale Rajani, Bloomstein Joshua, Zha Beth Shoshana, Maguire Cole P., Glascock Abigail, Sarma Aartik, Mourani Peter M., Kalantar Katrina L., Detweiler Angela, Neff Norma, Haller Sidney C., Ca... See more

Journal:

Nature Communications

October 2024

Chromatin remodelling drives immune cell–fibroblast communication in heart failure

Authors: Alexanian Michael, Padmanabhan Arun, Nishino Tomohiro, Travers Joshua G., Ye Lin, Pelonero Angelo, Lee Clara Youngna, Sadagopan Nandhini, Huang Yu, Auclair Kirsten, Zhu Ada, An Yuqian, Ekstrand Christina A., Martinez Cassandra, Teran Barbara Gonzalez, Flanigan Will R., Kim Charis Kee-Seon, Lumbao-Co... See more

Journal:

Nature

October 2024

A positive ReceptivaDx result for BCL6 does not correlate with abnormal ERA results or decreased expression of receptivity-associated markers: two sides of the endometrial receptivity coin in fertility evaluation and treatment

Authors: Huang David, Flynn Emily, Almonte-Loya Ana, Davidson Brittany, Chan Meagan, Casillas Amber, Irwin Juan C., Fragiadakis Gabriela K., Cakmak Hakan, Combes Alexis J., Cedars Marcelle I., Sirota Marina, Giudice Linda C.

Journal:

F&S Science

October 2024

Proinflammatory immune cells disrupt angiogenesis and promote germinal matrix hemorrhage in prenatal human brain

Authors: Chen Jiapei, Crouch Elizabeth E., Zawadzki Miriam E., Jacobs Kyle A., Mayo Lakyn N., Choi Jennifer Ja-Yoon, Lin Pin-Yeh, Shaikh Saba, Tsui Jessica, Gonzalez-Granero Susana, Waller Shamari, Kelekar Avani, Kang Gugene, Valenzuela Edward J., Birrueta Janeth Ochoa, Diafos Loukas N., Wedderburn-Pugh Kayl... See more

Journal:

Nature Neuroscience

September 2024

An adaptive Epithelial-Mesenchymal Transition Program Enables Basal Epithelial Cells to Bypass Stress-Induced Stasis and Contributes to Metaplastic Breast Cancer Progenitor State

Authors: Caruso Joseph A., Tlsty Thea D.

September 2024

Single-cell RNA-seq analysis reveals cell subsets and gene signatures associated with Rheumatoid Arthritis Disease Activity

Authors: Binvignat Marie, Miao Brenda Y., Wibrand Camilla, Yang Monica M., Rychkov Dmitry, Flynn Emily, Nititham Joanne, Tamaki Whitney, Khan Umair, Carvidi Alexander, Krueger Melissa, Niemi Erene C., Sun Yang, Fragiadakis Gabriela K., Sellam Jérémie, Mariotti-Ferrandiz Encarnita, Klatzmann David, Gross Andr... See more

Journal:

JCI Insight

July 2024

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19

Authors: Neyton Lucile P. A., Patel Ravi K., Sarma Aartik, Ansel K. Mark, Christenson Stephanie, Adkisson Michael, Eckalbar Walter, Maliskova Lenka, Schroeder Andrew, Bueno Raymund, Gordon Gracie, Hartoularos George, Kushnoor Divya, Lee David, McCarthy Elizabeth, Ogorodnikov Anton, Spitzer Matthew, Hiam Kami... See more

Journal:

Nature Communications

June 2024

Defective interferon signaling in the circulating monocytes of type 2 diabetic mice

Authors: Omodaka Shunsuke, Kato Yuya, Sato Yoshimichi, Falcone-Juengert Jaime, Zhang Hongxia, Kanoke Atsushi, Eckalbar Walter L., Endo Hidenori, Hsieh Christine L., Aran Dvir, Liu Jialing

June 2024

Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment

Authors: Tharp Kevin M., Kersten Kelly, Maller Ori, Timblin Greg A., Stashko Connor, Canale Fernando P., Menjivar Rosa E., Hayward Mary-Kate, Berestjuk Ilona, ten Hoeve Johanna, Samad Bushra, Ironside Alastrair J., di Magliano Marina Pasca, Muir Alexander, Geiger Roger, Combes Alexis J., Weaver Valerie M.

Journal:

Nature Cancer

June 2024

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells

Authors: Mowery Cody T., Freimer Jacob W., Chen Zeyu, Casaní-Galdón Salvador, Umhoefer Jennifer M., Arce Maya M., Gjoni Ketrin, Daniel Bence, Sandor Katalin, Gowen Benjamin G., Nguyen Vinh, Simeonov Dimitre R., Garrido Christian M., Curie Gemma L., Schmidt Ralf, Steinhart Zachary, Satpathy Ansuman T., Pollar... See more

Journal:

Nature Genetics

May 2024

Regulatory T cell-derived enkephalin imparts pregnancy-induced analgesia

Authors: Midavaine Élora, Moraes Beatriz C., Benitez Jorge, Rodriguez Sian R., Braz Joao M., Kochhar Nathan P., Eckalbar Walter L., Domingos Ana I., Pintar John E., Basbaum Allan I., Kashem Sakeen W.

May 2024

Coordinated immune dysregulation in juvenile dermatomyositis revealed by single-cell genomics

Authors: Rabadam Gabrielle, Wibrand Camilla, Flynn Emily, Hartoularos George C., Sun Yang, Madubata Chioma, Fragiadakis Gabriela K., Ye Chun Jimmie, Kim Susan, Gartner Zev J., Sirota Marina, Neely Jessica

Journal:

JCI Insight

May 2024

Dysregulation of CD4 Array and CD8 Array resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis

Authors: He Jun Yan, Kim Yang-Joon, Mennillo Elvira, Rusu Iulia, Bain Jared, Rao Arjun A, Andersen Christopher, Law Karen, Yang Hai, Tsui Jessica, Shen Alan, Davidson Brittany, Kushnoor Divyashree, Shi Yimin, Fan Frances, Cheung Alexander, Zhang Li, Fong Lawrence, Combes Alexis J, Pisco Angela O, Kattah Mich... See more

Journal:

Journal for ImmunoTherapy of Cancer

April 2024

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology

Authors: Phan Hoang Van, Tsitsiklis Alexandra, Maguire Cole P., Haddad Elias K., Becker Patrice M., Kim-Schulze Seunghee, Lee Brian, Chen Jing, Hoch Annmarie, Pickering Harry, van Zalm Patrick, Altman Matthew C., Augustine Alison D., Calfee Carolyn S., Bosinger Steve, Cairns Charles B., Eckalbar Walter, Guan... Phan Hoang Van, Tsitsiklis Alexandra, Maguire Cole P., Haddad Elias K., Becker Patrice M., Kim-Schulze Seunghee, Lee Brian, Chen Jing, Hoch Annmarie, Pickering Harry, van Zalm Patrick, Altman Matthew C., Augustine Alison D., Calfee Carolyn S., Bosinger Steve, Cairns Charles B., Eckalbar Walter, Guan Leying, Jayavelu Naresh Doni, Kleinstein Steven H., Krammer Florian, Maecker Holden T., Ozonoff Al, Peters Bjoern, Rouphael Nadine, Montgomery Ruth R., Reed Elaine, Schaenman Joanna, Steen Hanno, Levy Ofer, Diray-Arce Joann, Langelier Charles R., Erle David J., Hendrickson Carolyn M., Kangelaris Kirsten N., Nguyen Viet, Lee Deanna, Chak Suzanna, Ghale Rajani, Gonzalez Ana, Jauregui Alejandra, Leroux Carolyn, Altamirano Luz Torres, Rashid Ahmad Sadeed, Willmore Andrew, Woodruff Prescott G., Krummel Matthew F., Carrillo Sidney, Ward Alyssa, Patel Ravi, Wilson Michael, Dandekar Ravi, Alvarenga Bonny, Rajan Jayant, Schroeder Andrew W., Fragiadakis Gabriela K., Mick Eran, Guerrero Yanedth Sanchez, Love Christina, Maliskova Lenka, Adkisson Michael, Ehrlich Lauren I. R., Melamed Esther, Rousseau Justin F., Hurley Kerin C., Geltman Janelle N., Siles Nadia, Rogers Jacob E., Kutzler Michele A., Bernui Mariana, Cusimano Gina, Connors Jennifer, Woloszczuk Kyra, Joyner David, Edwards Carolyn, Lin Edward, Melnyk Nataliya, Powell Debra L., Kim James N., Goonewardene I. Michael, Simmons Brent, Smith Cecilia M., Martens Mark, Croen Brett, Semenza Nicholas C., Bell Mathew R., Furukawa Sara, McLin Renee, Tegos George P., Rogowski Brandon, Mege Nathan, Ulring Kristen, Holland Steven M., Rosen Lindsey B., Lee Serena, Vaysman Tatyana, Fernandez-Sesma Ana, Simon Viviana, Van Bakel Harm, Gonzalez-Reiche Ana Silvia, Qi Jingjing, Carreño Juan Manuel, Singh Gagandeep, Raskin Ariel, Tcheou Johnstone, Khalil Zain, van de Guchte Adriana, Farrugia Keith, Khan Zenab, Kelly Geoffrey, Srivastava Komal, Eaker Lily, Bermúdez González Maria Carolina, Mulder Lubbertus C. F., Beach Katherine, Fatou Benoit, Smolen Kinga, Viode Arthur, van Haren Simon, Jha Meenakshi, Kho Alvin, Milliren Carly E., Chang Ana C., McEnaney Kerry, Barton Brenda, Lentucci Claudia, Murphy Maimouna, Saluvan Mehmet, Shaheen Tanzia, Liu Shanshan, Syphurs Caitlin, Albert Marisa, Hayati Arash Nemati, Bryant Robert, Abraham James, Salehi-Rad Ramin, Rivera Adreanne M., Sen Subha, Elashoff David, Ward Dawn C., Presnell Scott, Kohr Bernard, Arnett Azlann, Boddapati Arun K., Tharp Greg K., Pellegrini Kathryn L., Johnson Brandi, Panganiban Bernadine, Huerta Christopher, Anderson Evan J., Samaha Hady, Sevransky Jonathan, Bristow Laurel, Beagle Elizabeth, Cowan David, Hamilton Sydney, Hodder Thomas, Esserman Denise, Brito Anderson, Rothman Jessica, Grubaugh Nathan, Ko Albert I., Hafler David A., Shaw Albert C., Gygi Jeremy, Pawar Shrikant, Konstorum Anna, Chen Ernie, Cotsapas Chris, Wang Xiaomei, Xu Leqi, Dela Cruz Charles, Iwasaki Akiko, Mohanty Subhasis, Nelson Allison, Zhao Yujiao, Farhadian Shelli, Asashima Hiromitsu, Pulendran Bali, Nadeau R. Kari C., Rosenberg-Hasson Yael, Leipold Michael, Sigal Natalia, Rogers Angela, Fernandez Andrea, Manohar Monali, Do Evan, Chang Iris, Vita Randi, Westendorf Kerstin, Corry David B., Kheradmand Farrah, Song Li-Zhen, Nelson Ebony, Baden Lindsey R., Mendez Kevin, Lasky-Su Jessica, Tong Alexandra, Rooks Rebecca, Sekaly Rafick-Pierre, Fourati Slim, McComsey Grace A., Harris Paul, Sieg Scott, Ribeiro Susan Pereira, Overton James A., Rahman Adeeb, Hutton Scott R., Michelotti Greg, Wong Kari, Seyfert-Margolis Vicki, Metcalf Jordan P., Agudelo Higuita Nelson I., Sinko Lauren, Booth J. Leland, Messer William B., Hough Catherine L., Siegel Sarah, Sullivan Peter, Lu Zhengchun, Kraft Monica, Bime Chris, Mosier Jarrod, Erickson Heidi, Schunk Ron, Kimura Hiroki, Conway Michelle, Atkinson Mark A., Brakenridge Scott C., Ungaro Ricardo F., Manning Brittany Roth, Oberhaus Jordan, Guirgis Faheem W., Borresen Brittany, Anderson Matthew L. See more

Journal:

Science Translational Medicine

April 2024

Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development

Authors: Shroff Neha Pincha, Xu Pengfei, Kim Sangwoo, Shelton Elijah R., Gross Ben J., Liu Yucen, Gomez Carlos O., Ye Qianlin, Drennon Tingsheng Yu, Hu Jimmy K., Green Jeremy B. A., Campàs Otger, Klein Ophir D.

Journal:

Nature Cell Biology

April 2024

IgG hexamers initiate complement-dependent acute lung injury

Authors: Cleary Simon J., Seo Yurim, Tian Jennifer J., Kwaan Nicholas, Bulkley David P., Bentlage Arthur E.H., Vidarsson Gestur, Boilard Éric, Spirig Rolf, Zimring James C., Looney Mark R.

Journal:

Journal of Clinical Investigation

March 2024

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains

Authors: Zwick Rachel K., Kasparek Petr, Palikuqi Brisa, Viragova Sara, Weichselbaum Laura, McGinnis Christopher S., McKinley Kara L., Rathnayake Asoka, Vaka Dedeepya, Nguyen Vinh, Trentesaux Coralie, Reyes Efren, Gupta Alexander R., Gartner Zev J., Locksley Richard M., Gardner James M., Itzkovitz Shalev, Bo... See more

Journal:

Nature Cell Biology

February 2024

Macrophage and CD8 T Cell Discordance are Associated with Acute Lung Allograft Dysfunction Progression

Authors: Calabrese Daniel R., Yellamilli Shivaram, Ekstrand Christina, Singer Jonathan P., Hays Steven R., Leard Lorriana E., Shah Rupal J., Venado Aida, Kolaitis Nicholas A., Perez Alyssa, Combes Alexis, Greenland John R.

Journal:

The Journal of Heart and Lung Transplantation

February 2024