Publications | UCSF CoLabs

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

February 2025

Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus

Authors: Narendra Rithwik, Phan Hoang Van, Patterson Sarah L., Almonte Loya Ana Laura, Lanata Cristina, Love Christina, Park Joonsuk, Lydon Emily C., Shimoda Michiko Ametani, Barcellos Lisa, Mekonen Honey, Detweiler Angela, Deosthale Padmini, Neff Norma, Criswell Lindsey A., Maliskova Lenka, Eckalbar Walter,... See more

January 2025

Host-microbe multiomic profiling identifies distinct COVID-19 immune dysregulation in solid organ transplant recipients

Authors: Pickering Harry, Schaenman Joanna, Phan Hoang Van, Maguire Cole, Tsitsiklis Alexandra, Rouphael Nadine, Higuita Nelson Iván Agudelo, Atkinson Mark A., Brakenridge Scott, Fung Monica, Messer William, Reed Elaine F., Rivera Adreanne M., Pickering Harry, Sen Subha, Elashoff David, Ward Dawn C., Brook J... See more

Journal:

Nature Communications

January 2025

Targeting CD206+ macrophages disrupts the establishment of a key antitumor immune axis

Authors: Ray Arja, Hu Kenneth H., Kersten Kelly, Courau Tristan, Kuhn Nicholas F., Zaleta-Linares Itzia, Samad Bushra, Combes Alexis J., Krummel Matthew F.

Journal:

Journal of Experimental Medicine

January 2025

CD38 expression by neonatal human naïve CD4 + T cells shapes their distinct metabolic state and tolerogenic potential

Authors: Dwyer Laura R., DeRogatis Andrea M., Clancy Sean, Gouirand Victoire, Chien Charles, Rogers Elizabeth E., Oltman Scott P., Jelliffe-Pawlowski Laura L., Lynch Susan V., Rutishauser Rachel L., Wagner Allon, Combes Alexis J., Scharschmidt Tiffany C.

January 2025

Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states

Authors: Babdor Joel, Patel Ravi K, Davidson Brittany, Noecker Cecilia, Rahim Maha, Bisanz Jordan E, Tenvooren Iliana, Marquez Diana, Calvo Maria, Johri Vrinda, McCarthy Elizabeth, Shaheed Avneet, Ekstrand Christina, Weakley Allison M, Yu Feiqiao B, Fiehn Oliver, Turnbaugh Peter J, Combes Alexis J, Fragiadak... See more

December 2024

Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping

Authors: Wang Kexin, Nie Yutong, Maguire Cole, Syphurs Caitlin, Sheen Heejune, Karoly Meagan, Lapp Linda, Gygi Jeremy P., Jayavelu Naresh Doni, Patel Ravi K., Hoch Annmarie, Corry David, Kheradmand Farrah, McComsey Grace A., Fernandez-Sesma Ana, Simon Viviana, Metcalf Jordan P., Higuita Nelson I Agudelo, Mes... See more

November 2024

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

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