Alexis Combes, PhD
Assistant Professor
Pathology
School of Medicine

Interests

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• System Immunology
• Immune metabolism
• Cancer immunity
• Single cell omics
• Cell biology

Websites

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• Disease-to-biology CoLab (colabs.ucsf.edu)
• ImmunoX (immunox.ucsf.edu)

Publications (48)

Top publication keywords:
EndosomesCD8-Positive T-LymphocytesMonocytesInterferon Type IToll-Like Receptor 9Cyclonic StormsTumor EscapeCensusesNeoplasmsAntibodies, ViralInterferonsDendritic CellsProtein Phosphatase 1TranscriptomeTumor Microenvironment

• Lack of TGFβ signaling competency predicts conversion of immune poor cancer to immune rich and response to checkpoint blockade.
  bioRxiv : the preprint server for biology 2024 Moore J, Gkantalis J, Guix I, Chou W, Yuen K, Lazar AA, Spitzer M, Combes AJ, Barcellos-Hoff MH
• Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
  Nature communications 2024 Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck …
• Decoding functional hematopoietic progenitor cells in the adult human lung.
  Research square 2024 Conrad C, Magnen M, Tsui J, Wismer H, Naser M, Venkataramani U, Samad B, Cleary SJ, Qiu L, Tian JJ, De Giovanni M, Mende N, Passegue E, Laurenti E, Combes AJ, Looney MR
• Macrophage and CD8 T cell discordance are associated with acute lung allograft dysfunction progression.
  The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation 2024 Calabrese DR, Ekstrand CA, Yellamilli S, Singer JP, Hays SR, Leard LE, Shah RJ, Venado A, Kolaitis NA, Perez A, Combes A, Greenland JR
• Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
  bioRxiv : the preprint server for biology 2024 Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck …

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• Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.
  bioRxiv : the preprint server for biology 2023 Karra L, Finger AM, Shechtman L, Krush M, Huang RM, Prinz M, Tennvooren I, Bahl K, Hysienaj L, Gonzalez PG, Combes AJ, Gonzalez H, Argüello RJ, Spitzer MH, Roose JP
• Critical role of CD206+ macrophages in organizing anti-tumor immunity.
  bioRxiv : the preprint server for biology 2023 Ray A, Hu KH, Kersten K, Kuhn NF, Samad B, Combes AJ, Krummel MF
• Multimodal identification of rare potent effector CD8 T cells in solid tumors.
  bioRxiv : the preprint server for biology 2023 Ray A, Bassette M, Hu KH, Pass LF, Samad B, Combes A, Johri V, Davidson B, Hernandez G, Zaleta-Linares I, Krummel MF
• Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data.
  Frontiers in immunology 2023 Patel RK, Jaszczak RG, Im K, Carey ND, Courau T, Bunis DG, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards AW, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, …
• A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling.
  iScience 2023 Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, …
• Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma.
  bioRxiv : the preprint server for biology 2023 Tanaka M, Lum L, Hu K, Ledezma-Soto C, Samad B, Superville D, Ng K, Adams Z, Kersten K, Fong L, Combes AJ, Krummel M, Reeves M
• Defining and using immune archetypes to classify and treat cancer.
  Nature reviews. Cancer 2023 Combes AJ, Samad B, Krummel MF
• Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer.
  Cell stem cell 2023 Hu KH, Kuhn NF, Courau T, Tsui J, Samad B, Ha P, Kratz JR, Combes AJ, Krummel MF
• Polyunsaturated Fatty Acid-Bound α-Fetoprotein Promotes Immune Suppression by Altering Human Dendritic Cell Metabolism.
  Cancer research 2023 Munson PV, Adamik J, Hartmann FJ, Favaro PMB, Ho D, Bendall SC, Combes AJ, Krummel MF, Zhang K, Kelley RK, Butterfield LH
• High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease.
  NPJ breast cancer 2023 Im KW, Huppert LA, Malevanchik L, Rugo HS, Combes AJ, Campbell MJ, Krummel MF, Melisko ME
• Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
  Cell 2023 Rahim MK, Okholm TLH, Jones KB, McCarthy EE, Liu CC, Yee JL, Tamaki SJ, Marquez DM, Tenvooren I, Wai K, Cheung A, Davidson BR, Johri V, Samad B, O'Gorman WE, Krummel MF, van Zante A, Combes AJ, Angelo…
• Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data.
  bioRxiv : the preprint server for biology 2023 Patel RK, Jaszczak RG, Kwok I, Carey ND, Courau T, Bunis D, Samad B, Avanesyan L, Chew NW, Stenske S, Jespersen JM, Publicover J, Edwards A, Naser M, Rao AA, Lupin-Jimenez L, Krummel MF, Cooper S, …
• SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.
  Stem cell reports 2023 Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, …
• Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells.
  Nature communications 2022 Adamik J, Munson PV, Hartmann FJ, Combes AJ, Pierre P, Krummel MF, Bendall SC, Argüello RJ, Butterfield LH
• Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer.
  Cancer cell 2022 Kersten K, Hu KH, Combes AJ, Samad B, Harwin T, Ray A, Rao AA, Cai E, Marchuk K, Artichoker J, Courau T, Shi Q, Belk J, Satpathy AT, Krummel MF
• Tumor-associated macrophage heterogeneity is driven by tissue territories in breast cancer.
  Cell reports 2022 Laviron M, Petit M, Weber-Delacroix E, Combes AJ, Arkal AR, Barthélémy S, Courau T, Hume DA, Combadière C, Krummel MF, Boissonnas A
• Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood.
  BMC medicine 2022 Vallvé-Juanico J, George AF, Sen S, Thomas R, Shin MG, Kushnoor D, Vásquez JJ, Vo KC, Irwin JC, Roan NR, Combes AJ, Giudice LC
• Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer.
  Cancer immunology research 2022 Mujal AM, Combes AJ, Rao AA, Binnewies M, Samad B, Tsui J, Boissonnas A, Pollack JL, Argüello RJ, Meng MV, Porten SP, Ruhland MK, Barry KC, Chan V, Krummel MF
• Discovering dominant tumor immune archetypes in a pan-cancer census.
  Cell 2021 Combes AJ, Samad B, Tsui J, Chew NW, Yan P, Reeder GC, Kushnoor D, Shen A, Davidson B, Barczak AJ, Adkisson M, Edwards A, Naser M, Barry KC, Courau T, Hammoudi T, Argüello RJ, Rao AA, Olshen AB, …
• The intersection of COVID-19 and autoimmunity.
  The Journal of clinical investigation 2021 Knight JS, Caricchio R, Casanova JL, Combes AJ, Diamond B, Fox SE, Hanauer DA, James JA, Kanthi Y, Ladd V, Mehta P, Ring AM, Sanz I, Selmi C, Tracy RP, Utz PJ, Wagner CA, Wang JY, McCune WJ
• Genetic and immunologic features of recurrent stage I lung adenocarcinoma.
  Scientific reports 2021 Kratz JR, Li JZ, Tsui J, Lee JC, Ding VW, Rao AA, Mann MJ, Chan V, Combes AJ, Krummel MF, Jablons DM
• Archetypes of checkpoint-responsive immunity.
  Trends in immunology 2021 Im K, Combes AJ, Spitzer MH, Satpathy AT, Krummel MF
• Active surveillance characterizes human intratumoral T cell exhaustion.
  The Journal of clinical investigation 2021 You R, Artichoker J, Fries A, Edwards AW, Combes AJ, Reeder GC, Samad B, Krummel MF
• Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.
  Science translational medicine 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19.
  Nature 2021 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.
  bioRxiv : the preprint server for biology 2021 Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, …
• DNGR-1 limits Flt3L-mediated antitumor immunity by restraining tumor-infiltrating type I conventional dendritic cells.
  Journal for immunotherapy of cancer 2021 Cueto FJ, Del Fresno C, Brandi P, Combes AJ, Hernández-García E, Sánchez-Paulete AR, Enamorado M, Bromley CP, Gomez MJ, Conde-Garrosa R, Mañes S, Zelenay S, Melero I, Iborra S, Krummel MF, Sancho D
• Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures.
  Communications biology 2021 Andreoletti G, Lanata CM, Trupin L, Paranjpe I, Jain TS, Nititham J, Taylor KE, Combes AJ, Maliskova L, Ye CJ, Katz P, Dall'Era M, Yazdany J, Criswell LA, Sirota M
• A tumor-specific mechanism of Treg enrichment mediated by the integrin αvβ8.
  Science immunology 2021 Seed RI, Kobayashi K, Ito S, Takasaka N, Cormier A, Jespersen JM, Publicover J, Trilok S, Combes AJ, Chew NW, Chapman J, Krummel MF, Lou J, Marks J, Cheng Y, Baron JL, Nishimura SL
• Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs.
  bioRxiv : the preprint server for biology 2021 van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, …
• Global absence and targeting of protective immune states in severe COVID-19.
  Nature 2021 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution.
  Cell metabolism 2020 Argüello RJ, Combes AJ, Char R, Gigan JP, Baaziz AI, Bousiquot E, Camosseto V, Samad B, Tsui J, Yan P, Boissonneau S, Figarella-Branger D, Gatti E, Tabouret E, Krummel MF, Pierre P
• Global Absence and Targeting of Protective Immune States in Severe COVID-19.
  bioRxiv : the preprint server for biology 2020 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• Global Absence and Targeting of Protective Immune States in Severe COVID-19.
  Research square 2020 Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, …
• Lessons of COVID-19: A roadmap for post-pandemic science.
  The Journal of experimental medicine 2020 Freedman TS, Headley MB, Serwas N, Ruhland M, Castellanos CA, Combes AJ, Krummel MF
• Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity.
  Cell 2019 Binnewies M, Mujal AM, Pollack JL, Combes AJ, Hardison EA, Barry KC, Tsui J, Ruhland MK, Kersten K, Abushawish MA, Spasic M, Giurintano JP, Chan V, Daud AI, Ha P, Ye CJ, Roberts EW, Krummel MF
• A natural killer-dendritic cell axis defines checkpoint therapy-responsive tumor microenvironments.
  Nature medicine 2018 Barry KC, Hsu J, Broz ML, Cueto FJ, Binnewies M, Combes AJ, Nelson AE, Loo K, Kumar R, Rosenblum MD, Alvarado MD, Wolf DM, Bogunovic D, Bhardwaj N, Daud AI, Ha PK, Ryan WR, Pollack JL, Samad B, …
• Guanabenz inhibits TLR9 signaling through a pathway that is independent of eIF2α dephosphorylation by the GADD34/PP1c complex.
  Science signaling 2018 Perego J, Mendes A, Bourbon C, Camosseto V, Combes A, Liu H, Manh TV, Dalet A, Chasson L, Spinelli L, Bardin N, Chiche L, Santos MAS, Gatti E, Pierre P
• BAD-LAMP controls TLR9 trafficking and signalling in human plasmacytoid dendritic cells.
  Nature communications 2017 Combes A, Camosseto V, N'Guessan P, Argüello RJ, Mussard J, Caux C, Bendriss-Vermare N, Pierre P, Gatti E
• MARCH9-mediated ubiquitination regulates MHC I export from the TGN.
  Immunology and cell biology 2017 De Angelis Rigotti F, De Gassart A, Pforr C, Cano F, N'Guessan P, Combes A, Camossetto V, Lehner PJ, Pierre P, Gatti E
• Protein synthesis inhibition and GADD34 control IFN-β heterogeneous expression in response to dsRNA.
  The EMBO journal 2017 Dalet A, Argüello RJ, Combes A, Spinelli L, Jaeger S, Fallet M, Vu Manh TP, Mendes A, Perego J, Reverendo M, Camosseto V, Dalod M, Weil T, Santos MA, Gatti E, Pierre P
• LAMP5 Fine-Tunes GABAergic Synaptic Transmission in Defined Circuits of the Mouse Brain.
  PloS one 2016 Tiveron MC, Beurrier C, Céni C, Andriambao N, Combes A, Koehl M, Maurice N, Gatti E, Abrous DN, Kerkerian-Le Goff L, Pierre P, Cremer H
• RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4.
  The Journal of cell biology 2015 Terawaki S, Camosseto V, Prete F, Wenger T, Papadopoulos A, Rondeau C, Combes A, Rodriguez Rodrigues C, Vu Manh TP, Fallet M, English L, Santamaria R, Soares AR, Weil T, Hammad H, Desjardins M, Gorvel…