Alexis Combes, PhD

Title(s)Assistant Professor, Pathology
SchoolSchool of Medicine
Address513 Parnassus Avenue, MSB, #836
San Francisco CA 94117
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease. NPJ Breast Cancer. 2023 Apr 07; 9(1):22. Im KW, Huppert LA, Malevanchik L, Rugo HS, Combes AJ, Campbell MJ, Krummel MF, Melisko ME. PMID: 37029150; PMCID: PMC10082042.
      View in: PubMed   Mentions:
    2. Dynamic CD8+ T�cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes. Cell. 2023 03 16; 186(6):1127-1143.e18. 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 M, Fong L, Algazi AP, Ha P, Spitzer MH. PMID: 36931243.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    3. Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data. bioRxiv. 2023 Mar 11. 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, Baron J, Combes AJ, Fragiadakis GK. PMID: 36945648; PMCID: PMC10028883.
      View in: PubMed   Mentions:
    4. Polyunsaturated fatty acid-bound alpha-fetoprotein promotes immune suppression by altering human dendritic cell metabolism. Cancer Res. 2023 Feb 27. Munson PV, Adamik J, Hartmann FJ, Favaro PMB, Ho D, Bendall SC, Combes AJ, Krummel MF, Zhang K, Kelley RK, Butterfield LH. PMID: 36847613.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports. 2023 03 14; 18(3):636-653. 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, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. PMID: 36827975; PMCID: PMC9948283.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    6. Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis. bioRxiv. 2023 Jan 22. Mennillo E, Kim YJ, Rusu I, Lee G, Dorman LC, Bernard-Vazquez F, Bain JL, Patel R, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Naser M, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. PMID: 36711576; PMCID: PMC9882264.
      View in: PubMed   Mentions:
    7. Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells. Nat Commun. 2022 09 02; 13(1):5184. Adamik J, Munson PV, Hartmann FJ, Combes AJ, Pierre P, Krummel MF, Bendall SC, Argüello RJ, Butterfield LH. PMID: 36056019; PMCID: PMC9440236.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    8. Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer. Cancer Cell. 2022 06 13; 40(6):624-638.e9. 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. PMID: 35623342; PMCID: PMC9197962.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    9. Tumor-associated macrophage heterogeneity is driven by tissue territories in breast cancer. Cell Rep. 2022 05 24; 39(8):110865. Laviron M, Petit M, Weber-Delacroix E, Combes AJ, Arkal AR, Barthélémy S, Courau T, Hume DA, Combadière C, Krummel MF, Boissonnas A. PMID: 35613577.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    10. Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood. BMC Med. 2022 04 15; 20(1):158. 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. PMID: 35421980; PMCID: PMC9011995.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    11. Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer. Cancer Immunol Res. 2022 04 01; 10(4):403-419. 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. PMID: 35181780; PMCID: PMC8982148.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    12. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022 01 06; 185(1):184-203.e19. 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, Immunoprofiler Consortium, Cai C, Zhan J, Davis KC, Kelley RK, Chapman JS, Atreya CE, Patel A, Daud AI, Ha P, Diaz AA, Kratz JR, Collisson EA, Fragiadakis GK, Erle DJ, Boissonnas A, Asthana S, Chan V, Krummel MF. PMID: 34963056; PMCID: PMC8862608.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    13. The intersection of COVID-19 and autoimmunity. J Clin Invest. 2021 12 15; 131(24). 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. PMID: 34710063; PMCID: PMC8670833.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimalsCells
    14. Genetic and immunologic features of recurrent stage I lung adenocarcinoma. Sci Rep. 2021 12 08; 11(1):23690. Kratz JR, Li JZ, Tsui J, Lee JC, Ding VW, Rao AA, Mann MJ, Chan V, Combes AJ, Krummel MF, Jablons DM. PMID: 34880292; PMCID: PMC8654957.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    15. Archetypes of checkpoint-responsive immunity. Trends Immunol. 2021 11; 42(11):960-974. Im K, Combes AJ, Spitzer MH, Satpathy AT, Krummel MF. PMID: 34642094; PMCID: PMC8724347.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    16. Active surveillance characterizes human intratumoral T cell exhaustion. J Clin Invest. 2021 09 15; 131(18). You R, Artichoker J, Fries A, Edwards AW, Combes AJ, Reeder GC, Samad B, Krummel MF. PMID: 34292884; PMCID: PMC8439597.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    17. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med. 2021 Sep 22; 13(612):eabh2624. 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, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium. PMID: 34429372; PMCID: PMC8601717.
      View in: PubMed   Mentions: 85     Fields:    Translation:Humans
    18. Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 Aug; 596(7872):E8. 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, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 34341540; PMCID: PMC8328349.
      View in: PubMed   Mentions: 1     Fields:    
    19. SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator. bioRxiv. 2021 Jun 02. 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, Jablons DM, Langelier CR, Matthay M, Ott M, Krummel M, Combes AJ, Sil A, Erle DJ, Kratz JR, Roose JP. PMID: 34100012; PMCID: PMC8183007.
      View in: PubMed   Mentions: 1  
    20. DNGR-1 limits Flt3L-mediated antitumor immunity by restraining tumor-infiltrating type I conventional dendritic cells. J Immunother Cancer. 2021 05; 9(5). 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. PMID: 33980589; PMCID: PMC8118081.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    21. Transcriptomic analysis of immune cells in a multi-ethnic cohort of systemic lupus erythematosus patients identifies ethnicity- and disease-specific expression signatures. Commun Biol. 2021 04 21; 4(1):488. 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. PMID: 33883687; PMCID: PMC8060402.
      View in: PubMed   Mentions: 4  Translation:HumansCells
    22. A tumor-specific mechanism of Treg enrichment mediated by the integrin αvβ8. Sci Immunol. 2021 03 26; 6(57). 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. PMID: 33771888; PMCID: PMC8425767.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    23. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10. 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, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. PMID: 33758859; PMCID: PMC7987018.
      View in: PubMed   Mentions:
    24. Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 03; 591(7848):124-130. 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, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33494096; PMCID: PMC8567458.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansCells
    25. SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution. Cell Metab. 2020 12 01; 32(6):1063-1075.e7. 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. PMID: 33264598; PMCID: PMC8407169.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansAnimalsCells
    26. Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv. 2020 Oct 29. 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, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33140050; PMCID: PMC7605559.
      View in: PubMed   Mentions:
    27. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Res Sq. 2020 Oct 28. 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, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. PMID: 33140041; PMCID: PMC7605560.
      View in: PubMed   Mentions:
    28. Lessons of COVID-19: A roadmap for post-pandemic science. J Exp Med. 2020 09 07; 217(9). Freedman TS, Headley MB, Serwas N, Ruhland M, Castellanos CA, Combes AJ, Krummel MF. PMID: 32735669; PMCID: PMC7392636.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    29. Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity. Cell. 2019 04 18; 177(3):556-571.e16. 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. PMID: 30955881; PMCID: PMC6954108.
      View in: PubMed   Mentions: 207     Fields:    Translation:HumansAnimalsCells
    30. A natural killer-dendritic cell axis defines checkpoint therapy-responsive tumor microenvironments. Nat Med. 2018 08; 24(8):1178-1191. 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, Asthana S, Chan V, Krummel MF. PMID: 29942093; PMCID: PMC6475503.
      View in: PubMed   Mentions: 370     Fields:    Translation:HumansCells
    31. Guanabenz inhibits TLR9 signaling through a pathway that is independent of eIF2α dephosphorylation by the GADD34/PP1c complex. Sci Signal. 2018 01 23; 11(514). 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. PMID: 29363586.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    32. BAD-LAMP controls TLR9 trafficking and signalling in human plasmacytoid dendritic cells. Nat Commun. 2017 10 13; 8(1):913. Combes A, Camosseto V, N'Guessan P, Argüello RJ, Mussard J, Caux C, Bendriss-Vermare N, Pierre P, Gatti E. PMID: 29030552; PMCID: PMC5640662.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    33. MARCH9-mediated ubiquitination regulates MHC I export from the TGN. Immunol Cell Biol. 2017 10; 95(9):753-764. De Angelis Rigotti F, De Gassart A, Pforr C, Cano F, N'Guessan P, Combes A, Camossetto V, Lehner PJ, Pierre P, Gatti E. PMID: 28559542.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    34. Protein synthesis inhibition and GADD34 control IFN-β heterogeneous expression in response to dsRNA. EMBO J. 2017 03 15; 36(6):761-782. 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. PMID: 28100675; PMCID: PMC5350567.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    35. LAMP5 Fine-Tunes GABAergic Synaptic Transmission in Defined Circuits of the Mouse Brain. PLoS One. 2016; 11(6):e0157052. 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. PMID: 27272053; PMCID: PMC4896627.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    36. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. J Cell Biol. 2015 Sep 28; 210(7):1133-52. 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 JP, Santos MA, Gatti E, Pierre P. PMID: 26416964; PMCID: PMC4586740.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
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