Alexis Combes, PhD

Assistant Professor
Pathology
Publications: 

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

The Journal of experimental medicine

Ray A, Hu KH, Kersten K, Courau T, Kuhn NF, Zaleta-Linares I, Samad B, Combes AJ, Krummel MF

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.

bioRxiv : the preprint server for biology

Mennillo E, Lotstein ML, Lee G, Johri V, Ekstrand C, Tsui J, Hou J, Leet DE, He JY, Mahadevan U, Eckalbar W, Oh DY, Fragiadakis GK, Kattah MG, Combes AJ

Chromatin remodelling drives immune cell-fibroblast communication in heart failure.

Nature

Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Pelonero A, Lee CY, Sadagopan N, Huang Y, Auclair K, Zhu A, An Y, Ekstrand CA, Martinez C, Teran BG, Flanigan WR, Kim CK, Lumbao-Conradson K, Gardner Z, Li L, Costa MW, Jain R, Charo I, Combes AJ, Haldar SM, Pollard KS, Vagnozzi RJ, McKinsey TA, Przytycki PF, Srivastava D

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.

F&S science

Huang D, Flynn E, Almonte-Loya A, Davidson B, Chan M, Casillas A, Irwin JC, Fragiadakis GK, Cakmak H, Combes AJ, Cedars MI, Sirota M, Giudice LC

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

Nature neuroscience

Chen J, Crouch EE, Zawadzki ME, Jacobs KA, Mayo LN, Choi JJ, Lin PY, Shaikh S, Tsui J, Gonzalez-Granero S, Waller S, Kelekar A, Kang G, Valenzuela EJ, Birrueta JO, Diafos LN, Wedderburn-Pugh K, Di Marco B, Xia W, Han CZ, Coufal NG, Glass CK, Fancy SPJ, Alfonso J, Kriegstein AR, Oldham MC, Garcia-Verdugo JM, Kutys ML, Lehtinen MK, Combes AJ, Huang EJ

Critical role of CD206+ macrophages in organizing anti-tumor immunity.

bioRxiv : the preprint server for biology

Ray A, Hu KH, Kersten K, Kuhn NF, Samad B, Combes AJ, Krummel MF

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

Nature Cancer

Tharp KM, Kersten K, Maller O, Timblin GA, Stashko C, Canale FP, Menjivar RE, Hayward MK, Berestjuk I, Ten Hoeve J, Samad B, Ironside AJ, di Magliano MP, Muir A, Geiger R, Combes AJ, Weaver VM

Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade.

bioRxiv : the preprint server for biology

Moore J, Gkantalis J, Guix I, Chou W, Yuen K, Lazar AA, Spitzer M, Combes AJ, Barcellos-Hoff MH

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

Journal for immunotherapy of cancer

He JY, Kim YJ, Mennillo E, Rusu I, Bain J, Rao AA, Andersen C, Law K, Yang H, Tsui J, Shen A, Davidson B, Kushnoor D, Shi Y, Fan F, Cheung A, Zhang L, Fong L, Combes AJ, Pisco AO, Kattah MG, Oh DY

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.

Nature communications

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 K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG

Decoding functional hematopoietic progenitor cells in the adult human lung.

Research square

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

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 identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis.

bioRxiv : the preprint server for biology

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

Single cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions.

bioRxiv : the preprint server for biology

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

Multimodal identification of rare potent effector CD8 T cells in solid tumors.

bioRxiv : the preprint server for biology

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

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, Baron JL, Combes AJ, Fragiadakis GK

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling.

iScience

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, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MGP, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, UCSF COMET Consortium, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma.

bioRxiv : the preprint server for biology

Tanaka M, Lum L, Hu K, Ledezma-Soto C, Superville D, Ng K, Adams Z, Kersten K, Fong L, Krummel M, Reeves M

Defining and using immune archetypes to classify and treat cancer.

Nature reviews. Cancer

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

Hu KH, Kuhn NF, Courau T, Tsui J, Samad B, Ha P, Kratz JR, Combes AJ, Krummel MF

Polyunsaturated fatty acid-bound alpha-fetoprotein promotes immune suppression by altering human dendritic cell metabolism.

Cancer research

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

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

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

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data.

bioRxiv : the preprint server for biology

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

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

Stem cell reports

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

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells.

Nature communications

Adamik J, Munson PV, Hartmann FJ, Combes AJ, Pierre P, Krummel MF, Bendall SC, Arg?ello RJ, Butterfield LH

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer.

Cancer cell

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

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

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

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

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

The intersection of COVID-19 and autoimmunity.

The Journal of clinical investigation

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

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

Im K, Combes AJ, Spitzer MH, Satpathy AT, Krummel MF

Active surveillance characterizes human intratumoral T cell exhaustion.

The Journal of clinical investigation

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

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

Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19.

Nature

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

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.

bioRxiv : the preprint server for biology

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

DNGR-1 limits Flt3L-mediated antitumor immunity by restraining tumor-infiltrating type I conventional dendritic cells.

Journal for immunotherapy of cancer

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

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

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.

bioRxiv : the preprint server for biology

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

Global absence and targeting of protective immune states in severe COVID-19.

Nature

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

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution.

Cell metabolism

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

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

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

Research square

Krummel M, Combes A, Courau T, Kuhn N, Hu K, Ray A, Chen W, Cleary S, Chew N, Kushnoor D, Reeder G, Shen A, Tsui J, Hiam K, Sandoval PM, Zhu W, Lee D, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik C, Loudermilk R, Wilson M, Ye C, Fragiadakis G, Looney M, Chan V, Ward A, Carrillo S, Matthay M, Erle D, Woodruff P, Langelier C, Kangelaris K, Hendrickson C, Calfee C, Rao A

Lessons of COVID-19: A roadmap for post-pandemic science.

The Journal of experimental medicine

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

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

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

Guanabenz inhibits TLR9 signaling through a pathway that is independent of eIF2α dephosphorylation by the GADD34/PP1c complex.

Science signaling

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

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

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

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

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

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

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