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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, 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
Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27.

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs)...

Cite
Combes AJ, Samad B, Tsui J, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021;185(1):184-203.e19doi: 10.1016/j.cell.2021.12.004.
Combes, A. J., Samad, B., Tsui, J., Chew, N. W., Yan, P., Reeder, G. C., Kushnoor, D., Shen, A., Davidson, B., Barczak, A. J., Adkisson, M., Edwards, A., Naser, M., Barry, K. C., Courau, T., Hammoudi, T., Argüello, R. J., Rao, A. A., Olshen, A. B., Cai, C., Zhan, J., Davis, K. C., Kelley, R. K., Chapman, J. S., Atreya, C. E., Patel, A., Daud, A. I., Ha, P., Diaz, A. A., Kratz, J. R., Collisson, E. A., Fragiadakis, G. K., Erle, D. J., Boissonnas, A., Asthana, S., Chan, V., & Krummel, M. F. (2022). Discovering dominant tumor immune archetypes in a pan-cancer census. Cell, 185(1), 184-203.e19. https://doi.org/10.1016/j.cell.2021.12.004
Combes, Alexis J, et al. "Discovering dominant tumor immune archetypes in a pan-cancer census." Cell vol. 185,1 (2022): 184-203.e19. doi: https://doi.org/10.1016/j.cell.2021.12.004
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, 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. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27. PMID: 34963056.
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Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions.

Molecular neurobiology

Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M.
PMID: 34669146
Mol Neurobiol. 2021 Oct 20; doi: 10.1007/s12035-021-02591-8. Epub 2021 Oct 20.

Alzheimer's disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can inform new therapeutic approaches for both sexes. Previous bulk human brain...

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Belonwu SA, Li Y, Bunis D, et al. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Mol Neurobiol. 2021;doi: 10.1007/s12035-021-02591-8.
Belonwu, S. A., Li, Y., Bunis, D., Rao, A. A., Solsberg, C. W., Tang, A., Fragiadakis, G. K., Dubal, D. B., Oskotsky, T., & Sirota, M. (2021). Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Molecular neurobiology, . https://doi.org/10.1007/s12035-021-02591-8
Belonwu, Stella A, et al. "Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions." Molecular neurobiology vol. (2021). doi: https://doi.org/10.1007/s12035-021-02591-8
Belonwu SA, Li Y, Bunis D, Rao AA, Solsberg CW, Tang A, Fragiadakis GK, Dubal DB, Oskotsky T, Sirota M. Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer's Disease Across Two Brain Regions. Mol Neurobiol. 2021 Oct 20; doi: 10.1007/s12035-021-02591-8. Epub 2021 Oct 20. PMID: 34669146.
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Global Absence and Targeting of Protective Immune States in Severe COVID-19.

Research square

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: 33140041
Res Sq. 2020 Oct 28; doi: 10.21203/rs.3.rs-97042/v1.

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a wholeblood preserving single-cell analysis protocol...

Cite
Combes AJ, Courau T, Kuhn NF, et al. Global Absence and Targeting of Protective Immune States in Severe COVID-19. Res Sq. 2020;doi: 10.21203/rs.3.rs-97042/v1.
Combes, A. J., Courau, T., Kuhn, N. F., Hu, K. H., Ray, A., Chen, W. S., Cleary, S. J., Chew, N. W., Kushnoor, D., Reeder, G. C., Shen, A., Tsui, J., Hiam-Galvez, K. J., Muñoz-Sandoval, P., Zhu, W. S., Lee, D. S., Sun, Y., You, R., Magnen, M., Rodriguez, L., Leligdowicz, A., Zamecnik, C. R., Loudermilk, R. P., Wilson, M. R., Ye, C. J., Fragiadakis, G. K., Looney, M. R., Chan, V., Ward, A., Carrillo, S., Matthay, M., Erle, D. J., Woodruff, P. G., Langelier, C., Kangelaris, K., Hendrickson, C. M., Calfee, C., Rao, A. A., & Krummel, M. F. (2020). Global Absence and Targeting of Protective Immune States in Severe COVID-19. Research square, . https://doi.org/10.21203/rs.3.rs-97042/v1
Combes, Alexis J, et al. "Global Absence and Targeting of Protective Immune States in Severe COVID-19." Research square vol. (2020). doi: https://doi.org/10.21203/rs.3.rs-97042/v1
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. Res Sq. 2020 Oct 28; doi: 10.21203/rs.3.rs-97042/v1. PMID: 33140041; PMCID: PMC7605560.
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Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.

EClinicalMedicine

Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, Comet C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Poller W, Borodina T, Pa-Covid SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B.
PMID: 34490415
EClinicalMedicine. 2021 Oct;40:101099. doi: 10.1016/j.eclinm.2021.101099. Epub 2021 Sep 02.

BACKGROUND: Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been increasing urgency to identify pathophysiological characteristics leading to severe clinical course in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human leukocyte antigen...

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Weiner J, Suwalski P, Holtgrewe M, et al. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine. 2021;40:101099doi: 10.1016/j.eclinm.2021.101099.
Weiner, J., Suwalski, P., Holtgrewe, M., Rakitko, A., Thibeault, C., Müller, M., Patriki, D., Quedenau, C., Krüger, U., Ilinsky, V., Popov, I., Balnis, J., Jaitovich, A., Helbig, E. T., Lippert, L. J., Stubbemann, P., Real, L. M., Macías, J., Pineda, J. A., Fernandez-Fuertes, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J. M., Hübner, R. H., Hinzmann, B., Salvo, M., Blueher, A., Siemann, S., Jurisic, S., Beer, J. H., Rutishauser, J., Wiggli, B., Schmid, H., Danninger, K., Binder, R., Corman, V. M., Mühlemann, B., Arjun Arkal, R., Fragiadakis, G. K., Mick, E., Comet, C., Calfee, C. S., Erle, D. J., Hendrickson, C. M., Kangelaris, K. N., Krummel, M. F., Woodruff, P. G., Langelier, C. R., Venkataramani, U., García, F., Zyla, J., Drosten, C., Alice, B., Jones, T. C., Suttorp, N., Witzenrath, M., Hippenstiel, S., Zemojtel, T., Skurk, C., Poller, W., Borodina, T., Pa-Covid, S. G., Ripke, S., Sander, L. E., Beule, D., Landmesser, U., Guettouche, T., Kurth, F., & Heidecker, B. (2021). Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine, 40101099. https://doi.org/10.1016/j.eclinm.2021.101099
Weiner, January, et al. "Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01." EClinicalMedicine vol. 40 (2021): 101099. doi: https://doi.org/10.1016/j.eclinm.2021.101099
Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, Comet C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Poller W, Borodina T, Pa-Covid SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B. Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01. EClinicalMedicine. 2021 Oct;40:101099. doi: 10.1016/j.eclinm.2021.101099. Epub 2021 Sep 02. PMID: 34490415; PMCID: PMC8410317.
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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.
PMID: 33140050
bioRxiv. 2020 Oct 29; doi: 10.1101/2020.10.28.359935.

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol...

Cite
Combes AJ, Courau T, Kuhn NF, et al. Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv. 2020;doi: 10.1101/2020.10.28.359935.
Combes, A. J., Courau, T., Kuhn, N. F., Hu, K. H., Ray, A., Chen, W. S., Cleary, S. J., Chew, N. W., Kushnoor, D., Reeder, G. C., Shen, A., Tsui, J., Hiam-Galvez, K. J., Muñoz-Sandoval, P., Zhu, W. S., Lee, D. S., Sun, Y., You, R., Magnen, M., Rodriguez, L., Leligdowicz, A., Zamecnik, C. R., Loudermilk, R. P., Wilson, M. R., Ye, C. J., Fragiadakis, G. K., Looney, M. R., Chan, V., Ward, A., Carrillo, S., Matthay, M., Erle, D. J., Woodruff, P. G., Langelier, C., Kangelaris, K., Hendrickson, C. M., Calfee, C., Rao, A. A., & Krummel, M. F. (2020). Global Absence and Targeting of Protective Immune States in Severe COVID-19. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.10.28.359935
Combes, Alexis J, et al. "Global Absence and Targeting of Protective Immune States in Severe COVID-19." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.10.28.359935
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. bioRxiv. 2020 Oct 29; doi: 10.1101/2020.10.28.359935. PMID: 33140050; PMCID: PMC7605559.
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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, 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
Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27.

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs)...

Cite
Combes AJ, Samad B, Tsui J, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021;185(1):184-203.e19doi: 10.1016/j.cell.2021.12.004.
Combes, A. J., Samad, B., Tsui, J., Chew, N. W., Yan, P., Reeder, G. C., Kushnoor, D., Shen, A., Davidson, B., Barczak, A. J., Adkisson, M., Edwards, A., Naser, M., Barry, K. C., Courau, T., Hammoudi, T., Argüello, R. J., Rao, A. A., Olshen, A. B., Cai, C., Zhan, J., Davis, K. C., Kelley, R. K., Chapman, J. S., Atreya, C. E., Patel, A., Daud, A. I., Ha, P., Diaz, A. A., Kratz, J. R., Collisson, E. A., Fragiadakis, G. K., Erle, D. J., Boissonnas, A., Asthana, S., Chan, V., & Krummel, M. F. (2022). Discovering dominant tumor immune archetypes in a pan-cancer census. Cell, 185(1), 184-203.e19. https://doi.org/10.1016/j.cell.2021.12.004
Combes, Alexis J, et al. "Discovering dominant tumor immune archetypes in a pan-cancer census." Cell vol. 185,1 (2022): 184-203.e19. doi: https://doi.org/10.1016/j.cell.2021.12.004
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, 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. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27. PMID: 34963056.
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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, 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
Cell. 2021 Dec 22; doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 22.

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs)...

Cite
Combes AJ, Samad B, Tsui J, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021;doi: 10.1016/j.cell.2021.12.004.
Combes, A. J., Samad, B., Tsui, J., Chew, N. W., Yan, P., Reeder, G. C., Kushnoor, D., Shen, A., Davidson, B., Barczak, A. J., Adkisson, M., Edwards, A., Naser, M., Barry, K. C., Courau, T., Hammoudi, T., Argüello, R. J., Rao, A. A., Olshen, A. B., Cai, C., Zhan, J., Davis, K. C., Kelley, R. K., Chapman, J. S., Atreya, C. E., Patel, A., Daud, A. I., Ha, P., Diaz, A. A., Kratz, J. R., Collisson, E. A., Fragiadakis, G. K., Erle, D. J., Boissonnas, A., Asthana, S., Chan, V., & Krummel, M. F. (2021). Discovering dominant tumor immune archetypes in a pan-cancer census. Cell, . https://doi.org/10.1016/j.cell.2021.12.004
Combes, Alexis J, et al. "Discovering dominant tumor immune archetypes in a pan-cancer census." Cell vol. (2021). doi: https://doi.org/10.1016/j.cell.2021.12.004
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, 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. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021 Dec 22; doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 22. PMID: 34963056.
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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, 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
Cell. 2021 Dec 22; doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 22.

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs)...

Cite
Combes AJ, Samad B, Tsui J, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021;doi: 10.1016/j.cell.2021.12.004.
Combes, A. J., Samad, B., Tsui, J., Chew, N. W., Yan, P., Reeder, G. C., Kushnoor, D., Shen, A., Davidson, B., Barczak, A. J., Adkisson, M., Edwards, A., Naser, M., Barry, K. C., Courau, T., Hammoudi, T., Argüello, R. J., Rao, A. A., Olshen, A. B., Cai, C., Zhan, J., Davis, K. C., Kelley, R. K., Chapman, J. S., Atreya, C. E., Patel, A., Daud, A. I., Ha, P., Diaz, A. A., Kratz, J. R., Collisson, E. A., Fragiadakis, G. K., Erle, D. J., Boissonnas, A., Asthana, S., Chan, V., & Krummel, M. F. (2021). Discovering dominant tumor immune archetypes in a pan-cancer census. Cell, . https://doi.org/10.1016/j.cell.2021.12.004
Combes, Alexis J, et al. "Discovering dominant tumor immune archetypes in a pan-cancer census." Cell vol. (2021). doi: https://doi.org/10.1016/j.cell.2021.12.004
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, 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. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021 Dec 22; doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 22. PMID: 34963056.
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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, 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
bioRxiv. 2021 Mar 10; doi: 10.1101/2021.03.09.434529.

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we...

Cite
van der Wijst MGP, Vazquez SE, Hartoularos GC, et al. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021;doi: 10.1101/2021.03.09.434529.
van der Wijst, M. G. P., Vazquez, S. E., Hartoularos, G. C., Bastard, P., Grant, T., Bueno, R., Lee, D. S., Greenland, J. R., Sun, Y., Perez, R., Ogorodnikov, A., Ward, A., Mann, S. A., Lynch, K. L., Yun, C., Havlir, D. V., Chamie, G., Marquez, C., Greenhouse, B., Lionakis, M. S., Norris, P. J., Dumont, L. J., Kelly, K., Zhang, P., Zhang, Q., Gervais, A., Voyer, T. L., Whatley, A., Si, Y., Byrne, A., Combes, A. J., Rao, A. A., Song, Y. S., Fragiadakis, G. K., Kangelaris, K., Calfee, C. S., Erle, D. J., Hendrickson, C., Krummel, M. F., Woodruff, P. G., Langelier, C. R., Casanova, J. L., Derisi, J. L., Anderson, M. S., & Ye, C. J. (2021). 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, . https://doi.org/10.1101/2021.03.09.434529
van der Wijst, Monique G P, et al. "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 vol. (2021). doi: https://doi.org/10.1101/2021.03.09.434529
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, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10; doi: 10.1101/2021.03.09.434529. PMID: 33758859; PMCID: PMC7987018.
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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, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF.
PMID: 34341540
Nature. 2021 Aug;596(7872):E8. doi: 10.1038/s41586-021-03718-6.

No abstract available.

Cite
Combes AJ, Courau T, Kuhn NF, et al. Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021;596(7872):E8doi: 10.1038/s41586-021-03718-6.
Combes, A. J., Courau, T., Kuhn, N. F., Hu, K. H., Ray, A., Chen, W. S., Chew, N. W., Cleary, S. J., Kushnoor, D., Reeder, G. C., Shen, A., Tsui, J., Hiam-Galvez, K. J., Muñoz-Sandoval, P., Zhu, W. S., Lee, D. S., Sun, Y., You, R., Magnen, M., Rodriguez, L., Im, K. W., Serwas, N. K., Leligdowicz, A., Zamecnik, C. R., Loudermilk, R. P., Wilson, M. R., Ye, C. J., Fragiadakis, G. K., Looney, M. R., Chan, V., Ward, A., Carrillo, S., Matthay, M., Erle, D. J., Woodruff, P. G., Langelier, C., Kangelaris, K., Hendrickson, C. M., Calfee, C., Rao, A. A., & Krummel, M. F. (2021). Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19. Nature, 596(7872), E8. https://doi.org/10.1038/s41586-021-03718-6
Combes, Alexis J, et al. "Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19." Nature vol. 596,7872 (2021): E8. doi: https://doi.org/10.1038/s41586-021-03718-6
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, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF. Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19. Nature. 2021 Aug;596(7872):E8. doi: 10.1038/s41586-021-03718-6. PMID: 34341540; PMCID: PMC8328349.
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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, 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
bioRxiv. 2021 Mar 10; doi: 10.1101/2021.03.09.434529.

Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we...

Cite
van der Wijst MGP, Vazquez SE, Hartoularos GC, et al. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021;doi: 10.1101/2021.03.09.434529.
van der Wijst, M. G. P., Vazquez, S. E., Hartoularos, G. C., Bastard, P., Grant, T., Bueno, R., Lee, D. S., Greenland, J. R., Sun, Y., Perez, R., Ogorodnikov, A., Ward, A., Mann, S. A., Lynch, K. L., Yun, C., Havlir, D. V., Chamie, G., Marquez, C., Greenhouse, B., Lionakis, M. S., Norris, P. J., Dumont, L. J., Kelly, K., Zhang, P., Zhang, Q., Gervais, A., Voyer, T. L., Whatley, A., Si, Y., Byrne, A., Combes, A. J., Rao, A. A., Song, Y. S., Fragiadakis, G. K., Kangelaris, K., Calfee, C. S., Erle, D. J., Hendrickson, C., Krummel, M. F., Woodruff, P. G., Langelier, C. R., Casanova, J. L., Derisi, J. L., Anderson, M. S., & Ye, C. J. (2021). 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, . https://doi.org/10.1101/2021.03.09.434529
van der Wijst, Monique G P, et al. "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 vol. (2021). doi: https://doi.org/10.1101/2021.03.09.434529
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, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10; doi: 10.1101/2021.03.09.434529. PMID: 33758859; PMCID: PMC7987018.
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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, 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
Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27.

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs)...

Cite
Combes AJ, Samad B, Tsui J, et al. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2021;185(1):184-203.e19doi: 10.1016/j.cell.2021.12.004.
Combes, A. J., Samad, B., Tsui, J., Chew, N. W., Yan, P., Reeder, G. C., Kushnoor, D., Shen, A., Davidson, B., Barczak, A. J., Adkisson, M., Edwards, A., Naser, M., Barry, K. C., Courau, T., Hammoudi, T., Argüello, R. J., Rao, A. A., Olshen, A. B., Cai, C., Zhan, J., Davis, K. C., Kelley, R. K., Chapman, J. S., Atreya, C. E., Patel, A., Daud, A. I., Ha, P., Diaz, A. A., Kratz, J. R., Collisson, E. A., Fragiadakis, G. K., Erle, D. J., Boissonnas, A., Asthana, S., Chan, V., & Krummel, M. F. (2022). Discovering dominant tumor immune archetypes in a pan-cancer census. Cell, 185(1), 184-203.e19. https://doi.org/10.1016/j.cell.2021.12.004
Combes, Alexis J, et al. "Discovering dominant tumor immune archetypes in a pan-cancer census." Cell vol. 185,1 (2022): 184-203.e19. doi: https://doi.org/10.1016/j.cell.2021.12.004
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, 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. Discovering dominant tumor immune archetypes in a pan-cancer census. Cell. 2022 Jan 06;185(1):184-203.e19. doi: 10.1016/j.cell.2021.12.004. Epub 2021 Dec 27. PMID: 34963056.
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