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Marcus Ramsay Clark

Professor
mclark@medicine.bsd.uchicago.edu
Websites
Research Summary
Our laboratory has a long-standing interest in B cell antigen receptor (BCR) signaling and how BCR dependent processes regulate specific cell fate decisions. In the bone marrow, we have been working to understand how signals initiated through the pre-BCR, in conjunction with those delivered through the IL-7 receptor, coordinate cell cycle progression with immunoglobulin light chain gene recombination. These studies resulted in discovery of the epigenetic reader BRWD1 as critical for both regulating Ig-kappa accessibility and in coordinating broad transcriptional programs in early and late B lymphopoiesis. Recently, we have demonstrated that the pre-BCR initiates an IRF4-CXCR4 feedforward loop and that it is CXCR4 that directly signals Ig-kappa recombination. These latter findings fundamentally rewrite the canonical model of B lymphopoiesis. Furthermore, they are the first demonstration of a direct and independent role for CXCR4 in driving an important biological process. In the periphery, we have focused on the molecular control of germinal centers (GCs). Recently, we have recently defined two novel B cell populations within the dark zone that both allow compartmentalization of fundamental GC functions and reveal the molecular programs of the GC cycle. This new three population model fundamentally rewrites the GC paradigm. In all these areas, we have derived novel in vivo models, and have performed directed in vitro studies, to obtain definitive insights into these processes. Our translational studies have focused on how in situ adaptive immune responses drive tubulointerstitial inflammation in human lupus nephritis. For these studies, we have used deep machine learning to develop novel image analysis tools to quantify and identify functional relationships between different T cell and antigen presenting cell populations in situ. Remarkably, this bioinformatics platform approaches the sensitivity and specificity of two-photon excitation microscopy (TPEM). However, unlike TPEM, it can be applied to the study of human disease. We have also used single cell technologies to understand B cell selection at sites of inflammation and determine the interrelationships between transcriptional state and antigenic specificity.
Keywords
B Cells, Molecular Biology, Developmental Biology, gene regulation, Autoimmunity, Lupus Nephritis, Adaptive Immunity, chromatin organization
Biosciences Graduate Program Association
Publications

  1. Abraham R, Durkee MS, Ai J, Veselits M, Casella G, Asano Y, Chang A, Ko K, Oshinsky C, Peninger E, Giger ML, Clark MR. Specific in situ inflammatory states associate with progression to renal failure in lupus nephritis. J Clin Invest. 2022 May 24. View in: PubMed

  2. Chen JW, Schickel JN, Tsakiris N, Sng J, Arbogast F, Bouis D, Parisi D, Gera R, Boeckers JM, Delmotte FR, Veselits M, Schuetz C, Jacobsen EM, Posovszky C, Schulz AS, Schwarz K, Clark MR, Menard L, Meffre E. Positive and negative selection shape the human naive B cell repertoire. J Clin Invest. 2022 01 18; 132(2). View in: PubMed

  3. Asano Y, Daccache J, Jain D, Ko K, Kinloch A, Veselits M, Wolfgeher D, Chang A, Josephson M, Cunningham P, Tambur A, Khan AA, Pillai S, Chong AS, Clark MR. Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. Nat Commun. 2021 07 16; 12(1):4372. View in: PubMed

  4. Durkee MS, Abraham R, Clark MR, Giger ML. Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images. Am J Pathol. 2021 10; 191(10):1693-1701. View in: PubMed

  5. Kennedy DE, Clark MR. Compartments and Connections Within the Germinal Center. Front Immunol. 2021; 12:659151. View in: PubMed

  6. Durkee MS, Abraham R, Ai J, Veselits M, Clark MR, Giger ML. Quantifying the effects of biopsy fixation and staining panel design on automatic instance segmentation of immune cells in human lupus nephritis. J Biomed Opt. 2021 01; 26(2). View in: PubMed

  7. Chang A, Clark MR, Ko K. Cellular aspects of the pathogenesis of lupus nephritis. Curr Opin Rheumatol. 2021 03 01; 33(2):197-204. View in: PubMed

  8. Kinloch AJ, Asano Y, Mohsin A, Henry C, Abraham R, Chang A, Labno C, Wilson PC, Clark MR. Machine Learning to Quantify In Situ Humoral Selection in Human Lupus Tubulointerstitial Inflammation. Front Immunol. 2020; 11:593177. View in: PubMed

  9. Zheng Z, Zhang L, Cui XL, Yu X, Hsu PJ, Lyu R, Tan H, Mandal M, Zhang M, Sun HL, Sanchez Castillo A, Peng J, Clark MR, He C, Huang H. Control of Early B Cell Development by the RNA N6-Methyladenosine Methylation. Cell Rep. 2020 06 30; 31(13):107819. View in: PubMed

  10. Kennedy DE, Okoreeh MK, Maienschein-Cline M, Ai J, Veselits M, McLean KC, Dhungana Y, Wang H, Peng J, Chi H, Mandal M, Clark MR. Novel specialized cell state and spatial compartments within the germinal center. Nat Immunol. 2020 06; 21(6):660-670. View in: PubMed

  11. Chen PM, Wilson PC, Shyer JA, Veselits M, Steach HR, Cui C, Moeckel G, Clark MR, Craft J. Kidney tissue hypoxia dictates T cell-mediated injury in murine lupus nephritis. Sci Transl Med. 2020 04 08; 12(538). View in: PubMed

  12. Wong JB, Hewitt SL, Heltemes-Harris LM, Mandal M, Johnson K, Rajewsky K, Koralov SB, Clark MR, Farrar MA, Skok JA. B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage. Nat Commun. 2019 10 18; 10(1):4768. View in: PubMed

  13. Mandal M, Okoreeh MK, Kennedy DE, Maienschein-Cline M, Ai J, McLean KC, Kaverina N, Veselits M, Aifantis I, Gounari F, Clark MR. CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis. Nat Immunol. 2019 10; 20(10):1393-1403. View in: PubMed

  14. Karki S, Banerjee S, Mclean K, Dinner A, Clark MR. Transcription factories in Ig? allelic choice and diversity. Adv Immunol. 2019; 141:33-49. View in: PubMed

  15. Liarski VM, Sibley A, van Panhuys N, Ai J, Chang A, Kennedy D, Merolle M, Germain RN, Giger ML, Clark MR. Quantifying in situ adaptive immune cell cognate interactions in humans. Nat Immunol. 2019 04; 20(4):503-513. View in: PubMed

  16. Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Nat Commun. 2018 09 24; 9(1):3888. View in: PubMed

  17. Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR. Regulated Capture of V? Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 2018 08 28; 24(9):2443-2456. View in: PubMed

  18. Kennedy DE, Clark MR. PI3Kd: Too much of a good thing. Nat Immunol. 2018 09; 19(9):910-911. View in: PubMed

  19. Veselits M, Tanaka A, Chen Y, Hamel K, Mandal M, Kandasamy M, Manicassamy B, O'Neill SK, Wilson P, Sciammas R, Clark MR. Igß ubiquitination activates PI3K signals required for endosomal sorting. J Exp Med. 2017 Dec 04; 214(12):3775-3790. View in: PubMed

  20. Jacobsen JA, Woodard J, Mandal M, Clark MR, Bartom ET, Sigvardsson M, Kee BL. EZH2 Regulates the Developmental Timing of Effectors of the Pre-Antigen Receptor Checkpoints. J Immunol. 2017 06 15; 198(12):4682-4691. View in: PubMed

  21. Ko K, Wang J, Perper S, Jiang Y, Yanez D, Kaverina N, Ai J, Liarski VM, Chang A, Peng Y, Lan L, Westmoreland S, Olson L, Giger ML, Chun Wang L, Clark MR. Bcl-2 as a Therapeutic Target in Human Tubulointerstitial Inflammation. Arthritis Rheumatol. 2016 11; 68(11):2740-2751. View in: PubMed

  22. Henault J, Riggs JM, Karnell JL, Liarski VM, Li J, Shirinian L, Xu L, Casey KA, Smith MA, Khatry DB, Izhak L, Clarke L, Herbst R, Ettinger R, Petri M, Clark MR, Mustelin T, Kolbeck R, Sanjuan MA. Self-reactive IgE exacerbates interferon responses associated with autoimmunity. Nat Immunol. 2016 Feb; 17(2):196-203. View in: PubMed

  23. Mandal M, Hamel KM, Maienschein-Cline M, Tanaka A, Teng G, Tuteja JH, Bunker JJ, Bahroos N, Eppig JJ, Schatz DG, Clark MR. Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nat Immunol. 2015 Oct; 16(10):1094-103. View in: PubMed

  24. Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG. RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell. 2015 Aug 13; 162(4):751-65. View in: PubMed

  25. Kinloch AJ, Chang A, Ko K, Henry Dunand CJ, Henderson S, Maienschein-Cline M, Kaverina N, Rovin BH, Salgado Ferrer M, Wolfgeher D, Liarski V, Haddon DJ, Utz PJ, Wilson PC, Clark MR. Vimentin is a dominant target of in situ humoral immunity in human lupus tubulointerstitial nephritis. Arthritis Rheumatol. 2014 Dec; 66(12):3359-70. View in: PubMed

  26. Hamel KM, Mandal M, Karki S, Clark MR. Balancing Proliferation with Ig? Recombination during B-lymphopoiesis. Front Immunol. 2014; 5:139. View in: PubMed

  27. Liarski VM, Kaverina N, Chang A, Brandt D, Yanez D, Talasnik L, Carlesso G, Herbst R, Utset TO, Labno C, Peng Y, Jiang Y, Giger ML, Clark MR. Cell distance mapping identifies functional T follicular helper cells in inflamed human renal tissue. Sci Transl Med. 2014 Apr 02; 6(230):230ra46. View in: PubMed

  28. Chang A, Ko K, Clark MR. The emerging role of the inflammasome in kidney diseases. Curr Opin Nephrol Hypertens. 2014 May; 23(3):204-10. View in: PubMed

  29. Clark MR, Mandal M, Ochiai K, Singh H. Orchestrating B cell lymphopoiesis through interplay of IL-7 receptor and pre-B cell receptor signalling. Nat Rev Immunol. 2014 Feb; 14(2):69-80. View in: PubMed

  30. Powers SE, Mandal M, Matsuda S, Miletic AV, Cato MH, Tanaka A, Rickert RC, Koyasu S, Clark MR. Subnuclear cyclin D3 compartments and the coordinated regulation of proliferation and immunoglobulin variable gene repression. J Exp Med. 2012 Nov 19; 209(12):2199-213. View in: PubMed

  31. Sawai CM, Freund J, Oh P, Ndiaye-Lobry D, Bretz JC, Strikoudis A, Genesca L, Trimarchi T, Kelliher MA, Clark M, Soulier J, Chen-Kiang S, Aifantis I. Therapeutic targeting of the cyclin D3:CDK4/6 complex in T cell leukemia. Cancer Cell. 2012 Oct 16; 22(4):452-65. View in: PubMed

  32. Ochiai K, Maienschein-Cline M, Mandal M, Triggs JR, Bertolino E, Sciammas R, Dinner AR, Clark MR, Singh H. A self-reinforcing regulatory network triggered by limiting IL-7 activates pre-BCR signaling and differentiation. Nat Immunol. 2012 Jan 22; 13(3):300-7. View in: PubMed

  33. Mandal M, Powers SE, Maienschein-Cline M, Bartom ET, Hamel KM, Kee BL, Dinner AR, Clark MR. Epigenetic repression of the Igk locus by STAT5-mediated recruitment of the histone methyltransferase Ezh2. Nat Immunol. 2011 Oct 30; 12(12):1212-20. View in: PubMed

  34. Clark MR. Flippin' lipids. Nat Immunol. 2011 May; 12(5):373-5. View in: PubMed

  35. Hsieh C, Chang A, Brandt D, Guttikonda R, Utset TO, Clark MR. Predicting outcomes of lupus nephritis with tubulointerstitial inflammation and scarring. Arthritis Care Res (Hoboken). 2011 Jun; 63(6):865-74. View in: PubMed

  36. Chang A, Henderson SG, Brandt D, Liu N, Guttikonda R, Hsieh C, Kaverina N, Utset TO, Meehan SM, Quigg RJ, Meffre E, Clark MR. In situ B cell-mediated immune responses and tubulointerstitial inflammation in human lupus nephritis. J Immunol. 2011 Feb 01; 186(3):1849-60. View in: PubMed

  37. Ma S, Pathak S, Mandal M, Trinh L, Clark MR, Lu R. Ikaros and Aiolos inhibit pre-B-cell proliferation by directly suppressing c-Myc expression. Mol Cell Biol. 2010 Sep; 30(17):4149-58. View in: PubMed

  38. Mandal M, Powers SE, Ochiai K, Georgopoulos K, Kee BL, Singh H, Clark MR. Ras orchestrates exit from the cell cycle and light-chain recombination during early B cell development. Nat Immunol. 2009 Oct; 10(10):1110-7. View in: PubMed

  39. O'Neill SK, Veselits ML, Zhang M, Labno C, Cao Y, Finnegan A, Uccellini M, Alegre ML, Cambier JC, Clark MR. Endocytic sequestration of the B cell antigen receptor and toll-like receptor 9 in anergic cells. Proc Natl Acad Sci U S A. 2009 Apr 14; 106(15):6262-7. View in: PubMed

  40. Mandal M, Crusio KM, Meng F, Liu S, Kinsella M, Clark MR, Takeuchi O, Aifantis I. Regulation of lymphocyte progenitor survival by the proapoptotic activities of Bim and Bid. Proc Natl Acad Sci U S A. 2008 Dec 30; 105(52):20840-5. View in: PubMed

  41. Zhang M, Veselits M, O'Neill S, Hou P, Reddi AL, Berlin I, Ikeda M, Nash PD, Longnecker R, Band H, Clark MR. Ubiquitinylation of Ig beta dictates the endocytic fate of the B cell antigen receptor. J Immunol. 2007 Oct 01; 179(7):4435-43. View in: PubMed

  42. Gomez TS, McCarney SD, Carrizosa E, Labno CM, Comiskey EO, Nolz JC, Zhu P, Freedman BD, Clark MR, Rawlings DJ, Billadeau DD, Burkhardt JK. HS1 functions as an essential actin-regulatory adaptor protein at the immune synapse. Immunity. 2006 Jun; 24(6):741-752. View in: PubMed

  43. Hou P, Araujo E, Zhao T, Zhang M, Massenburg D, Veselits M, Doyle C, Dinner AR, Clark MR. B cell antigen receptor signaling and internalization are mutually exclusive events. PLoS Biol. 2006 Jul; 4(7):e200. View in: PubMed

  44. Cooper AB, Sawai CM, Sicinska E, Powers SE, Sicinski P, Clark MR, Aifantis I. A unique function for cyclin D3 in early B cell development. Nat Immunol. 2006 May; 7(5):489-97. View in: PubMed

  45. Clark MR, Cooper AB, Wang LD, Aifantis I. The pre-B cell receptor in B cell development: recent advances, persistent questions and conserved mechanisms. Curr Top Microbiol Immunol. 2005; 290:87-103. View in: PubMed

  46. Wang LD, Lopes J, Cooper AB, Dang-Lawson M, Matsuuchi L, Clark MR. Selection of B lymphocytes in the periphery is determined by the functional capacity of the B cell antigen receptor. Proc Natl Acad Sci U S A. 2004 Jan 27; 101(4):1027-32. View in: PubMed

  47. Kabak S, Skaggs BJ, Gold MR, Affolter M, West KL, Foster MS, Siemasko K, Chan AC, Aebersold R, Clark MR. The direct recruitment of BLNK to immunoglobulin alpha couples the B-cell antigen receptor to distal signaling pathways. Mol Cell Biol. 2002 Apr; 22(8):2524-35. View in: PubMed

  48. Sun T, Clark MR, Storb U. A point mutation in the constant region of Ig lambda1 prevents normal B cell development due to defective BCR signaling. Immunity. 2002 Feb; 16(2):245-55. View in: PubMed

  49. Siemasko K, Skaggs BJ, Kabak S, Williamson E, Brown BK, Song W, Clark MR. Receptor-facilitated antigen presentation requires the recruitment of B cell linker protein to Igalpha. J Immunol. 2002 Mar 01; 168(5):2127-38. View in: PubMed

  50. Siemasko K, Clark MR. The control and facilitation of MHC class II antigen processing by the BCR. Curr Opin Immunol. 2001 Feb; 13(1):32-6. View in: PubMed

  51. Wang LD, Clark MR. Igalpha: B all that you can B. J Clin Invest. 1999 Oct; 104(8):1011-2. View in: PubMed

  52. Siemasko K, Eisfelder BJ, Stebbins C, Kabak S, Sant AJ, Song W, Clark MR. Ig alpha and Ig beta are required for efficient trafficking to late endosomes and to enhance antigen presentation. J Immunol. 1999 Jun 01; 162(11):6518-25. View in: PubMed

  53. Garrett-Sinha LA, Su GH, Rao S, Kabak S, Hao Z, Clark MR, Simon MC. PU.1 and Spi-B are required for normal B cell receptor-mediated signal transduction. Immunity. 1999 Apr; 10(4):399-408. View in: PubMed
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