Selected Publications
2024
BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function. bioRxiv [Preprint]. Wright NE, Kennedy DE, Ai J, Veselits ML, Attaway M, Yoon YM, Durkee MS, Veselits J, Maienschein-Cline M, Mandal M, Clark MR. B. 2024 Apr 28:2024.04.25.591154. PMID: 38712068.
Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data. Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data. Durkee MS, Ai J, Casella G, Cao T, Chang A, Halper-Stromberg A, Jabri B, Clark MR, Giger ML. IEEE Medical Imaging. 2024 Jan 11:2024.01.09.574920. PMID: 38260318
2023
Molecular mechanisms insulating proliferation from genotoxic stress in B lymphocytes. Trends Immunol. 2023 Aug 10:S1471-4906(23)00134-5. Online ahead of print. PMID: 37573227
Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies. medRxiv. 2023 May 11:2023.05.08.23289640. PMID: 37214861
STAT3 signaling in B cells controls germinal center zone organization and recycling. Cell Rep. 2023 May 30;42(5):112512. PMID: 37200190
The endogenous repertoire harbors self-reactive CD4+ T cell clones that adopt a follicular helper T cell-like phenotype at steady state. Nat Immunol. 2023 Mar;24(3):487-500. PMID: 36759711
The ion transporter Na+-K+-ATPase enables pathological B cell survival in the kidney microenvironment of lupus nephritis. Sci Adv. 2023 Feb 3;9(5):eadf8156. PMID: 36724234
2022
IRF4 expression by lung dendritic cells drives acute but not Trm cell-dependent memory Th2 responses. JCI Insight. 2022 Nov 8;7(21):e140384. PMID: 36194494
Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing. Sci Immunol. 2022 Aug 5;7(74):eabm1664. PMID: 35930652
Specific in situ inflammatory states associate with progression to renal failure in lupus nephritis. J Clin Invest. 2022 Jul 1;132(13):e155350. PMID: 35608910
Positive and negative selection shape the human naive B cell repertoire.
2021
Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. Nat Commun. 2021 Jul 16;12(1):4372. PMID: 34272370
Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images. Am J Pathol. 2021 Oct;191(10):1693-1701. PMID: 34129842
Compartments and Connections Within the Germinal Center. Front Immunol. 2021 Mar 31;12:659151. PMID: 33868306
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 Jan;26(2):022910. PMID: 33420765
Cellular aspects of the pathogenesis of lupus nephritis. Curr Opin Rheumatol. 2021 Mar 1;33(2):197-204. PMID: 33394604
2020
Machine Learning to Quantify In Situ Humoral Selection in Human Lupus Tubulointerstitial Inflammation. Front Immunol. 2020 Nov 27;11:593177. PMID: 33329582
Control of Early B Cell Development by the RNA N6-Methyladenosine Methylation. Cell Rep. 2020 Jun 30;31(13):107819. PMID: 32610122
Antibodies in cerebral cavernous malformations react with cytoskeleton autoantigens in the lesional milieu. J Autoimmun. 2020 Sep;113:102469. PMID: 32362501
Novel specialized cell state and spatial compartments within the germinal center. Kennedy DE, Okoreeh MK, Maienschein-Cline M, Ai J, Veselits, M, McLean KC, Dhugana, Y, Wang, H, Peng, J, Chi, H, Mandal, M, Clark MR. Nat Immunol. 2020. Jun;21(6):660-670. PMID: 32341509
Kidney tissue hypoxia dictates T cell-mediated injury in murine lupus nephritis. Sci Transl Med. 2020 Apr 8;12(538):eaay1620. PMID: 32269165
Anti-vimentin antibodies: a unique antibody class associated with therapy-resistant lupus nephritis. Kinloch AJ, Cascino MD, Dai J, Bermea RS, Ko K, Vesselits M, Dragone LL, Mor Vaknin N, Legendre M, Markovitz DM, Okoreeh MK, Townsend MJ, Clark MR. Lupus. 2020;29(6):569-577. PMID: 32216516
2019
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage. Nat Commun. 2019 Oct 18;10(1):4768. PMID: 31628339
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis. Mandal M, Okoreeh MK, Kennedy DE, Maienschein-Cline M, Ai J, McLean KC, Kaverina N, Veselits M, Aifantis I, Gounari F, Clark MR. Nat Immunol. 2019 Oct;20(10):1393-1403. PMID: 31477919
Transcription factories in Igκ allelic choice and diversity. Karki S, Banerjee S, Mclean K, Dinner A, Clark MR. Adv Immunol. 2019;141:33-49. PMID: 30904132
Quantifying in situ adaptive immune cell cognate interactions in humans. Liarski VM, Sibley A, van Panhuys N, Ai J, Chang A, Kennedy D, Merolle M, Germain RN, Giger ML, Clark MR. Nat Immunol. 2019 Apr;20(4):503-513. PMID: 30778242
2018
BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. Nat Commun. 2018 Sep 24;9(1):3888. PMID: 30250168
Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. 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. Cell Rep. 2018 Aug 28;24(9):2443-2456. PMID: 30157436
PI3Kδ: Too much of a good thing. Kennedy DE, Clark MR. Nat Immunol. 2018 Sep;19(9):910-911. PMID: 30127436
In Situ Humoral Immunity to Vimentin in HLA-DRB1*03+ Patients With Pulmonary Sarcoidosis. Kinloch AJ, Kaiser Y, Wolfgeher D, Ai J, Eklund A, Clark MR, Grunewald J. Front Immunol. 2018 Jul 9;9:1516. PMID: 30038611
2017
Igβ ubiquitination activates PI3K signals required for endosomal sorting. Veselits M, Tanaka A, Chen Y, Hamel K, Mandal M, Kandasamy M, Manicassamy B, O’Neill SK, Wilson P, Sciammas R, Clark MR. J Exp Med. 2017 Dec 4;214(12):3775-3790. PMID: 29141870
EZH2 Regulates the Developmental Timing of Effectors of the Pre-Antigen Receptor Checkpoints. Jacobsen JA, Woodard J, Mandal M, Clark MR, Bartom ET, Sigvardsson M, Kee BL. Immunol. 2017 Jun 15;198(12):4682-4691. PMID: 28490575
2016
Bcl-2 as a Therapeutic Target in Human Tubulointerstitial Inflammation. 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. Arthritis Rheumatol. 2016 Nov;68(11):2740-2751. PMID: 27159593
Overview of pathophysiology and treatment of human lupus nephritis. Trotter K, Clark MR, Liarski VM. Curr Opin Rheumatol. 2016 Sep;28(5):460-7. PMID: 27341623
Self-reactive IgE exacerbates interferon responses associated with autoimmunity. Nat Immunol. 2016 Feb;17(2):196-203. PMID: 26692173
2015
The Pathogenesis and Therapeutic Implications of Tubulointerstitial Inflammation in Human Lupus Nephritis. Semin Nephrol. 2015 Sep;35(5):455-64. PMID: 26573548
Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nat Immunol. 2015 Oct;16(10):1094-103. PMID: 26301565
RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell. 2015 Aug 13;162(4):751-65. PMID: 26234156
2024
BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function. bioRxiv [Preprint]. Wright NE, Kennedy DE, Ai J, Veselits ML, Attaway M, Yoon YM, Durkee MS, Veselits J, Maienschein-Cline M, Mandal M, Clark MR. B. 2024 Apr 28:2024.04.25.591154. PMID: 38712068.
2023
Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell. 2023 Nov 22;186(24):5269-5289.e22. PMID: 37995656
BRWD1 orchestrates small pre-B cell chromatin topology by converting static to dynamic cohesin. Nat Immunol. 2023 Nov 20. doi: 10.1038/s41590-023-01666-z. PMID: 37985858
Molecular mechanisms insulating proliferation from genotoxic stress in B lymphocytes. Trends Immunol. 2023 Aug 10:S1471-4906(23)00134-5. Online ahead of print. PMID: 37573227
Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies. medRxiv. 2023 May 11:2023.05.08.23289640. PMID: 37214861
STAT3 signaling in B cells controls germinal center zone organization and recycling. Cell Rep. 2023 May 30;42(5):112512. PMID: 37200190
The endogenous repertoire harbors self-reactive CD4+ T cell clones that adopt a follicular helper T cell-like phenotype at steady state. Nat Immunol. 2023 Mar;24(3):487-500. PMID: 36759711
The ion transporter Na+-K+-ATPase enables pathological B cell survival in the kidney microenvironment of lupus nephritis. Sci Adv. 2023 Feb 3;9(5):eadf8156. PMID: 36724234
2022
IRF4 expression by lung dendritic cells drives acute but not Trm cell-dependent memory Th2 responses. JCI Insight. 2022 Nov 8;7(21):e140384. PMID: 36194494
Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing. Sci Immunol. 2022 Aug 5;7(74):eabm1664. PMID: 35930652
Specific in situ inflammatory states associate with progression to renal failure in lupus nephritis. J Clin Invest. 2022 Jul 1;132(13):e155350. PMID: 35608910
Positive and negative selection shape the human naive B cell repertoire.
2021
Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection. Nat Commun. 2021 Jul 16;12(1):4372. PMID: 34272370
Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images. Am J Pathol. 2021 Oct;191(10):1693-1701. PMID: 34129842
Compartments and Connections Within the Germinal Center. Front Immunol. 2021 Mar 31;12:659151. PMID: 33868306
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 Jan;26(2):022910. PMID: 33420765
Cellular aspects of the pathogenesis of lupus nephritis. Curr Opin Rheumatol. 2021 Mar 1;33(2):197-204. PMID: 33394604
2020
Machine Learning to Quantify In Situ Humoral Selection in Human Lupus Tubulointerstitial Inflammation. Front Immunol. 2020 Nov 27;11:593177. PMID: 33329582
Control of Early B Cell Development by the RNA N6-Methyladenosine Methylation. Cell Rep. 2020 Jun 30;31(13):107819. PMID: 32610122
Antibodies in cerebral cavernous malformations react with cytoskeleton autoantigens in the lesional milieu. J Autoimmun. 2020 Sep;113:102469. PMID: 32362501
Novel specialized cell state and spatial compartments within the germinal center. Kennedy DE, Okoreeh MK, Maienschein-Cline M, Ai J, Veselits, M, McLean KC, Dhugana, Y, Wang, H, Peng, J, Chi, H, Mandal, M, Clark MR. Nat Immunol. 2020. Jun;21(6):660-670. PMID: 32341509
Kidney tissue hypoxia dictates T cell-mediated injury in murine lupus nephritis. Sci Transl Med. 2020 Apr 8;12(538):eaay1620. PMID: 32269165
Anti-vimentin antibodies: a unique antibody class associated with therapy-resistant lupus nephritis. Kinloch AJ, Cascino MD, Dai J, Bermea RS, Ko K, Vesselits M, Dragone LL, Mor Vaknin N, Legendre M, Markovitz DM, Okoreeh MK, Townsend MJ, Clark MR. Lupus. 2020;29(6):569-577. PMID: 32216516
2019
B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage. Nat Commun. 2019 Oct 18;10(1):4768. PMID: 31628339
CXCR4 signaling directs Igk recombination and the molecular mechanisms of late B lymphopoiesis. Mandal M, Okoreeh MK, Kennedy DE, Maienschein-Cline M, Ai J, McLean KC, Kaverina N, Veselits M, Aifantis I, Gounari F, Clark MR. Nat Immunol. 2019 Oct;20(10):1393-1403. PMID: 31477919
Transcription factories in Igκ allelic choice and diversity. Karki S, Banerjee S, Mclean K, Dinner A, Clark MR. Adv Immunol. 2019;141:33-49. PMID: 30904132
Quantifying in situ adaptive immune cell cognate interactions in humans. Liarski VM, Sibley A, van Panhuys N, Ai J, Chang A, Kennedy D, Merolle M, Germain RN, Giger ML, Clark MR. Nat Immunol. 2019 Apr;20(4):503-513. PMID: 30778242
2018
BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. Nat Commun. 2018 Sep 24;9(1):3888. PMID: 30250168
Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. 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. Cell Rep. 2018 Aug 28;24(9):2443-2456. PMID: 30157436
PI3Kδ: Too much of a good thing. Kennedy DE, Clark MR. Nat Immunol. 2018 Sep;19(9):910-911. PMID: 30127436
In Situ Humoral Immunity to Vimentin in HLA-DRB1*03+ Patients With Pulmonary Sarcoidosis. Kinloch AJ, Kaiser Y, Wolfgeher D, Ai J, Eklund A, Clark MR, Grunewald J. Front Immunol. 2018 Jul 9;9:1516. PMID: 30038611
2017
Igβ ubiquitination activates PI3K signals required for endosomal sorting. Veselits M, Tanaka A, Chen Y, Hamel K, Mandal M, Kandasamy M, Manicassamy B, O’Neill SK, Wilson P, Sciammas R, Clark MR. J Exp Med. 2017 Dec 4;214(12):3775-3790. PMID: 29141870
EZH2 Regulates the Developmental Timing of Effectors of the Pre-Antigen Receptor Checkpoints. Jacobsen JA, Woodard J, Mandal M, Clark MR, Bartom ET, Sigvardsson M, Kee BL. Immunol. 2017 Jun 15;198(12):4682-4691. PMID: 28490575
2016
Bcl-2 as a Therapeutic Target in Human Tubulointerstitial Inflammation. 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. Arthritis Rheumatol. 2016 Nov;68(11):2740-2751. PMID: 27159593
Overview of pathophysiology and treatment of human lupus nephritis. Trotter K, Clark MR, Liarski VM. Curr Opin Rheumatol. 2016 Sep;28(5):460-7. PMID: 27341623
Self-reactive IgE exacerbates interferon responses associated with autoimmunity. Nat Immunol. 2016 Feb;17(2):196-203. PMID: 26692173
2015
The Pathogenesis and Therapeutic Implications of Tubulointerstitial Inflammation in Human Lupus Nephritis. Semin Nephrol. 2015 Sep;35(5):455-64. PMID: 26573548
Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nat Immunol. 2015 Oct;16(10):1094-103. PMID: 26301565
RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell. 2015 Aug 13;162(4):751-65. PMID: 26234156