Peer-Reviewed Journal Articles
Published in Internationally Recognized Peer-Reviewed Journals
Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications
Molecular mechanisms governing the progression of nephritis in lupus prone mice and human lupus patients
Altered expression of genes controlling metabolism characterizes the tissue response to immune injury in lupus
The pathogenesis of systemic lupus erythematosus: Harnessing big data to understand the molecular basis of lupus
Deconvoluting the heterogeneity of SLE: The contribution of ancestry
Analysis of Trans-Ancestral SLE Risk Loci Identifies Unique Biologic Networks and Drug Targets in African and European Ancestries
Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry
COVID-19 Patients Exhibit Unique Transcriptional Signatures Indicative of Disease Severity
Transcriptomics data: pointing the way to subclassification and personalized medicine in systemic lupus erythematosus
Molecular endotypes of type 1 and type 2 SLE
Medelian Randomization and Pathway Analysis Demonstrate Shared Genetic Associations Between Systemic Lupus Erythematosus and Coronary Artery Disease
Machine learning reveals distinct gene signature profiles in lesional and nonlesional regions of inflammatory skin diseases
AMPEL Relationships in Lupus, Derm, RA, IBD, Nephritis
Patient Stratification Optimizes Drug Development & Cell Therapy Treatments
Sanofi – Derm
Confirmation of AMPEL’s ability to predict drug responders
S. Shrotri, A. Daamen, P. Bachali, A. Grammer and P. Lipsky
Blood gene expression reveals endotypes of atopic dermatitis patients with distinct responses to Dupilumab (Dupixent, FDA approved for AD)
J Invest Derm 145: 98, 2025
Avalo – Derm
Confirmation of AMPEL’s ability to predict drug responders
Integrative Transcriptomic Profiling Identifies a Dominant Macrophage-Derived IL-1ß/NLRP3 Inflammasome Axis in HS (Hidradenitis Suppurativa)
J. Invest. Derm, in press.
Lilly – Lupus
Confirmation of AMPEL’s ability to predict drug responders
P.Bachali, A. Grammer and P.E. Lipsky
Subsets of patients with Lupus identified by gene expression profiles exhibit differential clinical responsiveness to Baricitinib
Arthritis Rheum 10:1002, 2026.
AMPEL’s Technology Enriched for Baricitinib Responders in the Ph2 Trial
Lilly PMWC2024 presentation – View Video
P. Bachali, A. Grammer and P. Lipsky.
Identification of subsets of systemic lupus erythematosus patients responsive to baricitinib targeting JAK1,2 by transcriptomic analysis at baseline.
Arthritis Rheumatol. 75: 9, 2023.
BMS/Celgene – Lupus & Derm
Confirmation of AMPEL’s ability to predict drug responders
P. Bachali, A. Daamen, S. Korish, Y. Hu, P. Schafer, A. Grammer and P.E. Lipsky
Responsiveness of SLE to Iberdomide based on molecular endotypes
Ann Rheum Dis 84: 1001, 2025
V.P. Werth, J.T. Merrill, R. Furie, T. Dorner, R. van Vollenhoven, P. Lipsky . . .N. Delev
Effect of Iberdomide on cutaneous manifestations of SLE: a randomized Ph2 trial
J Amer Acad Derm 92:425, 2025.
AMPEL’s Technology Enriched for Iberdomide Responders in the Ph2 Trial
BMS PMWC2024 presentation – View Video
P. Bachali, Y. Hu, N. Delev, P. Schafer and P. Lipsky
Identification of subsets of SLE patients responsive to Iberdomide by transcriptomic analysis of baseline samples
Ann. Rheum. Dis. 10:4878, 2023.
P.E. Lipsky, R. van Vollenhoven, T. Doerner, V.P. Werth, J.T. Merrill, R. Furie, M. Petronijevic, B.V. Zamora, M. Majdan, F. Irazoque-Palazuelos, R. Terbrueggen, N. Delev, M. Weiswasser, S. Korish, M. Stern, S. Hersey, Y. Ye, A. Gaudy, Z. Liu, R. Gagnon, S. Tang and P.H. Schafer
The biological impact of Iberdomide in patients with active Systemic Lupus Erythematosus
Ann. Rheum. Dis. 10:1136, 2022.
Werth, J. Merrill, R. Furie, T. Dorner, R. van Vollenhoven, P. Lipsky, M. Weiswasser, S. Korish, P. Schafer, M. Stern, Z. Liu, S. Tang and N. Delev
Effect of Iberdomide on cutaneous manifestations in SLE: results of a 24-week, placebo-controlled, Phase 2 study
Ann.Rheum.Dis. 80: 76, 2021.
P.E. Lipsky, R. van Vollenhoven, T. Doerner, V. Werth, J. Merrill, R. Furie . . .and P. Schafer
Iberdomide decreases B cells and plasmacytoid DCs, increases regulatory T cells and IL2, and has enhanced clinical efficacy in active systemic lupus erythematosus patients with high aiolos or the IFN gene expression signature
Arthritis Rheumatol.2020; 72 (suppl 10).
UCB/Biogen – Lupus & Derm
Confirmation of AMPEL’s ability to predict drug responders
C. Gunther, P. Lipsky . . .T. Carlile, J.D. Jaffe, J.A. Hurt, S. Treusch, T.L. Reynolds, M.K. Moseley, M.L. Broz and J.M. Kahlenberg.
Characterization of Litifilimab Treatment Response in Patients with Cutaneous Lupus Erythematosus using RNASeq from Lilac Ph2b blood samples
J European Academy Dermatology V, in press.
I.Cutcutache, A.S. Powelesland . . . P.E. Lipsky, A. Skowera and C. Stach
Dapriolizumab Pegol impacts important immunologic pathways in SLE: pharmacodynamic analysis of B cell and Type I IFN pathways from a Ph2B trial
Ann Rheum Dis 83: 334, 2025.
I. Cutcuache, A.S. Powlesland, A. Skelton . . .P. Lipsky, A. Skowera and C. Stach.
Dapirolizumab pegol targeting CD40-ligand impacts important immunologic pathways in systemic lupus erythematosus: pharmacodynamic analysis of B cell and type I
Ann. Rheum. Dis 83:265, 2024.
UCB & Biogen Announce Publication in Lancet of Positive Dapirolizumab Pegol Ph3 Results in SLE
AMGEN/Horizon – Lupus
J. Zent, K. Bell, B. William, P. Bachali and P. Lipsky
Unsupervised Clustering of Lupus Patient-Reported Outcome Data Identifies Patient Groups with Differences in SLEDAI and Physician Global Assessment
Arthritis Rheumatol. 74: 1473, 2022.
K. Bell, C. Dykas, B. Muckian, B. Williams, H. Rainey, M. Comberg, M. Mora, K.A. Owen and P.E. Lipsky
Patient-Reported Outcome Information Collected from Lupus Patients Using a Mobile Application: Compliance and Validation
ACR Open Rheumatology, 2021.
AMPEL BioSolutions, Horizon, and Lupus Research Alliance Partner on Unique Clinical Trial for Patients with Lupus
https://www.pharmaadvancement.com/drug-development/clinical-trials/ampel-biosolutions-horizon-pharma-plc-and-lupus-research-alliance-partner-on-unique-clinical-trial-for-patients-with-lupus/
Janssen/Johnson&Johnson – Lupus
Confirmation of AMPEL’s scoring system to predict drugs for Lupus
R.F. van Vollenhoven, B.H. Hahn, G.C. Tsokos, P. Lipsky, R.M. Gordon, K. Fei, H. Lo, M. Chevrier, S. Rose, P. Berry, Z. Yao, C.S. Karyekar, Q. Zuraw
Efficacy and Safety of Ustekinumab in Patients With Active Systemic Lupus Erythematosus: Results of a Phase II Open-label Extension Study.” J. Rheumatology 49(4): 380-387, 2022.
R.F. van Vollenhoven, B.H. Hahn, G.C. Tsokos, P.E. Lipsky, K. Fei, R.M. Gordon, I. Gregen, K.M. Lo, M. Chevrier and S. Rose
Maintenance of Efficacy and Safety of Ustekinumab Through One Year in a Phase II Multicenter, Prospective, Randomized, Double-Blind Placebo-Controlled Crossover Trial of Patients with Active SLE
Arthritis Rheum. 72:761, 2020.
R.F. van Vollenhoven, B.H. Hahn, G.C. Tsokos, C.L. Wagner, P.E. Lipsky, Z. Touma, V.P. Werth, R.M Gordon, B. Zhou, B. Hsu, M. Chevrier, M. Triebel, J.L. Jordan and S. Rose
Efficacy and safety of ustekinumab, an IL-12 and IL-23 inhibitor, in patients with active systemic lupus erythematosus: results of a multicentre, double-blind, phase 2, randomised, controlled study.
Lancet 392:1330, 2018.
AMPEL’s System For Drug Repositioning Confirmed By Success Of Phase 2 Trial Of Stelara In Lupus
Virginia Catalyst Grant for LuGENE – Lupus
A. Daamen, C. Rival, M. Mandal, S. Jean, A. Grammer, L. Erickson and P.E. Lipsky
Dual BAFF and APRIL inhibition with TACI.Fc depletes IgA plasma cells and ameliorates Lupus Nephritis
iScience, in press 2026.
R. Alajoleen, A. Daamen, P. Timilesena, S. Li, P.E. Lipsky and X.M. Luo
Single-cell RNA sequencing analysis reveals disease stage-dependent transcriptomic profiles of regulatory B cells in Systemic Lupus Erythematosus
J. Immunol. 210: 15505, 2024
A. Daamen, R. Alajoleen, A. Grammer, X.M. Luo and P.E Lipsky
Lupus: scRNA-Seq analysis reveals heterogeneity of IL10 producing regulatory B cells
Frontiers Immunol 14: 128770, 2023
J. Wilson, J. Wei, A. Daamen, C. Mayberry, A. Grammer, P. Lipsky, D. Roopenian and C.-H. Chang
Unveiling metabolic vulnerabilities in Lupus B cells: targeting BCMA and glucose dependency for therapeutic strategies
Lupus Sci & Med 11:1136, 2023
CAR-T Cells
Peter E Lipsky, Andrea R Daamen
Potential and pitfalls of repurposing the CAR-T cell regimen for the treatment of autoimmune disease
Ann. Rheum. Dis. 83:, 696, 2024.
NIH: Lupus Stem Cell Transplantation (autologous)
Sencer Goklemez, S. Hasni, F.T. Hakim . .. G.G. Illei, P.E. Lipsky and S.Z. Pavletic
Long-term follow-up after lymphodepleting autologous haematopoietic cell transplantation for treatment-resistant SLE
Rheumatology 61:3317-3328, 2022. | https://clinicaltrials.gov/ct2/show/NCT00076752
Pfizer
Confirmation of AMPEL’s ability to validate drug targets
M.D. Catalina, P. Bachali, N.S. Geraci, A.C. Grammer and P.E. Lipsky
Gene Expression Analysis Delineates the Potential Role of Multiple Interferons in Systemic Lupus Erythematosus
Nature Communications Biology 2:140, 2019
Astra Zenaca – Lupus
Background paper for Anifrolumab (2021 FDA approval for Lupus)
R.W. Maul, M.D. Catalina, V. Kumar, P. Bachali, A.C. Grammer, S. Wang, W. Yang, S. Hasni, R. Ettinger, P.E. Lipsky and P.J. Gearhart
Transcriptome and IgH Repertoire Analyses Show that CD11chi B Cells Are a Distinct Population with Similarity to B Cells Arising in Autoimmunity and Infection
Frontiers in Immunology 12:649458, 2021.
Aker BioPharma – Lupus
J. Salmon, D. Wallace, V. Rus, A. Cox, C. Dykas, B. Williams, Y. Ding, P.-A. Hals, L. Johnsen and P.E. Lipsky.
Correction of omega-3 fatty acid deficiency and improvement in disease activity in patients with systemic lupus erythematosus treated with krill oil concentrate: a multicentre, randomised, double-blind, placebo-controlled trial
Lupus Science & Medicine 11:e001201, 2024.
J.E. Salmon, D.J. Wallace, V. Rus and P. Lipsky
Correction of omega-3 fatty acid deficiency and improvement in disease activity in SLE patients treated in a concentrated extract of krill oil
Ann. Rheum. Dis. 82:1467, 2024.
Lupus Research Alliance (formerly ALR and LRI)
Dr. Lipsky Reports Positive Results LuCIN-LRA studies at ACR & EULAR
- https://www.lupusresearch.org/two-lupus-therapeutics-studies-report-positive-results-at-2019-acr-arp-annual-meeting/
- https://www.lupusresearch.org/value-study-results-reported-at-eular/
NYU-AMPEL-LRA collaboration expands the landscape of Lupus Clinical Trials
AMPEL leads outcome measure development for Lupus (rescue failed trials)
Abrahamowicz, M.I. Abrahamowicz and P.E. Lipsky
External Validation of the Lupus Multivariable Outcome Score (LuMOS®) for Systemic Lupus Erythematosus Trials
Open Rhematology 8:1-8, 2022.
Abrahamowicz, J.M. Sedalia, R. Goldman-Ramsey, L.S. Simon, V. Strand and P.E. Lipsky
Development of a novel evidence-based LuMOS for clinical trials
Arthritis and Rheumatism 70:1450, 2018
Abrahamowicz and P.E. Lipsky
Validation of a LuMOS® as an outcome measure for SLE trials
Lupus Science & Medicine 8:1136, 2021.
Pre-Clinical Animal Models for Drug Development – Lupus, Derm, OA/RA, Infection
Hospital for Special Surgery NYC – Derm
T.M. Li, V. Zyulina, E.S. Seltzer, M. Dacic, Y. Chinenov, A. Daamen. . .P.E. Lipsky and T. Lu,
Interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in Lupus
eLife 13:e85914, 2024.
Feinstein Institutes for Med Research, NYC – Arthritis
K.Gu, R. Robl, I. Rector, A Grammer and P. Lipsky
Novel gene expression analysis documents significant differences in Osteoarthritis Cartilage based on presence of mutations in ALDH1A2
Rheumatol 51: 46, 2024
UCSF – Lupus
I. Rector, K.A. Owen, P. Bachali, E. Hubbard, J. Yazdany, M. Dall’era, A.C. Grammer and P.E. Lipsky
Differential regulation of the interferon response in Lupus distinguishes patients of Asian ancestry
RMD Open 9:e003475, 2023.
University of Virginia – Lupus
A.R. Daamen, H.W. Wang, P. Bachali, N. Shen, K.M. Kingsmore, R.D. Robl, A.C. Grammer, S.M. Fu, and P.E. Lipsky
Molecular mechanisms governing the progression of nephritis in lupus-prone mice and human lupus patients
Frontiers in Immunology 14:1147526, 2023.
Preprint: https://lupus.bmj.com/content/9/Suppl_3/A78
Wang, N. Geraci, P. Bachali, B. Kegerreis, M. Catalina, E. Hubbard, S.S. Sung, F. Gaskin, A. Grammer, P. Lipsky and S.M. Fu
Glomerular and Tubular Transcriptional Profiles Reveal Gene Clusters Specific for Different Stages of Glomerulonephritis in NZM2328 Mice
Arthritis Rheumatol. 70:10, 2018
Jackson Labs/Tufts University – Lupus
A.R. Daamen, C. Chang, D.C. Roopenian, A.C. Grammer and P.E. Lipsky
Transcriptomic analysis reveals a critical regulatory role for CD8 T cells in a mouse model of SLE
Lupus Science & Medicine 8: 1136, 2021.
https://lupus.bmj.com/content/8/Suppl_2/A6.2.abstract
U. Mass-Chan & GWU-DC – Lupus
T. Dawson, K. Crandall and P. Lipsky
Dysregulated HERV expression in Systemic Lupus Erythematosus binds cytoplasmic RNA resulting in a inflammatory positive feedback loop
Rheumatol 52: 137, 2025
Sun, Z. Liu . . . N. Stearrett, K. A. Crandall, P. Bachali, A.C. Grammer and P.E. Lipsky
Abnormalities in intron retention characterize patients with Systemic Lupus Erythematosus
Nature Sci Reports 13: 5141, 2023
N. Stearrett, T. Dawson, A. Rahnvard, P. Bachali, M.L. Bendall, C. Zheng, R. Caricchio, M. Perez-Losada, A.C. Grammer, P.E. Lipsky and K.A. Crandall
Expression of human endogenous retroviruses in Systemic Lupus Erythematosus: multiomic integration with gene expression
Frontiers Immunol 12: 661437, 2021
Virginia Tech – Lupus, Infection, Metabolic/Wellness, Microbiome
M. Hameed, P. Rai, M Shakhawat-Hossain, S Coutermarsh-Ott, A. Daamen, PE Lipsky and J Weger-Lucarelli
G-CSF protects against arthritogenic alphavirus pathogenesis in a type I IFN-dependent manner
Frontier Immunol 16: 1606053, 2025.
M. Hameed, A.R. Daamen, M Shakhawat-Hossain, S Coutermarsh-Ott, PE Lipsky and J Weger-Lucarelli
Obesity-associated changes in immune cell dynamics during Alphavirus infection revealed by single cell transcriptomic analysis
Preprint bioRxiv 2024
P. Rai, J.M. Marano, L. Kang, S. Coutermarsh-Ott, A. Daamen, P.E. Lipsky and J. Weger-Lucarelli
Obesity fosters severe disease outcomes in a mouse model of cornovirus infection associated with transcriptomic abnormalities
J. Med. Virol. 96: e29587, 2024
D.N. Oakland, M. Appiah, J. Zhu, P. Lipsky and X.M. Luo
Bacterial DNA mediated protection from Systemic Lupus Erythematosus
J. Immunol. 210: 7716, 2023.
Abdelhamid, R. Alajoleen, K.M. Kingsmore, X. Cabana-Puig, R. Lu, J. Zhu, J.C. Testerman, Y. Li, A.C. Ross, T. E. Cecere, C.M. Reilly, A.C. Grammer, P.E. Lipsky and X.M. Luo
Hypovitaminosis A Drives the Progression of Tubulointerstitial Lupus Nephritis through Potentiating Predisease Cellular Autoreactivity
Immunohorizons 7:17, 2023.
M. Appiah, D.N. Oakland, J. Zhu, X. Cabana-Puig, R. Lu, R. Alajoleen, C. Armstrong, D. Xu, C.M. Reilly, A.C. Grammer, M.J. Shlomchik, P.E. Lipsky and X.M. Luo
Bacterial DNA induces regulatory B cells and attenuates lupus through a B cell-extrinsic, TLR9-dependent mechanism
Lupus Science and Medicine 9:1303, 2022.
Mu, B.K. Swartwout, X.C. Puig, J. Grieco, T.E. Cecere, H. Wang, C. Puglisi, C.M. Reilly, A.C. Grammer, P.E. Lipsky*, X.M. Luo* (*co-corresponding authors)
Gut microbiota and bacterial DNA suppress autoimmunity by stimulating regulatory B cells in a murine model of lupus
Frontiers in Immunology 11:593353, 2020.
J. Ren*, M. Catalina*, K. Eden, X. Liao, K. Read, X. Luo, R. McMillan, M. Hulver, M. Jarpe, P. Bachali, A. Grammer, P. Lipsky and C. Reilly (*co-first authors)
Selective HDAC6 inhibition normalizes B cell activation and germinal center formation in SLE
Frontiers in Immunology 10:2512, 2019.
Ren, E. Panther, X. Liao, A.C. Grammer, P.E. Lipsky and C.M. Reilly
The impact of protein acetylation/deacetylation on systemic lupus erythematosus
Int. J. Molec. Sci. 19: E4007, 2018.