Lupus Flare Forecast & Abnormal Drug Target Prediction
(LuGENE^® blood test & LuPRO^® mobile app )

LuGENE^® Prognostic blood test for Lupus (“potentially revolutionary”, Lupus Foundation of America)

Validation of eight endotypes of lupus based on whole-blood RNA profiles
Lupus Sci Med 12:e001526, 2025.
https://lupus.bmj.com/content/12/1/e001526

Genes causative of PID are risk factors for and are over-expressed in systemic lupus erythematosus
Frontiers in Immunol 17: 1494343, 2025.
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2026.1494343/full

Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications
Genome Medicine 14: 84, 2023.
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01237-9

Machine learning to determine the endotype of SLE patients: a validation study
Lupus Sci Med 11:1136, 2024.
https://lupus.bmj.com/content/11/Suppl_2/A100

Validation of a Transcriptomic-Based Machine Learning Model to Establish the Endotype of SLE Patients. 
Arthritis Rheum 75:9, 2023.
https://acr23.eventscribe.net/fsPopup.asp?PresentationID=1324897&mode=presInfo

An interpretable machine learning pipeline based on transcriptomics predicts phenotypes of lupus patients
iScience 26 (10): 108042, 2023.
https://www.cell.com/iscience/fulltext/S2589-0042(23)02119-3?

Single-cell RNA sequencing analysis reveals disease stage-dependent transcriptomic profiles of regulatory B cell in Systemic Lupus Erythematosus
J. Immunol. 210: 15505, 2023.
https://academic.oup.com/jimmunol/article-abstract/210/Supplement_1/155.05/7946433?redirectedFrom=fulltext

Identification of subsets/endotypes of SLE patients responsive to Iberdomide by transcriptomic analysis of baseline samples
Ann. Rheum. Dis. 10:4878, 2023.
https://ard.bmj.com/content/82/Suppl_1/387.2

Glucose oxidation-dependent survival of activated B cells provides a putative novel therapeutic target for lupus treatment.
iScience 26: 107487, 2023.
https://www.sciencedirect.com/science/article/pii/S258900422301564X

Differential regulation of the interferon response in SLE distinguishes patients of Asian ancestry
RMD Open 9:e003475, 2023.
https://rmdopen.bmj.com/content/9/3/e003475.abstract

The Molecular Endotypes of Type1 and Type2 Lupus
Lupus Science & Medicine 0:e00861, 2023.
https://lupus.bmj.com/content/10/1/e000861.full

Recent advances in the use of machine learning and artificial intelligence to improve diagnosis, predict flares and enrich trials in lupus
Curr Opin Rheum 32, 2022.
https://pubmed.ncbi.nlm.nih.gov/36001343/

Anti-RNP antibodies are associated with the interferon gene signature but not decreased complement levels in SLE
Ann Rheum Dis 81:632, 2022.
http://dx.doi.org/10.1136/annrheumdis-2021-221662

Transcriptomics data: Pointing the way to subclassification and personalized medicine in SLE
Current Opinion in Rheumatology 33: 579, 2021.
https://pubmed.ncbi.nlm.nih.gov/34410228/

The pathogenesis of systemic lupus erythematosus: harnessing Big Data to understand the molecular basis of lupus
J. Autoimmunity 110:102359-102369, 2020.
https://pubmed.ncbi.nlm.nih.gov/31806421/

Current Status of the Evaluation and Management of Lupus Patients with Future Prospects
Frontiers in Medicine 8: 682544, 2021.
https://www.frontiersin.org/articles/10.3389/fmed.2021.682544/full

Deconvoluting the heterogeneity of SLE: the contribution of ancestry
J. Aller. and Clin. Immunol., 2021.
https://doi.org/10.1016/j.jaci.2021.11.005

Patient  ancestry significantly contributes to molecular heterogeneity of Systemic Lupus Erythematosus
JCI Insights 5(15) e140380, 2020.
10.1172/jci.insight.140380.

Biomarkers as entry criteria for clinical trials of new therapies for systemic lupus erythematosus
Arthritis and Rheumatism 69:487, 2017.
https://onlinelibrary.wiley.com/doi/epdf/10.1002/art.40008

Identification of alterations in macrophage polarization associated with disease activity in systemic lupus erythematosus
PLoS One 13(12):e0208132, 2018.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208132

Molecular Characterization of Circulating Plasma Cells in Patients with Active Systemic Lupus Erythematosus
PLoS One 10: e0044362, 2013.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044362

LuPRO^® mobile app for Lupus

P.E. Lipsky, A.C. Grammer and K. Bell
Systems and methods for analysis of Patient-Reported Outcome Data
https://patents.google.com/patent/US20250006370A1/en

Unsupervised Clustering of Lupus Patient-Reported Outcome Data Identifies Patient Groups with Differences in SLEDAI and Physician Global Assessment
Arthritis Rheumatol. 74: 1473, 2022.
https://acrabstracts.org/abstract/unsupervised-clustering-of-lupus-patient-reported-outcome-data-identifies-patient-groups-with-differences-in-sledai-and-physician-global-assessment/

Patient-Reported Outcome Information Collected from Lupus Patients Using a Mobile Application: Compliance and Validation
ACR Open Rheumatology, 2021.
https://doi.org/10.1002/acr2.11370

LuGENE-Dx^® for Lupus

Examination of the shared genetic architecture between MS and SLE facilitates discovery of novel lupus risk loci
Hum. Genetics. 143: 703, 2024.
https://link.springer.com/article/10.1007/s00439-024-02672-3

An interpretable machine learning pipeline based on transcriptomics predicts phenotypes of lupus patients
iScience 26 (10): 108042, 2023.
https://www.cell.com/iscience/fulltext/S2589-0042(23)02119-3?

Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry
Nature Sci. Rep., 2023.
https://www.nature.com/articles/s41598-023-32569-6

Differential regulation of the interferon response in SLE distinguishes patients of Asian ancestry
RMD Open 9:e003475, 2023.
https://rmdopen.bmj.com/content/9/3/e003475.abstract

Analysis of Trans-Ancestral SLE Risk Loci Identifies Unique Biologic Networks and Drug Targets in African and European Ancestries
Am. J. Human Genetics 107:1-18, 2020.
doi.org/10.1016/j.ajhg.2020.09.007

DermaGENE®
Psoriasis, Atopic Dermatitis, Scleroderma, Lupus, Hidradenitis suppurativa, Alopecia areata, Vitiligo

Comprehensive transcriptomic analysis of atopic dermatitis patients documents the spectrum of molecular abnormalities and the response to treatment
J Investigative Derm, in press.
Preprint at bioRxiv 04.709610, 2026.
https://www.biorxiv.org/content/10.64898/2026.03.04.709610v1.full

A.Daamen, J. Hamdan, A. Grammer and P. Lipsky
Delineation of skin barrier abnormalities in atopic dermatitis and psoriasis
J Invest Derm 144: 64, 2024

Transcriptomic analysis identifies disease severity and therapeutic response in psoriasis
JID Innovations 2: 100333, 2024
https://www.jidinnovations.org/article/S2667-0267(24)00081-X/fulltext

S.Shrotri, K. Allison, P. Bachali, A. Grammer and P. Lipsky
Heterogeneity of psoriatic skin identified by a novel transcriptomic based psoriasis cell and immune score (PsoriaCIS)
J Invest Derm 144: 58, 2024

Machine learning reveals distinct gene expression profiles in lesional and nonlesional regions of inflammatory skin diseases
Science Advances 8: 4776, 2022.
https://www.science.org/doi/10.1126/sciadv.abn4776

Altered expression of genes controlling metabolism characterizes  the tissue response to immune injury in Lupus
Nature Scientific Reports 11: 14789, 2021.
https://www.nature.com/articles/s41598-021-93034-w

NephroGENE®, in discussion for licensing, co-development and/or partnering
Lupus Nephritis, IgA Nephropathy and other Chronic Kidney Diseases

Linking transcriptomic profiles of kidney and blood samples provides insight into identification of lupus nephritis
J. Rheum 52:51, 2025.
https://www.jrheum.org/content/52/Suppl_1/51.2.abstract

Relating transcriptomic profiles of human lupus nephritis and glomerulonephritis in lupus-prone mice
J. Rheum. 52:85, 2025.
https://www.jrheum.org/content/52/Suppl_1/85.1.abstract

An NTE5E loss-of-function variant permits tissue inflammation and hypertension in SLE
iScience 29: 116017, 2026.
https://www.sciencedirect.com/science/article/pii/S2589004226013921

The role of adenosine receptor modulation in SLE disease progression
J Immunol 214:1763, 2025.
https://academic.oup.com/jimmunol/article/214/Supplement_1/vkaf283.1763/8331011

Testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis
Briefings in Bioinformatics 24:322, 2023.
https://academic.oup.com/bib/article/24/5/bbad322/7260519

Molecular mechanisms governing the progression of nephritis in lupus-prone mice and human lupus patients
Frontiers in Immunology 14:1147526, 2023.
https://www.frontiersin.org/articles/10.3389/fimmu.2023.1147526/full
Preprint https://lupus.bmj.com/content/9/Suppl_3/A78

Altered expression of genes controlling metabolism characterizes  the tissue response to immune injury in Lupus
Nature Scientific Reports 11: 14789, 2021.
https://www.nature.com/articles/s41598-021-93034-w

FibroGENE®, in discussion for licensing, co-development and/or partnering
Diagnostic for Fibromyalgia with decision support for drug options

Pain in systemic lupus erythematosus: emerging insights and paradigms
Nature Rev Rheum 21: 626, 2025.
https://www.nature.com/articles/s41584-025-01290-1

Nociplasticity: a proposed concept to understand the symptomatology of SLE
Arthritis and Rheum 77:966, 2025.
https://acrjournals.onlinelibrary.wiley.com/doi/10.1002/art.43152

Assessment of Fibromyalgia with and without the background of Lupus
R.D. Robl, A.M. Eudy, P.S. Bachali, J.L Rogers, M.E.B. Clowse, D.S. Pisetsky and P.E. Lipsky,
The Molecular Endotypes of Type1 and Type2 Lupus
Lupus Science & Medicine 0:e00861, 2023.
https://lupus.bmj.com/content/10/1/e000861.full

CardioGENE®,  in discussion for licensing, co-development and/or partnering
Predicts risk and drug options for CAD/CVD

Genetic Association with Autoimmune Diseases Identifies Molecular Mechanisms of Coronary Artery Disease
iScience 27 (9): 110715, 2024
https://www.cell.com/iscience/fulltext/S2589-0042(24)01940-0

Medelian Randomization and Pathway Analysis Demonstrate Shared Genetic Associations Between Systemic Lupus Erythematosus and Coronary Artery Disease
Cell Reports Medicine 3: 100805, 2022
http://doi.org/10.1016/j.xcrm.2022.100805

Commentary on N. Gao et. al. “Systemic Lupus Erythematosus and Cardiovascular Disease: A Mendelian Randomization Study.”
Frontiers Immunology 13: 1075400, 2022.
www.frontiersin.org/articles/10.3389/fimmu.2022.908831/full)

ArthroGENE®
Rheumatoid Arthritis, Osteoarthritis, Lupus Arthritis
Decision support for drug options

Utility of baseline transcriptomic analysis of RA Synovium as an indicator for long-term clinical outcomes
Frontiers in Medicine 10:3889, 2022.
https://www.frontiersin.org/articles/10.3389/fmed.2022.823244/full

Single-cell sequencing of immune cells from anticitrullinated peptide antibody positive and negative rheumatoid arthritis
Nature Communications 12:4977, 2021.
https://www.nature.com/articles/s41467-021-25246-7

Analysis of Gene Expression from SLE, RA, OA, Synovium Reveals a Profile of Activated Immune Cells and Inflammatory Pathways
Nature Scientific Reports 10:71361, 2020.
https://www.nature.com/articles/s41598-020-74391-4

Can we cure rheumatoid arthritis?
Curr Opin Immunol 94: 102561, 2025.
https://www.sciencedirect.com/science/article/pii/
S0952791525000378

2023 International consensus guidance for use of Tripterygium Wilfordii Hook F in the treatment of active rheumatoid arthritis
J. Autoimmunity 142:103148, 2023.
https://doi.org/10.1016/j.jaut.2023.103148

Efficacy and safety of Tripterygium Wilfordii Hook F plus TNF inhibitor for active rheumatoid arthritis (a multicenter, randomized, double-blind, triple-dummy controlled trial)
Clinical Immunology 255:109749, 2023.
https://www.sciencedirect.com/science/article/abs/pii/S1521661623005120

Nurse-like cells in rheumatoid arthritis: Formation of survival niches cooperating between the cell types
Mod Rheumatol. 29:401, 2019.
https://doi.org/10.1080/14397595.2018.1483305

Induction of sustained remission in early inflammatory arthritis with the combination of infliximab  (TNF biologic) plus methotrexate: the DINORA trial
Arthritis Res. Ther. 20:174. 2018.
https://doi.org/10.1186/s13075-018-1667-z

Comparison of the impact of Tripterygium wilfordii Hook F and Methotrexate treatment on radiological progression in active rheumatoid arthritis: 2-year follow up of a randomized, non-blinded, controlled study
Arthritis Res. Ther. 20:70, 2018.
10.1186/s13075-018-1563-6

Comparison of Tripterygium wilfordii Hook F with methotrexate in the treatment of active rheumatoid arthritis (TRIFRA): a randomised, controlled clinical trial.
Ann. Rheum. Dis. 74:1078, 2014.
doi: 10.1136/annrheumdis-2013-204807

Blood Test Market Ready and Open for Commercialization Partner
COVID used as proof-of-concept but test is applicable across infections

March 2023: CovGENE^® is a market-ready blood test measuring twenty human genes (mRNAs) that predicts patients who may progress to life-threatening disease

A.R. Daamen, P. Bachali, A.C. Grammer and P.E. Lipsky
Classification of COVID-19 Patients into Clinically Relevant Subsets by a Novel Machine Learning Pipeline Using Transcriptomic Features
International Journal of Molecular Sciences 24: 4905, 2023
https://www.mdpi.com/1422-0067/24/5/4905

September 2022: Clinical validation/utility study with data from three independent sites confirms CovGENE^® predicts patients who may progress to life-threatening disease

A.R. Daamen, P. Bachali, C.A. Bonham, L. Somerville, J.M Sturek, A.C. Grammer, A. Kadl and P.E Lipsky
COVID-19 Patients Exhibit Unique Transcriptional Signatures Indicative of Disease Severity
Frontiers Immunology 13: 989556, 2022.
https://www.frontiersin.org/articles/10.3389/fimmu.2022.989556/full

June2020-March 2021: Proof-of-Concept (Blood of COVID patients predict severity of disease course (lung and brochiolar lavage)

A.R. Daamen, P. Bachali, K.A. Owen, K.M. Kingsmore, E.L. Hubbard, A.C. Labonte, R. Robl, S. Shroti, A.C. Grammer and P.E. Lipsky.
Comprehensive transcriptomic analysis of COVID-19 Blood, Lung and Airway
Nature Scientific Reports 11:7052, 2021
https://www.nature.com/articles/s41598-021-86002-x
Preprint in bioRxiv. 2020 Jun 2: 2020.05.28.121889. doi: 10.1101.2020.05.28.121889.

NeuroGENE®, in discussion for licensing, co-development and/or partnering

S. Kerns, K.A. Owen, D. Schwalbe, A.C. Grammer and P.E. Lipsky
Examination of shared architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel risk loci
Human Genetics 143: 703, 2024