Peer-Reviewed Journal Articles

Published in Internationally Recognized Peer-Reviewed Journals

LUPUS

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

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

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://journals.aai.org/jimmunol/article/210/1_Supplement/155.05/264956

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

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.

LuPRO® mobile app for Lupus

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, expected launch TBD

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

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

DERMATOLOGY

DermaGENE®, expected launch 2025
Psoriasis, Atopic Dermatitis, Scleroderma, Lupus

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

NEPHROLOGY

NephroGENE®, expected launch TBD
Lupus Nephritis and other Chronic Kidney Diseases

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

FIBROMYALGIA

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

CARDIOLOGY

CardioGENE®, open for co-development partner
Predicts early risk of serious heart attack or stroke

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)

ARTHRITIS

ArthroGENE®, open for co-development partner
Rheumatoid Arthritis, Osteoarthritis, Lupus Arthritis

2023 International consensus guidance for use of Tripterygium Wilfordii Hook F in the treatment of active rheumatoid arthritis
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

Utility of baseline transcriptomic analytis 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 Systemic Lupus Erythematosus 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

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

INFECTIONS

CovGENE®, market ready and open for commercialization partner
Predicts life-threatening disease as well as long-COVID

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.

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