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
LUPUS
LuGENE® blood test for Lupus
(LuGENE® blood test & LuPRO® mobile app )
LuGENE® 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?
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, 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
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
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/
LuGENE-Dx® for Lupus, expected launch TBD
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
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 Q3 2024
Lupus, Psoriasis, Atopic Dermatitis, Scleroderma
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
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 Pharma Partnering
Lupus Arthritis, Rheumatoid Arthritis, Osteoarthritis
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
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.
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 bioRxiv. 2020 Jun 2: 2020.05.28.121889. doi: 10.1101.2020.05.28.121889.