Peer-Reviewed Journal Articles
Published in Internationally Recognized Peer-Reviewed Journals
Molecular mechanisms governing the progression of nephritis in lupus prone mice and human lupus patients
Machine learning reveals distinct gene signature profiles in lesional and nonlesional regions of inflammatory skin diseases
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
COVID-19 Patients Exhibit Unique Transcriptional Signatures Indicative of Disease Severity
Medelian Randomization and Pathway Analysis Demonstrate Shared Genetic Associations Between Systemic Lupus Erythematosus and Coronary Artery Disease
Transcriptomics data: pointing the way to subclassification and personalized medicine in systemic lupus erythematosus
Molecular endotypes of type 1 and type 2 SLE
Technology Papers
AMPEL Genomic Platform (AGP®) Bioinformatic Tools and Machine Learning Analytics
Sun, Z. Liu, A. Li, Z. Zeng, W. Peng, J. Zhu, J. Zhao, C. Zhu, C. Zeng, N. Stearett, K. Crandall, P. Bachali, A. Grammer and P. Lipsky, “Abnormalities in intron retention characterize patients with Systemic Lupus Erythematosus,” Nature Sci. Rep. 13:5141, 2023. https://www.nature.com/articles/s41598-023-31890-4
E.L. Hubbard, D.S. Pisetsky and P.E. Lipsky, “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
K.M. Kingsmore, C. Puglisi, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “Application of machine learning for patient classification and outcome prediction in RAIDS (Rheumatic Autoimmune Inflammatory Diseases)”, Nature Reviews Rheumatology 17: 710, 2021. https://www.nature.com/articles/s41584-021-00708-w
(featured on printed cover and website landing page, December 2021).
Miranda C. Marion, Paula S. Ramos, Prathyusha Bachali, Adam C. Labonte, Kip D. Zimmerman, Hannah C. Ainsworth, Sarah E. Heuer, Robert D. Robl, Michelle D. Catalina, Jennifer A. Kelly, Timothy D. Howard, P.E. Lipsky, C.D. Langefeld* and A.C. Grammer (*co-corresponding authors), “Nucleic acid sensing and interferon-inducible pathways show differential methylation in MZ twins discordant for lupus and overexpression in independent lupus samples: Implications for pathogenic mechanism and drug targeting,” Genes 12: 1898, 2021. https://www.mdpi.com/2073-4425/12/12/1898
N. Stearrett, T. Dawson, G. Rahnavard, P. Bachali, M. Bendell, C. Zhen, 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 in Immunology 4:661437, 2021. doi: 10.3389/fimmu.2021.661437.
L. Pengchong, J. Mengdi. . . P.E. Lipsky, G.C. Tsokos and X. Zhang. “Glutathione peroxidase 4-regulated neutrophil ferroptosis induces systemic autoimmunity, Nature Immunology 22:1107, 2021. https://www.nature.com/articles/s41590-021-00993-3
K.M. Kingsmore, P.E. Lipsky and A.C. Grammer, “Repositioning Drugs for Systemic Lupus Erythematosus,” SLE: Basic, Applied and Clinical Aspects, pp. 641, 2020.
M. Wang, H. Chen, J. Qiu . . .X. Zhang and P.E, Lipsky, “Antagonizing miR-7 suppresses B cell hyperresponsiveness and inhibits lupus development.” J. Autoimmun. 109:102440, 2020. https://www.sciencedirect.com/science/article/abs/pii/S0896841120300536.
K.M. Kingsmore, A.C. Grammer and P.E. Lipsky, “Drug Repurposing to Improve the Treatment of Patients with Rheumatic Autoimmune Inflammatory Diseases (RAIDs)”, Nature Reviews Rheumatology 16:32, 2020. https://www.nature.com/articles/s41584-019-0337-0
P.E. Lipsky, B. Kegerreis and A.C. Grammer, “Systems and methods for single-cell RNA-Seq dataanalysis,” US202000090787A1.
B.J. Kegerreis, M.D. Catalina, P. Bachali, N. Geraci, A. Labonte, C. Zeng, N. Stearrett, K. Crandall and A.C. Grammer, “Machine Learning Approaches to Predict Disease Activity from Gene Expression Data,” Nature Scientific Reports 9:9617, 2019. https://www.nature.com/articles/s41598-019-45989-0
https://www.jimmunol.org/content/early/2019/04/23/jimmunol.1801512
B.J. Kegerreis, M.D. Catalina, N.S. Geraci, P. Bachali, P.E. Lipsky and A.C. Grammer. “Genomic Identification of Low-Density Granulocytes and Analysis of their Role in the Pathogenesis of Systemic Lupus Erythematosus,” J. Immunol. 202:3309, 2019. https://www.jimmunol.org/content/202/11/3309
S.Y. Weissenberg . . . P. Bachali, M.D. Catalina, A. Grammer, P. Lipsky, A.C. Lino* and T. Doerner* (*co-corresponding authors), “Identification and characterization of post-activated B cells in systemic autoimmune diseases,” Frontiers in Immunology 10:2136, 2019. https://www.frontiersin.org/articles/10.3389/fimmu.2019.02136
A.C. Labonte, B. Kegerreis, N. Geraci, P. Bachali, S. Madamanchi, R. Robl, M.D. Catalina, P.E. Lipsky and A.C. Grammer. “Identification of alterations in macrophage polarization associated with disease activity in systemic lupus erythematosus,” PLoS One 13(12):e0208132, 2018. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478921/
Y. Chen . . .W. Zhang and P.E. Lipsky, “Aberrant Expansion and Function of Follicular Helper T Cell Subsets in IgG4-Related Disease.” Arthritis Rheumatol.70:1853, 2018. . doi: 10.1002/art.40556. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220938/
A.C. Grammer and P.E. Lipsky, “Drug Repositioning Strategies for the Identification of Novel Therapies for Rheumatic Autoimmune Inflammatory Diseases,” Rheum Dis Clin. 43:467-480, 2017. https://pubmed.ncbi.nlm.nih.gov/28711146/
A.C. Grammer, M.M. Ryals, S.E. Heuer, R.D. Robl, S. Madamanchi, L.S. Davis, B. Lauwerys, M.D Catalina and P.E. Lipsky, “Drug Repositioning in SLE: Crowd-Sourcing, Literature-Mining and Big Data Analysis.” Lupus 25:1150-1170, 2016. https://pubmed.ncbi.nlm.nih.gov/27497259/
A.C. Grammer, M.M. Ryals, M.D. Catalina and P.E. Lipsky, “Repositioning Drugs for SLE” in SLE: Basic, Applied and Clinical Aspects, pp. 567-575, 2016. https://www.sciencedirect.com/science/article/pii/B9780128019177000668
R. Dietert and A.C. Grammer, “The Epigenetics of Autoimmunity & Immune Disorders” in The Epigenome and Developmental Origins of Adult Health and Disease, pp. 211-234, 2015.
A.C. Grammer, M. Ryals and Peter E. Lipsky, “A comprehensive approach to identify approved drugs and treatments for repositioning as therapies for systemic lupus erythematosus.” Arthr. Res. Ther. 16: 51, 2014. https://arthritis-research.biomedcentral.com/articles/10.1186/ar4667
S.J. Fleischer, C. Giesecke, H.E. Mei, P.E. Lipsky, C. Daridon and T. Dörner, “Increased frequency of a unique spleen tyrosine kinase bright memory B cell population in systemic lupus erythematosus.
Arthritis Rheumatol. 66:3424, 2014. https://onlinelibrary.wiley.com/doi/epdf/10.1002/art.38854
S. Hasni, G. Illei, N. Nikolov, F. Hakim, S. Leitman, J. Balow, H. Austin, J. Gea-Banacloche, U. Oh, P. Muraro, C. Sportes, P. Lipsky. R. Gress, S. Pavletic, A. Grammer, “Lymphoablation including B cell depletion and autologous hematopoietic stem cell transplantation leads to long remissions in treatment- resistant Systemic Lupus Erythemstosus Patients” Arthritis and Rheum. 65: 1610, 2013.
Lugar, P., C. Love., A.C. Grammer, Sandeep S. Dave and P.E. Lipsky. “Molecular Characterization of Circulating Plasma Cells in Patients with Active Systemic Lupus Erythematosus.” PLoS One 10: e0044362, 2012.
Medical Affairs Papers
Lupus Precision Medicine Products (setting the stage for LuGENE®)
M.D Catalina, K.A. Owen, A.C. Labonte, A.C. Grammer and P.E. Lipsky. “The pathogenesis of systemic lupus erythematosus: Harnessing big data to understand the molecular basis of lupus” https://www.sciencedirect.com/science/article/abs/pii/S0896841119307218?via%3Dihub/
S. Yavuz and P.E. Lipsky. “Diagnosis of Systemic Lupus Erythematosus in the Age of Precision Medicine.” Diagnoses Without Names, pp. 77-87, 2022. https://link.springer.com/chapter/10.1007/978-3-031-04935-4_8/
S. Yavuz and P.E. Lipsky, “Current Status of the Evaluation and Management of Lupus Patients and Future Prospects.” Frontiers in Medicine 8:682544, 2021. https://www.frontiersin.org/articles/10.3389/fmed.2021.682544/full
D.S. Pisetsky, D.M. Spencer, B. Rovin and P.E. Lipsky, “ANA testing in the classification of patients with SLE.” Ann. Rheum. Dis. 80:e124, 2021.
D.S. Pisetsky and P.E. Lipsky, “New insights into the role of antinuclear antibodies in SLE.” Nat. Rev. Rheumatol. 16:565, 2020.
M. Dall’Era, I.N. Bruce, C. Gordon, S. Manzi, J. McCaffrey and P.E. Lipsky, “Current challenges in the development of new treatments for lupus.” Ann. Rheum. Dis. 78:729, 2019.
D.S. Pisetsky, B.H. Rovin and P.E. Lipsky, “Biomarkers as entry criteria for clinical trials of new therapies for systemic lupus erythematosus,” Arthritis and Rheumatism 69:487, 2017.
D.S. Pisetsky, A.C. Grammer, T.C. Ning and P.E. Lipsky. “Are Autoantibodies the Targets of B Cell Directed Therapy?” Nature Reviews Rheumatology 7: 1610, 2013.
Product Papers
LuGENE Manage®, expected launch Q2 2023 (LuPRO® mobile app & LuGENE® blood test)
LuPRO® mobile app for Lupus
K. Bell, C. Dykas, B. Muckian, B. Williams, 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. https://doi.org/10.1002/acr2.11370
LuGENE® blood test for 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
E.L. Hubbard, A.C. Grammer and P.E. Lipsky, “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/
M.D. Catalina, K.A. Owen, A.C. Labonte, A.C. Grammer and P.E. Lipsky, “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/
S. Yavuz and P.E. Lipsky, “Current Status of the Evaluation and Management of Lupus Patients and Future Prospects.” Frontiers in Medicine 8:682544, 2021.
https://www.frontiersin.org/articles/10.3389/fmed.2021.682544/full
K.A. Owen, A. C. Grammer and P.E. Lipsky, “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
Catalina, M.D., P. Bachali, A.E. Yeo, N.S. Geraci, M.A. Petri, A.C. Grammer and P.E. Lipsky, “Patient ancestry significantly contributes to molecular heterogeneity of Systemic Lupus Erythematosus,” JCI Insights 5(15) e140380, 2020. 10.1172/jci.insight.140380.
DermaGENE®, expected launch Q4 2023
Lupus, Psoriasis, Atopic Dermatitis, Scleroderma
B.A. Martinez, K.M. Kingsmore, S. Shrotri, P. Bachali, A.C. Grammer and P.E. Lipsky. “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
CardioGENE®, expected launch TBD
Coronary Artery Disease with and without an autoimmune background like Lupus
J. Kain, K.A. Owen, M.C. Marion, C.D. Langefeld, A.C. Grammer and P.E. Lipsky, “Medelian Randomization and Pathway Analysis Demonstrate Shared Genetic Associations Between Systemic Lupus Erythematosus and Coronary Artery Disease,”
http://doi.org/10.1016/j.xcrm.2022.100805
CovGENE®, expected launch with co-development partner 2023
Predicts severity of COVID disease course
March 2021: the blood of COVID patients predicts severity of disease course (lung and bronchiolar lavage)
https://www.nature.com/articles/s41598-021-86002-x
September 2022: validation of CovGENE to predict COVID disease severity
https://www.frontiersin.org/articles/10.3389/fimmu.2022.989556/full
NephroGENE®, expected launch TBD
Lupus Nephritis and other Chronic Kidney Diseases
K.M. Kingsmore, P. Bachali, M.D. Catalina, A.R. Daamen, S.E. Heuer, R.D. Robl, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “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
ArthroGENE®, expected launch TBD
Lupus Arthritis, Rheumatoid Arthritis, Osteoarthritis
V. Anaparti, D. Wiens, L.J. O’Neill, E. Hubbard, R. Robl, I. Smolik, C. Hitchen, P.E. Lipsky and H. El-Gabalawy, “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
X. Wu, Y. Liu. . .P.E. Lipsky, G.C. Tsokos, F. Bai and X. Zhang. “Single-cell sequencing of immune cells from anticitrullinated peptide antibody positive and negative rheumatoid arthritis,” https://www.nature.com/articles/s41467-021-25246-7
E.L. Hubbard, M.D. Catalina, S. Heuer, P. Bachali, R. Robl, N.S. Geraci, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “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
T. Ochi, T. Sawai, K. Murakami, A. Kamataki, M. Uzuki, T. Tomita, H. Tsuboi, K. Ochi, K. Ebina, S. Hirohata, P.E. Lipsky, “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
T.A. Stamm, K.P. Machold, D. Aletaha, F. Alasti, P. Lipsky . . . J. Smolen. “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.
Y.Z. Zhou, J.D. Zhao, H. Chen, Y. Zhang, D.F. Wang, L.F. Huang . . .P.E. Lipsky and X. Zhang, “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
Q.W. Lv, W. Zhang. . . P.E. Lipsky and X. Zhang, “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
LuGENE-Dx® for Lupus, expected launch TBD
K.A. Owen, A. Price, H. Ainsworth, B.N. Aidukaitis, P. Bachali, M.D. Catalina, J.M. Dittman, T.D. Howard, Kathryn M. Kingsmore, A.C. Labonte, Robert D. Robl, Kip D. Zimmerman, C.D. Langefeld, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors),“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
Medical Affairs for LuGENE-Dx®
J.N. Williams, M. Dall’Era, S.S. Lim, C.H. Feldman, K.A. Arntsen, A.D. Blazer, T. Goode, J.T. Merrill, S. Sheikh, A.M. Stevens, P.E. Lipsky and K.H. Costenbader, “Increasing Ancestral Diversity in Systemic Lupus Erythematosus Clinical Studies.” Arthritis Care Res. 74:420, 2022. doi: 10.1002/acr.24474.
K.A. Owen, A. C. Grammer and P.E. Lipsky, “Deconvoluting the heterogeneity of SLE: the contribution of ancestry,” Journal of Allergy and Clinical Immunology, 2021. https://doi.org/10.1016/j.jaci.2021.11.005
Catalina, M.D., P. Bachali, A.E. Yeo, N.S. Geraci, M.A. Petri, A.C. Grammer and P.E. Lipsky, “Patient ancestry significantly contributes to molecular heterogeneity of Systemic Lupus Erythematosus,” JCI Insights 5(15) e140380, 2020. 10.1172/jci.insight.140380.
A. Anjorin and P. Lipsky, “Engaging African ancestry participants in SLE clinical trials.” Lupus Sci. Med. 5:e000297, 2018. doi: 10.1136/lupus-2018-000297.
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.
LuGENE Mouse (utilized with Clients and Collaborators)
Jackson Labs/Tufts University
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
Virginia Tech University
L. 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. https://doi.org/10.4049/immunohorizons.2200015Q. 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. https://www.frontiersin.org/articles/10.3389/fimmu.2020.593353.
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. https://www.frontiersin.org/articles/10.3389/fimmu.2019.02512
J. 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.
University of Virginia
H. 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. https://acrabstracts.org/abstract/glomerular-and-tubular-transcriptional-profiles-reveal-gene-clusters-specific-for-different-stages-of-glomerulonephritis-in-nzm2328-mice/
Mylan: Multiple Sclerosis mouse model work
P. Lipsky, P.T. Vallano . . .and H. Li, “Demonstration of Equivalence of Generic Glatiramer Acetate and Copaxone for MS.” Front. Pharmacol. 12:760726, 2021. doi: 10.3389/fphar.2021.760726.
Collaborative/Client Papers
Clinical Trials (AMPEL has 50+ sites in the US and Canada)
NIH: Lupus Stem Cell Transplantation (autologous)
Alliance for Lupus Research
Rescue “failed” trials with LuMOS® using “mathematical machine learning”
Development/validation of evidence-based LUpus Multivariable Outcome Score for clinical trials
M. 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. https://onlinelibrary.wiley.com/doi/epdf/10.1002/acr2.11451
M. 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. https://www.ncbi.nlm.nih.gov/pubmed/29648686
M. Abrahamowicz and P.E. Lipsky, “Validation of a LuMOS® as an outcome measure for SLE trials,” Lupus Science & Medicine 8:1136, 2021. https://lupus.bmj.com/content/8/Suppl_2/A44.2.abstract
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. doi.org/10.3389/fimmu.2021.649458.
Image Analysis, Lupus DIVINE trial to test 2D-MRI to replace invasive biopsy, AMPEL 2018–2021. Gene expression RNA collected for CLIA validation of LuGENE® Product, expected Q42022. https://www.cvilletomorrow.org/articles/local-biomedical-company-battling-lupus-on-many Ongoing analysis of gene expression in Lupus Nephritis kidney for future paper.
Aker, Lupus ORKIDS trial (Omega-3 Krill Oil Inhibits Disease Activity in SLE), AMPEL 2018-2021. Gene expression RNA collected for CLIA validation of LuGENE® Product, expected Q42022. Ongoing analysis of gene expression before & during treatment with Krill Oil for future paper. AMPEL’s LuSEC® site education empowers patients and providers
Example instructional video https://ampelbiosolutions.com/whats-new/lupus-krill-oil-new-trial-looks-tiny-crustaceans-help/
Horizon, Lupus RIFLE trial for Rayos (delayed release prednisone), AMPEL 2016-2020. Prednisone with short half-life was FDA-approved for Lupus in 1950
https://richmond.com/life/health/charlottesville-company-works-to-improve-clinical-trial-experience-for-patients/article_75ad1e5b-4a4d-5d88-a51c-bfd12a647fd1.html
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. https://www.jrheum.org/content/early/2022/01/25/jrheum.210805
R.F. van Vollenhoven, B.H. Hahn, G.C. Tsokos, P.E. Lipsky, K. Fei, R.M. Gordon, I. Gregen, K.M. Lo, 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. https://ard.bmj.com/content/early/2022/04/26/annrheumdis-2022-222212.abstract
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.
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. https://ard.bmj.com/content/early/2022/04/26/annrheumdis-2022-222212
V. 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. https://ard.bmj.com/content/80/Suppl_1/76
P. 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). https://www.investorvillage.com/smbd.asp?mb=4235&mn=4575&pt=msg&mid=21227365
Lilly
Tabalumab anti-BAFF (DiD for Lupus)
“Transcriptomics data: Subclassification and personalized med in SLE,” Curr Opin Rheum 33: 579, 2021. “The pathogenesis of SLE: harnessing Big Data to understand the molecular basis of lupus,” J. Autoimmun. 110:102359, 2020.
Pfizer
Lupus VALUE trial, AMPEL 2017-2018, “Validation of a Pfizer Mobile Phone EPRO Tool” https://www.nbc29.com/story/40646159/value-study-results-show-custom-mobile-app-lets-patients-accurately-report-response-to-treatment
Anti-IFNbeta for Lupus, PF-07321332 DiD
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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478921/
Horizon, Gout TRIPLE trial (Pegloticase) and post-marketing work
Horizon-HVH/Eversana Collaboration:
Current Disease Management from Claims-Based Research
L. Brunetti, J. Vekaria, P.E. Lipsky and N. Schlesinger, “Treatment of Acute Gout Flares in the Emergency Department: Prescribing Patterns and Revisit Rates.” Ann. Pharmacotherapy. 56:422, 2022. doi:10.1177/10600280211032295
N.L. Edwards, N. Schlesinger, S. Clark, T. Arndt and P.E. Lipsky, “Management of Gout in the United States: A Claims-based Analysis. ACR Open Rheumatol. 2:180, 2020. doi: 10.1002/acr2.11121.
Horizon-Rutgers:
AMPEL gout trial for cherry juice effectiveness
Schlesinger, P.E. Lipsky, K. Jablonski, W. Jarjour, L. Brunetti and N.A. Young, “Components of tart cherry juice inhibit NFκB activation and inflammation in acute gout.” Clin. Exp. Rheum. 40(7):1293, 2022. https://europepmc.org/article/med/34369352
GoutPRO®
N. Schlesinger, N.L. Edwards, A.E. Yeo and P.E. Lipsky, “Development of a multivariable improvement measure for gout.” Arthritis Res. Ther. 22:164, 2020. doi: 10.1186/s13075-020-02254-4.
N. Schlesinger, N.L. Edwards, P.P. Khanna, A.E. Yeo and P.E Lipsky. “Evaluation of Proposed Criteria for Remission and Evidence-Based Development of Criteria for Complete Response in Patients With Chronic Refractory Gout.” ACR Open Rheumatol. 1:236, 2019. doi: 10.1002/acr2.1025.
Horizon-GCAN: AMPEL facilitated consensus statement re disease states of gout
D. Bursill, P.E. Lipsky et al., “Hyperuricaemia and Crystal-Associated Disease Network (G-CAN) consensus statement regarding labels and definitions of disease states of gout.” Ann. Rheum. Dis. 78:1592, 2019. doi: 10.1136/annrheumdis
Brunetti, J. Vekaria, P.E. Lipsky and N. Schlesinger. “Treatment of Acute Gout Flares in the Emergency Department: Prescribing Patterns and Revisit Rates, “ Ann. Pharmacother. 56(4):422-429, 2022. https://pubmed.ncbi.nlm.nih.gov/34282640/
R.T. Keenan, A.E. Yeo and P.E. Lipsky, “Pegloticase causes prolonged improvement in multiple disease parameters in patients with chronic refractory gout who maintain low serum urate levels.” Clin. Exp. Rheumatol. 40:1006, 2022. https://pubmed.ncbi.nlm.nih.gov/35238750/
N. Schlesinger, V.K. Rustgi, A.E. Yeo and P.E. Lipsky, “Improvement in hepatic fibrosis estimated by Fibrosis-4 index in pegloticase treated chronic refractory gout patients.” Clin. Exp. Rheumatol. 10: 55563, 2022. https://pubmed.ncbi.nlm.nih.gov/35349415/
P.E. Lipsky, N.L. Edwards, T.R. Fields, R.T. Keenan, B.F. Mandell and N. Schlesinger, “Response to the 2020 ACR Guideline for the Management of Gout.” Arthritis Care Res. 72:1506, 2020. doi: 10.1002/acr.24379.
N. Schlesinger and P.E. Lipsky, “Pegloticase treatment of chronic refractory gout: Update on efficacy and safety.” Semin. Arthritis Rheum. 50:S31, 2020. doi: 10.1016/j.semarthrit.2020.04.011.
M.H. Pillinger, T.R. Fields, A.E. Yeo and P.E. Lipsky, “Dissociation Between Clinical Benefit and Persistent Urate Lowering in Patients with Chronic Refractory Gout Treated with Pegloticase.” Rheumatol. 47:605, 2020. doi: 10.3899/jrheum.190161.
R.J. Johnson, H.K. Choi, A.E. Yeo and P.E. Lipsky, “Pegloticase Treatment Significantly Decreases Blood Pressure in Patients With Chronic Gout. Hypertension.” Hypertension 74:95, 2019. doi: 10.1161/HYPERTENSIONAHA.119.12727.
E.N. Lawrence, J.A. Singh, O. Troum, A.E. Yeo and P.E. Lipsky, “Characterization of patients with chronic refractory gout who do and do not have clinically apparent tophi and their response to pegloticase.” Rheumatology doi: 10.1093/rheumatology/kez017. PMID: 30843588.
B.F. Mandell, A.E. Yeo and P.E. Lipsky, “Tophus resolution in patients with chronic refractory gout who have persistent urate-lowering responses to pegloticase.” Arthritis Res. Ther. 20:286, 2018. doi: 10.1186/s13075-018-1782-x.
AMPEL Genomic Platform (AGP®) Bioinformatic Tools and Machine Learning Analytics
Sun, Z. Liu, A. Li, Z. Zeng, W. Peng, J. Zhu, J. Zhao, C. Zhu, C. Zeng, N. Stearett, K. Crandall, P. Bachali, A. Grammer and P. Lipsky, “Abnormalities in intron retention characterize patients with Systemic Lupus Erythematosus,” Nature Sci. Rep. 13:5141, 2023. https://www.nature.com/articles/s41598-023-31890-4
E.L. Hubbard, D.S. Pisetsky and P.E. Lipsky, “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
K.M. Kingsmore, C. Puglisi, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “Application of machine learning for patient classification and outcome prediction in RAIDS (Rheumatic Autoimmune Inflammatory Diseases)”, Nature Reviews Rheumatology 17: 710, 2021. https://www.nature.com/articles/s41584-021-00708-w
(featured on printed cover and website landing page, December 2021).
Miranda C. Marion, Paula S. Ramos, Prathyusha Bachali, Adam C. Labonte, Kip D. Zimmerman, Hannah C. Ainsworth, Sarah E. Heuer, Robert D. Robl, Michelle D. Catalina, Jennifer A. Kelly, Timothy D. Howard, P.E. Lipsky, C.D. Langefeld* and A.C. Grammer (*co-corresponding authors), “Nucleic acid sensing and interferon-inducible pathways show differential methylation in MZ twins discordant for lupus and overexpression in independent lupus samples: Implications for pathogenic mechanism and drug targeting,” Genes 12: 1898, 2021. https://www.mdpi.com/2073-4425/12/12/1898
N. Stearrett, T. Dawson, G. Rahnavard, P. Bachali, M. Bendell, C. Zhen, 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 in Immunology 4:661437, 2021. doi: 10.3389/fimmu.2021.661437.
L. Pengchong, J. Mengdi. . . P.E. Lipsky, G.C. Tsokos and X. Zhang. “Glutathione peroxidase 4-regulated neutrophil ferroptosis induces systemic autoimmunity, Nature Immunology 22:1107, 2021. https://www.nature.com/articles/s41590-021-00993-3
K.M. Kingsmore, P.E. Lipsky and A.C. Grammer, “Repositioning Drugs for Systemic Lupus Erythematosus,” SLE: Basic, Applied and Clinical Aspects, pp. 641, 2020.
M. Wang, H. Chen, J. Qiu . . .X. Zhang and P.E, Lipsky, “Antagonizing miR-7 suppresses B cell hyperresponsiveness and inhibits lupus development.” J. Autoimmun. 109:102440, 2020. https://www.sciencedirect.com/science/article/abs/pii/S0896841120300536.
K.M. Kingsmore, A.C. Grammer and P.E. Lipsky, “Drug Repurposing to Improve the Treatment of Patients with Rheumatic Autoimmune Inflammatory Diseases (RAIDs)”, Nature Reviews Rheumatology 16:32, 2020. https://www.nature.com/articles/s41584-019-0337-0
P.E. Lipsky, B. Kegerreis and A.C. Grammer, “Systems and methods for single-cell RNA-Seq dataanalysis,” US202000090787A1.
B.J. Kegerreis, M.D. Catalina, P. Bachali, N. Geraci, A. Labonte, C. Zeng, N. Stearrett, K. Crandall and A.C. Grammer, “Machine Learning Approaches to Predict Disease Activity from Gene Expression Data,” Nature Scientific Reports 9:9617, 2019. https://www.nature.com/articles/s41598-019-45989-0
https://www.jimmunol.org/content/early/2019/04/23/jimmunol.1801512
B.J. Kegerreis, M.D. Catalina, N.S. Geraci, P. Bachali, P.E. Lipsky and A.C. Grammer. “Genomic Identification of Low-Density Granulocytes and Analysis of their Role in the Pathogenesis of Systemic Lupus Erythematosus,” J. Immunol. 202:3309, 2019. https://www.jimmunol.org/content/202/11/3309
S.Y. Weissenberg . . . P. Bachali, M.D. Catalina, A. Grammer, P. Lipsky, A.C. Lino* and T. Doerner* (*co-corresponding authors), “Identification and characterization of post-activated B cells in systemic autoimmune diseases,” Frontiers in Immunology 10:2136, 2019. https://www.frontiersin.org/articles/10.3389/fimmu.2019.02136
A.C. Labonte, B. Kegerreis, N. Geraci, P. Bachali, S. Madamanchi, R. Robl, M.D. Catalina, P.E. Lipsky and A.C. Grammer. “Identification of alterations in macrophage polarization associated with disease activity in systemic lupus erythematosus,” PLoS One 13(12):e0208132, 2018. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478921/
Y. Chen . . .W. Zhang and P.E. Lipsky, “Aberrant Expansion and Function of Follicular Helper T Cell Subsets in IgG4-Related Disease.” Arthritis Rheumatol.70:1853, 2018. . doi: 10.1002/art.40556. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220938/
A.C. Grammer and P.E. Lipsky, “Drug Repositioning Strategies for the Identification of Novel Therapies for Rheumatic Autoimmune Inflammatory Diseases,” Rheum Dis Clin. 43:467-480, 2017. https://pubmed.ncbi.nlm.nih.gov/28711146/
A.C. Grammer, M.M. Ryals, S.E. Heuer, R.D. Robl, S. Madamanchi, L.S. Davis, B. Lauwerys, M.D Catalina and P.E. Lipsky, “Drug Repositioning in SLE: Crowd-Sourcing, Literature-Mining and Big Data Analysis.” Lupus 25:1150-1170, 2016. https://pubmed.ncbi.nlm.nih.gov/27497259/
A.C. Grammer, M.M. Ryals, M.D. Catalina and P.E. Lipsky, “Repositioning Drugs for SLE” in SLE: Basic, Applied and Clinical Aspects, pp. 567-575, 2016. https://www.sciencedirect.com/science/article/pii/B9780128019177000668
R. Dietert and A.C. Grammer, “The Epigenetics of Autoimmunity & Immune Disorders” in The Epigenome and Developmental Origins of Adult Health and Disease, pp. 211-234, 2015.
A.C. Grammer, M. Ryals and Peter E. Lipsky, “A comprehensive approach to identify approved drugs and treatments for repositioning as therapies for systemic lupus erythematosus.” Arthr. Res. Ther. 16: 51, 2014. https://arthritis-research.biomedcentral.com/articles/10.1186/ar4667
S.J. Fleischer, C. Giesecke, H.E. Mei, P.E. Lipsky, C. Daridon and T. Dörner, “Increased frequency of a unique spleen tyrosine kinase bright memory B cell population in systemic lupus erythematosus.
Arthritis Rheumatol. 66:3424, 2014. https://onlinelibrary.wiley.com/doi/epdf/10.1002/art.38854
S. Hasni, G. Illei, N. Nikolov, F. Hakim, S. Leitman, J. Balow, H. Austin, J. Gea-Banacloche, U. Oh, P. Muraro, C. Sportes, P. Lipsky. R. Gress, S. Pavletic, A. Grammer, “Lymphoablation including B cell depletion and autologous hematopoietic stem cell transplantation leads to long remissions in treatment- resistant Systemic Lupus Erythemstosus Patients” Arthritis and Rheum. 65: 1610, 2013.
Lugar, P., C. Love., A.C. Grammer, Sandeep S. Dave and P.E. Lipsky. “Molecular Characterization of Circulating Plasma Cells in Patients with Active Systemic Lupus Erythematosus.” PLoS One 10: e0044362, 2012.
Lupus Precision Medicine Products (setting the stage for LuGENE®)
M.D Catalina, K.A. Owen, A.C. Labonte, A.C. Grammer and P.E. Lipsky. “The pathogenesis of systemic lupus erythematosus: Harnessing big data to understand the molecular basis of lupus” https://www.sciencedirect.com/science/article/abs/pii/S0896841119307218?via%3Dihub/
S. Yavuz and P.E. Lipsky. “Diagnosis of Systemic Lupus Erythematosus in the Age of Precision Medicine.” Diagnoses Without Names, pp. 77-87, 2022. https://link.springer.com/chapter/10.1007/978-3-031-04935-4_8/
S. Yavuz and P.E. Lipsky, “Current Status of the Evaluation and Management of Lupus Patients and Future Prospects.” Frontiers in Medicine 8:682544, 2021. https://www.frontiersin.org/articles/10.3389/fmed.2021.682544/full
D.S. Pisetsky, D.M. Spencer, B. Rovin and P.E. Lipsky, “ANA testing in the classification of patients with SLE.” Ann. Rheum. Dis. 80:e124, 2021.
D.S. Pisetsky and P.E. Lipsky, “New insights into the role of antinuclear antibodies in SLE.” Nat. Rev. Rheumatol. 16:565, 2020.
M. Dall’Era, I.N. Bruce, C. Gordon, S. Manzi, J. McCaffrey and P.E. Lipsky, “Current challenges in the development of new treatments for lupus.” Ann. Rheum. Dis. 78:729, 2019.
D.S. Pisetsky, B.H. Rovin and P.E. Lipsky, “Biomarkers as entry criteria for clinical trials of new therapies for systemic lupus erythematosus,” Arthritis and Rheumatism 69:487, 2017.
D.S. Pisetsky, A.C. Grammer, T.C. Ning and P.E. Lipsky. “Are Autoantibodies the Targets of B Cell Directed Therapy?” Nature Reviews Rheumatology 7: 1610, 2013.
LuGENE Manage®, expected launch Q2 2023 (LuPRO® mobile app & LuGENE® blood test)
LuPRO® mobile app for Lupus
K. Bell, C. Dykas, B. Muckian, B. Williams, 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. https://doi.org/10.1002/acr2.11370
LuGENE® blood test for 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
E.L. Hubbard, A.C. Grammer and P.E. Lipsky, “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/
M.D. Catalina, K.A. Owen, A.C. Labonte, A.C. Grammer and P.E. Lipsky, “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/
S. Yavuz and P.E. Lipsky, “Current Status of the Evaluation and Management of Lupus Patients and Future Prospects.” Frontiers in Medicine 8:682544, 2021.
https://www.frontiersin.org/articles/10.3389/fmed.2021.682544/full
K.A. Owen, A. C. Grammer and P.E. Lipsky, “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
Catalina, M.D., P. Bachali, A.E. Yeo, N.S. Geraci, M.A. Petri, A.C. Grammer and P.E. Lipsky, “Patient ancestry significantly contributes to molecular heterogeneity of Systemic Lupus Erythematosus,” JCI Insights 5(15) e140380, 2020. 10.1172/jci.insight.140380.
DermaGENE®, expected launch Q4 2023
Lupus, Psoriasis, Atopic Dermatitis, Scleroderma
B.A. Martinez, K.M. Kingsmore, S. Shrotri, P. Bachali, A.C. Grammer and P.E. Lipsky. “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
CardioGENE®, expected launch TBD
Coronary Artery Disease with and without an autoimmune background like Lupus
J. Kain, K.A. Owen, M.C. Marion, C.D. Langefeld, A.C. Grammer and P.E. Lipsky, “Medelian Randomization and Pathway Analysis Demonstrate Shared Genetic Associations Between Systemic Lupus Erythematosus and Coronary Artery Disease,”
http://doi.org/10.1016/j.xcrm.2022.100805
CovGENE®, expected launch with co-development partner 2023
Predicts severity of COVID disease course
March 2021: the blood of COVID patients predicts severity of disease course (lung and bronchiolar lavage)
https://www.nature.com/articles/s41598-021-86002-x
September 2022: validation of CovGENE to predict COVID disease severity
https://www.frontiersin.org/articles/10.3389/fimmu.2022.989556/full
NephroGENE®, expected launch Q4 2023
Lupus Nephritis and other Chronic Kidney Diseases
K.M. Kingsmore, P. Bachali, M.D. Catalina, A.R. Daamen, S.E. Heuer, R.D. Robl, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “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
ArthroGENE®, expected launch TBD
Lupus Arthritis, Rheumatoid Arthritis, Osteoarthritis
V. Anaparti, D. Wiens, L.J. O’Neill, E. Hubbard, R. Robl, I. Smolik, C. Hitchen, P.E. Lipsky and H. El-Gabalawy, “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
X. Wu, Y. Liu. . .P.E. Lipsky, G.C. Tsokos, F. Bai and X. Zhang. “Single-cell sequencing of immune cells from anticitrullinated peptide antibody positive and negative rheumatoid arthritis,” https://www.nature.com/articles/s41467-021-25246-7
E.L. Hubbard, M.D. Catalina, S. Heuer, P. Bachali, R. Robl, N.S. Geraci, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors), “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
T. Ochi, T. Sawai, K. Murakami, A. Kamataki, M. Uzuki, T. Tomita, H. Tsuboi, K. Ochi, K. Ebina, S. Hirohata, P.E. Lipsky, “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
T.A. Stamm, K.P. Machold, D. Aletaha, F. Alasti, P. Lipsky . . . J. Smolen. “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.
Y.Z. Zhou, J.D. Zhao, H. Chen, Y. Zhang, D.F. Wang, L.F. Huang . . .P.E. Lipsky and X. Zhang, “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
Q.W. Lv, W. Zhang. . . P.E. Lipsky and X. Zhang, “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
LuGENE-Dx® for Lupus, expected launch TBD
K.A. Owen, A. Price, H. Ainsworth, B.N. Aidukaitis, P. Bachali, M.D. Catalina, J.M. Dittman, T.D. Howard, Kathryn M. Kingsmore, A.C. Labonte, Robert D. Robl, Kip D. Zimmerman, C.D. Langefeld, P.E. Lipsky* and A.C. Grammer* (*co-corresponding authors),“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
Medical Affairs for LuGENE-Dx®
J.N. Williams, M. Dall’Era, S.S. Lim, C.H. Feldman, K.A. Arntsen, A.D. Blazer, T. Goode, J.T. Merrill, S. Sheikh, A.M. Stevens, P.E. Lipsky and K.H. Costenbader, “Increasing Ancestral Diversity in Systemic Lupus Erythematosus Clinical Studies.” Arthritis Care Res. 74:420, 2022. doi: 10.1002/acr.24474.
K.A. Owen, A. C. Grammer and P.E. Lipsky, “Deconvoluting the heterogeneity of SLE: the contribution of ancestry,” Journal of Allergy and Clinical Immunology, 2021. https://doi.org/10.1016/j.jaci.2021.11.005
Catalina, M.D., P. Bachali, A.E. Yeo, N.S. Geraci, M.A. Petri, A.C. Grammer and P.E. Lipsky, “Patient ancestry significantly contributes to molecular heterogeneity of Systemic Lupus Erythematosus,” JCI Insights 5(15) e140380, 2020. 10.1172/jci.insight.140380.
A. Anjorin and P. Lipsky, “Engaging African ancestry participants in SLE clinical trials.” Lupus Sci. Med. 5:e000297, 2018. doi: 10.1136/lupus-2018-000297.
A. 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”, Science Advances.
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.
LuGENE Mouse (utilized with Clients and Collaborators)
Jackson Labs/Tufts University
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
Virginia Tech University
L. 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. https://doi.org/10.4049/immunohorizons.2200015
Q. 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. https://www.frontiersin.org/articles/10.3389/fimmu.2020.593353.
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. https://www.frontiersin.org/articles/10.3389/fimmu.2019.02512
J. 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.
University of Virginia
H. 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. https://acrabstracts.org/abstract/glomerular-and-tubular-transcriptional-profiles-reveal-gene-clusters-specific-for-different-stages-of-glomerulonephritis-in-nzm2328-mice/
Mylan: Multiple Sclerosis mouse model work
P. Lipsky, P.T. Vallano . . .and H. Li, “Demonstration of Equivalence of Generic Glatiramer Acetate and Copaxone for MS.” Front. Pharmacol. 12:760726, 2021. doi: 10.3389/fphar.2021.760726.
Clinical Trials (AMPEL has 50+ sites in the US and Canada)
NIH: Lupus Stem Cell Transplantation (autologous)
Alliance for Lupus Research
Rescue “failed” trials with LuMOS® using “mathematical machine learning”
Development/validation of evidence-based LUpus Multivariable Outcome Score for clinical trials
M. 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. https://onlinelibrary.wiley.com/doi/epdf/10.1002/acr2.11451
M. 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. https://www.ncbi.nlm.nih.gov/pubmed/29648686
M. Abrahamowicz and P.E. Lipsky, “Validation of a LuMOS® as an outcome measure for SLE trials,” Lupus Science & Medicine 8:1136, 2021. https://lupus.bmj.com/content/8/Suppl_2/A44.2.abstract
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. doi.org/10.3389/fimmu.2021.649458.
Image Analysis, Lupus DIVINE trial to test 2D-MRI to replace invasive biopsy, AMPEL 2018–2021. Gene expression RNA collected for CLIA validation of LuGENE® Product, expected Q42022. https://www.cvilletomorrow.org/articles/local-biomedical-company-battling-lupus-on-many Ongoing analysis of gene expression in Lupus Nephritis kidney for future paper.
Aker, Lupus ORKIDS trial (Omega-3 Krill Oil Inhibits Disease Activity in SLE), AMPEL 2018-2021. Gene expression RNA collected for CLIA validation of LuGENE® Product, expected Q42022. Ongoing analysis of gene expression before & during treatment with Krill Oil for future paper. AMPEL’s LuSEC® site education empowers patients and providers
Example instructional video https://ampelbiosolutions.com/whats-new/lupus-krill-oil-new-trial-looks-tiny-crustaceans-help/
Horizon, Lupus RIFLE trial for Rayos (delayed release prednisone), AMPEL 2016-2020. Prednisone with short half-life was FDA-approved for Lupus in 1950
https://richmond.com/life/health/charlottesville-company-works-to-improve-clinical-trial-experience-for-patients/article_75ad1e5b-4a4d-5d88-a51c-bfd12a647fd1.html
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. https://www.jrheum.org/content/early/2022/01/25/jrheum.210805
R.F. van Vollenhoven, B.H. Hahn, G.C. Tsokos, P.E. Lipsky, K. Fei, R.M. Gordon, I. Gregen, K.M. Lo, 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. https://ard.bmj.com/content/early/2022/04/26/annrheumdis-2022-222212.abstract
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.
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. https://ard.bmj.com/content/early/2022/04/26/annrheumdis-2022-222212
V. 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. https://ard.bmj.com/content/80/Suppl_1/76
P. 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). https://www.investorvillage.com/smbd.asp?mb=4235&mn=4575&pt=msg&mid=21227365
Lilly
Tabalumab anti-BAFF (DiD for Lupus)
“Transcriptomics data: Subclassification and personalized med in SLE,” Curr Opin Rheum 33: 579, 2021. “The pathogenesis of SLE: harnessing Big Data to understand the molecular basis of lupus,” J. Autoimmun. 110:102359, 2020.
Mylan: Multiple Sclerosis mouse model work
P. Lipsky, P.T. Vallano . . .and H. Li, “Demonstration of Equivalence of Generic Glatiramer Acetate and Copaxone for MS.” Front. Pharmacol. 12:760726, 2021. doi: 10.3389/fphar.2021.760726.
Pfizer
Lupus VALUE trial, AMPEL 2017-2018, “Validation of a Pfizer Mobile Phone EPRO Tool” https://www.nbc29.com/story/40646159/value-study-results-show-custom-mobile-app-lets-patients-accurately-report-response-to-treatment
Anti-IFNbeta for Lupus, PF-07321332 DiD
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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478921/
Horizon, Gout TRIPLE trial (Pegloticase) and post-marketing work
Horizon-HVH/Eversana Collaboration:
Current Disease Management from Claims-Based Research
L. Brunetti, J. Vekaria, P.E. Lipsky and N. Schlesinger, “Treatment of Acute Gout Flares in the Emergency Department: Prescribing Patterns and Revisit Rates.” Ann. Pharmacotherapy. 56:422, 2022. doi:10.1177/10600280211032295
N.L. Edwards, N. Schlesinger, S. Clark, T. Arndt and P.E. Lipsky, “Management of Gout in the United States: A Claims-based Analysis. ACR Open Rheumatol. 2:180, 2020. doi: 10.1002/acr2.11121.
Horizon-Rutgers:
AMPEL gout trial for cherry juice effectiveness
Schlesinger, P.E. Lipsky, K. Jablonski, W. Jarjour, L. Brunetti and N.A. Young, “Components of tart cherry juice inhibit NFκB activation and inflammation in acute gout.” Clin. Exp. Rheum. 40(7):1293, 2022. https://europepmc.org/article/med/34369352
GoutPRO®
N. Schlesinger, N.L. Edwards, A.E. Yeo and P.E. Lipsky, “Development of a multivariable improvement measure for gout.” Arthritis Res. Ther. 22:164, 2020. doi: 10.1186/s13075-020-02254-4.
N. Schlesinger, N.L. Edwards, P.P. Khanna, A.E. Yeo and P.E Lipsky. “Evaluation of Proposed Criteria for Remission and Evidence-Based Development of Criteria for Complete Response in Patients With Chronic Refractory Gout.” ACR Open Rheumatol. 1:236, 2019. doi: 10.1002/acr2.1025.
Horizon-GCAN: AMPEL facilitated consensus statement re disease states of gout
D. Bursill, P.E. Lipsky et al., “Hyperuricaemia and Crystal-Associated Disease Network (G-CAN) consensus statement regarding labels and definitions of disease states of gout.” Ann. Rheum. Dis. 78:1592, 2019. doi: 10.1136/annrheumdis
Brunetti, J. Vekaria, P.E. Lipsky and N. Schlesinger. “Treatment of Acute Gout Flares in the Emergency Department: Prescribing Patterns and Revisit Rates, “ Ann. Pharmacother. 56(4):422-429, 2022. https://pubmed.ncbi.nlm.nih.gov/34282640/
R.T. Keenan, A.E. Yeo and P.E. Lipsky, “Pegloticase causes prolonged improvement in multiple disease parameters in patients with chronic refractory gout who maintain low serum urate levels.” Clin. Exp. Rheumatol. 40:1006, 2022. https://pubmed.ncbi.nlm.nih.gov/35238750/
N. Schlesinger, V.K. Rustgi, A.E. Yeo and P.E. Lipsky, “Improvement in hepatic fibrosis estimated by Fibrosis-4 index in pegloticase treated chronic refractory gout patients.” Clin. Exp. Rheumatol. 10: 55563, 2022. https://pubmed.ncbi.nlm.nih.gov/35349415/
P.E. Lipsky, N.L. Edwards, T.R. Fields, R.T. Keenan, B.F. Mandell and N. Schlesinger, “Response to the 2020 ACR Guideline for the Management of Gout.” Arthritis Care Res. 72:1506, 2020. doi: 10.1002/acr.24379.
N. Schlesinger and P.E. Lipsky, “Pegloticase treatment of chronic refractory gout: Update on efficacy and safety.” Semin. Arthritis Rheum. 50:S31, 2020. doi: 10.1016/j.semarthrit.2020.04.011.
M.H. Pillinger, T.R. Fields, A.E. Yeo and P.E. Lipsky, “Dissociation Between Clinical Benefit and Persistent Urate Lowering in Patients with Chronic Refractory Gout Treated with Pegloticase.” Rheumatol. 47:605, 2020. doi: 10.3899/jrheum.190161.
R.J. Johnson, H.K. Choi, A.E. Yeo and P.E. Lipsky, “Pegloticase Treatment Significantly Decreases Blood Pressure in Patients With Chronic Gout. Hypertension.” Hypertension 74:95, 2019. doi: 10.1161/HYPERTENSIONAHA.119.12727.
E.N. Lawrence, J.A. Singh, O. Troum, A.E. Yeo and P.E. Lipsky, “Characterization of patients with chronic refractory gout who do and do not have clinically apparent tophi and their response to pegloticase.” Rheumatology doi: 10.1093/rheumatology/kez017. PMID: 30843588.
B.F. Mandell, A.E. Yeo and P.E. Lipsky, “Tophus resolution in patients with chronic refractory gout who have persistent urate-lowering responses to pegloticase.” Arthritis Res. Ther. 20:286, 2018. doi: 10.1186/s13075-018-1782-x.