{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T05:18:49Z","timestamp":1769318329392,"version":"3.49.0"},"reference-count":83,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T00:00:00Z","timestamp":1769126400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Cytokine and chemokine profiling is central to understanding inflammatory processes and the mechanisms driving diverse diseases. We introduce InCytokine, an open-source tool for semiquantitative analysis of cytokine and chemokine data generated by protein array technologies. InCytokine features robust and modular image-processing workflows, including automated spot detection, template alignment, normalization, quality control measures, and quantitative intensity summarization to deliver consistent and reliable readouts from profiling assays. We evaluated InCytokine by profiling wild-type microglia, TREM2 knockout, and Alzheimer\u2019s disease-associated TREM2 R47H variant cells in response to lipopolysaccharide and sulfatide exposure. Differential expression analysis revealed unique sulfatide-specific and genotype-specific cytokine signatures in TREM2 variants. We also report an intriguing modulation of DPP4 and a divergent expression pattern of ENA-78 in TREM2 variants in response to lipopolysaccharide and sulfatide treatment. Such distinct expression signatures raise the possibility that TREM2 variants may play a role in modulating inflammatory signaling relevant to cardio-metabolic and Alzheimer\u2019s disease. These signatures were corroborated using transcriptional profiling of the same microglia cells, revealing also a good concordance between protein array and RNA sequencing technologies. Taken together, InCytokine is an interactive, user-friendly web application for rapid, reproducible, and scalable analysis of protein array data, proven to generate meaningful insights for drug and biomarker discovery campaigns in pharmaceutical settings.<\/jats:p>","DOI":"10.3390\/ijms27031137","type":"journal-article","created":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T09:16:59Z","timestamp":1769159819000},"page":"1137","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["InCytokine, an Open-Source Software, Reveals a TREM2 Variant-Specific Cytokine Signature"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6657-5662","authenticated-orcid":false,"given":"Deepak","family":"Jha","sequence":"first","affiliation":[{"name":"Data and Genome Sciences, Merck & Co., Inc., Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4935-0071","authenticated-orcid":false,"given":"Marco","family":"Ancona","sequence":"additional","affiliation":[{"name":"Applied Research and Innovation, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filip","family":"Oplt","sequence":"additional","affiliation":[{"name":"Data Science and Scientific Informatics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonia L.","family":"Farmer","sequence":"additional","affiliation":[{"name":"Data and Genome Sciences, Merck & Co., Inc., Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Vagenknecht","sequence":"additional","affiliation":[{"name":"Data Science and Scientific Informatics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alejandro","family":"Vazquez-Otero","sequence":"additional","affiliation":[{"name":"Applied Research and Innovation, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Illia","family":"Prazdnyk","sequence":"additional","affiliation":[{"name":"Applied Research and Innovation, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jindrich","family":"Soukup","sequence":"additional","affiliation":[{"name":"Data Science and Scientific Informatics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebecca S.","family":"Mathew","sequence":"additional","affiliation":[{"name":"Data and Genome Sciences, Merck & Co., Inc., Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa","family":"Peterson","sequence":"additional","affiliation":[{"name":"Data and Genome Sciences, Merck & Co., Inc., Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3282-1017","authenticated-orcid":false,"given":"Danny A.","family":"Bitton","sequence":"additional","affiliation":[{"name":"Applied Research and Innovation, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1093\/gerona\/glu057","article-title":"Chronic inflammation (inflammaging) and its potential contribution to age-associated diseases","volume":"69","author":"Franceschi","year":"2014","journal-title":"J. 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