The four CCII Phase 1 Research Project Leaders (RPLs) and four Pilot Project Leaders (PPLs) have collectively published 96 peer-reviewed papers in the 4.3 years since the CCII was established. Fifteen of those publications have two RPL/PPL co-authors, illustrating how the CCII has catalyzed collaborations between members. Although not all the papers listed below relate directly to the Research/Pilot Projects funded by CCII, they have each been facilitated by the Center in some way, e.g., use of Core equipment, via CCII-catalyzed collaborations, or benefiting from training or expertise gained as a CCII participant. Moreover, almost all the publications are relevant to the CCII thematic area and are thus enhancing the Center�s reputation as a center of excellence for cancer immunology and immunotherapy research. 

RPL Yaddanapudi, Kavitha (15)

Mistry AM, Daneshmand J, Seo SJ, Lehman NL, Miller DM, Goodin DA, Frieboes HB, Chen J, Masters A, Williams BJ, Yaddanapudi K. Spatially Resolved Microglia/Macrophages in Recurrent Glioblastomas Overexpress Fatty Acid Metabolism and Phagocytic Genes. Curr Oncol. 2024 Feb 23;31(3):1183-1194. doi: 10.3390/curroncol31030088. PMID: 38534921 

Sun R, Lei C, Xu Z, Gu X, Huang L, Chen L, Tan Y, Peng M, Yaddanapudi K, Siskind L, Kong M, Mitchell R, Yan J, Deng Z. Neutral ceramidase regulates breast cancer progression by metabolic programming of TREM2-associated macrophages. Nat Commun. 2024 Feb 1;15(1):966. doi: 10.1038/s41467-024-45084-7. PMID: 38302493

Teer L, Yaddanapudi K, Chen J. Biophysical Control of the Glioblastoma Immunosuppressive Microenvironment: Opportunities for Immunotherapy. Bioengineering (Basel). 2024 Jan 18;11(1):93. doi: 10.3390/bioengineering11010093. PMID: 38247970

Sarkar OS, Donninger H, Al-Rayyan N, Chew LC, Stamp B, Zhang X, Whitt A, Li C, Hall M, Mitchell RA, Zippelius A, Eaton JW, Chesney JA, Yaddanapudi K. Monocytic MDSCs exhibit superior immune suppression via adenosine and depletion of adenosine improves efficacy of immunotherapy. Science Advances. 2023 Jun 30;9(26):eadg3736. doi: 10.1126/sciadv.adg3736. PMID: 37390211

Meng S, Whitt AG, Stamp BF, Eaton JW, Li C, Yaddanapudi K. Exosome-based cancer vaccine for prevention of lung cancer. Stem Cell Investig. 2023 Jan 9;10:2. doi: 10.21037/sci-2022-030. PMID: 36742283; PMCID: PMC9892015.

Whitt AG, Neely AM, Sarkar OS, Meng S, Arumugam S, Yaddanapudi K, Li C. Paraoxonase 2 (PON2) plays a limited role in murine lung tumorigenesis. Sci Rep. 2023 Jun 19;13(1):9929. doi: 10.1038/s41598-023-37146-5. PMID: 37337025

Yaddanapudi K, Stamp BF, Subrahmanyam PB, Smolenkov A, Waigel SJ, Gosain R, Egger ME, Martin RCG, Buscaglia R, Maecker HT, McMasters KM, Chesney JA. Single-Cell Immune Mapping of Melanoma Sentinel Lymph Nodes Reveals an Actionable Immunotolerant Microenvironment. Clin Cancer Res. 2022 May 13;28(10):2069-2081. doi: 10.1158/1078-0432.CCR-21-0664. PMID: 35046061; PMCID: PMC9840851.

Huxol H, Yaddanapudi K, Bushau-Sprinkle A, Palmer K, Bickel S, Morton R, Harris C. COVID-19 Disease in Children with Medical Complexity in a Pediatric Long-term Care Facility: A Case Series. Pediatr Infect Dis J. 2022 Sep 1;41(9):e403-e405. doi: 10.1097/INF.0000000000003587. Epub 2022 May 27. PMID: 35622420; PMCID: PMC9359677.

Banerjee M, Yaddanapudi K, States JC. Zinc supplementation prevents mitotic accumulation in human keratinocyte cell lines upon environmentally relevant arsenic exposure. Toxicol Appl Pharmacol. 2022 Nov 1;454:116255. doi:10.1016/j.taap.2022.116255. Epub 2022 Sep 24. PMID: 36162444.

Centner CS, Moore JT, Baxter ME, Yaddanapudi K, Bates PJ, Kopechek JA. Comparison of Acoustofluidic and Static Systems for Ultrasound-Mediated Molecular Delivery to T Lymphocytes. Ultrasound Med Biol. 2023 Jan;49(1):90-105. doi: 10.1016/j.ultrasmedbio.2022.08.005. Epub 2022 Oct 12. PMID: 36241589.

Centner CS, Murphy EM, Stamp BF, Priddy MC, Moore JT, Bates PJ, Menze MA, Yaddanapudi K, Kopechek JA. Assembly and Operation of an Acoustofluidic Device for Enhanced Delivery of Molecular Compounds to Cells. J Vis Exp. 2021 Jan 21;(167). doi: 10.3791/62035. PMID: 33554963.

Donninger H, Li C, Eaton JW, Yaddanapudi K. Cancer Vaccines: Promising Therapeutics or an Unattainable Dream. Vaccines (Basel). 2021 Jun 18;9(6):668. doi: 10.3390/vaccines9060668. PMID: 34207062; PMCID: PMC8233841.

Meng S, Whitt AG, Tu A, Eaton JW, Li C, Yaddanapudi K. Isolation of Exosome-Enriched Extracellular Vesicles Carrying Granulocyte-Macrophage Colony-Stimulating Factor from Embryonic Stem Cells. J Vis Exp. 2021 Nov 11;(177):10.3791/60170. doi: 10.3791/60170. PMID: 34842232; PMCID: PMC9127305.

Centner CS, Moore JT, Baxter ME, Long ZT, Miller JM, Kovatsenko ES, Xie B, Menze MA, Berson RE, Bates PJ, Yaddanapudi K, Kopechek JA. Acoustofluidic-mediated molecular delivery to human T cells with a three-dimensional-printed flow chamber. J Acoust Soc Am. 2021 Dec;150(6):4534. doi: 10.1121/10.0009054. PMID: 34972278.

Li C, Donninger H, Eaton J, Yaddanapudi K. Regulatory Role of Immune Cell-Derived Extracellular Vesicles in Cancer: The Message Is in the Envelope. Front Immunol. 2020 Jul 16;11:1525. doi: 10.3389/fimmu.2020.01525. PMID: 32765528; PMCID: PMC7378739.

(COBRE/CCII researcher, Dr. Kavitha Yaddanapudi obtained Research Project Grant (R01) from the National Institute of Health with a high-priority score of the top 2% percentile. Dr. Kavitha Yaddanapudi became the first graduate of the COBRE/CCII program - as a major accomplishment in line with COBRE/CCII's goal to support the research and career development of junior investigators in the thematic area.)

RPL Watson, Corey (37)

Watson CT, Rodriguez OL, Engelbrecht E, Safonova Y, Marasco WA, Smith ML. Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity. Genes Immun. 2024 Feb;25(1):92-94. doi: 10.1038/s41435-023-00238-3. Epub 2023 Dec 14. PMID: 38097744

Collins AM, Ohlin M, Corcoran M, Heather JM, Ralph D, Law M, Mart�nez-Barnetche J, Ye J, Richardson E, Gibson WS, Rodriguez OL, Peres A, Yaari G, Watson CT, Lees WD. AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol. 2024 Feb 9;14:1330153. doi: 10.3389/fimmu.2023.1330153. eCollection 2023. PMID: 38406579

Lees WD, Saha S, Yaari G, Watson CT. Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies. Bioinformatics. 2024 Mar 4;40(3):btae144. doi: 10.1093/bioinformatics/btae144. PMID: 38478393

Li F, Gragert L, Giovanni Biagini D, Patel JK, Kobashigawa JA, Tr�ck J, Rodriguez O, Watson CT, Gibb DR, Zhang X, Kransdorf EP. IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients. J Heart Lung Transplant. 2024 Feb;43(2):314-323. doi: 10.1016/j.healun.2023.09.022. Epub 2023 Oct 2. PMID: 37793509

Nickerson KM, Smita S, Hoehn KB, Marinov AD, Thomas KB, Kos JT, Yang Y, Bastacky SI, Watson CT, Kleinstein SH, Shlomchik MJ. Age-associated B cells are heterogeneous and dynamic drivers of autoimmunity in mice. J Exp Med. 2023 May 1;220(5):e20221346. doi: 10.1084/jem.20221346. Epub 2023 Feb 24. PMID: 36828389; PMCID: PMC9997508.

Ford EE, Tieri D, Rodriguez OL, Francoeur NJ, Soto J, Kos JT, Peres A, Gibson WS, Silver CA, Deikus G, Hudson E, Woolley CR, Beckmann N, Charney A, Mitchell TC, Yaari G, Sebra RP, Watson CT, Smith ML. FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires. J Immunol. 2023 May 15;210(10):1607-1619. doi: 10.4049/jimmunol.2200825. PMID: 37027017; PMCID: PMC10152037.

Lees WD, Christley S, Peres A, Kos JT, Corrie B, Ralph D, Breden F, Cowell LG, Yaari G, Corcoran M, Karlsson Hedestam GB, Ohlin M, Collins AM, Watson CT, Busse CE; AIRR Community. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics (Amst). 2023 Jun;10:100025. doi: 10.1016/j.immuno.2023.100025. Epub 2023 Feb 19. PMID: 37388275

Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun. 2023 Jul 21;14(1):4419. doi: 10.1038/s41467-023-40070-x. PMID: 37479682

Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein SH, Watson CT, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res. 2023 Sep 8;51(16):e86. doi: 10.1093/nar/gkad603. PMID: 37548401

Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol. 2023 Jan;44(1):7-21. doi: 10.1016/j.it.2022.11.001. Epub 2022 Dec 2. PMID: 36470826.

Gibson WS, Rodriguez OL, Shields K, Silver CA, Dorgham A, Emery M, Deikus G, Sebra R, Eichler EE, Bashir A, Smith ML, Watson CT. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun. 2023 Feb;24(1):21-31. doi: 10.1038/s41435-022-00188-2. Epub 2022 Dec 21. PMID: 36539592; PMCID: PMC10041605.

Babrak L, Marquez S, Busse CE, Lees WD, Miho E, Ohlin M, Rosenfeld AM, Stervbo U, Watson CT, Schramm CA; AIRR Community. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol. 2022;2453:279-296. doi: 10.1007/978-1-0716-2115-8_16. PMID: 35622332; PMCID: PMC9761530.

Omer A, Peres A, Rodriguez OL, Watson CT, Lees W, Polak P, Collins AM, Yaari G. T cell receptor beta germline variability is revealed by inference from repertoire data. Genome Med. 2022 Jan 7;14(1):2. doi: 10.1186/s13073-021-01008-4. PMID: 34991709; PMCID: PMC8740489.

Geller AE, Shrestha R, Woeste MR, Guo H, Hu X, Ding C, Andreeva K, Chariker JH, Zhou M, Tieri D, Watson CT, Mitchell RA, Zhang HG, Li Y, Martin Ii RCG, Rouchka EC, Yan J. The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. Nat Commun. 2022 Feb 9;13(1):759. doi: 10.1038/s41467-022-28407-4. PMID: 35140221; PMCID: PMC8828725.

Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 Apr;32(4):791-804. doi: 10.1101/gr.276027.121. Epub 2022 Mar 31. PMID: 35361626; PMCID: PMC8997358.

Jackson KJL, Kos JT, Lees W, Gibson WS, Smith ML, Peres A, Yaari G, Corcoran M, Busse CE, Ohlin M,

Watson CT, Collins AM. A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. Front Immunol. 2022 Jun 3;13:888555. doi: 10.3389/fimmu.2022.888555. PMID: 35720344; PMCID: PMC9205180. 

Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol. 2022 Aug;100(7):497-506. doi: 10.1111/imcb.12567. Epub 2022 Jul 4. PMID: 35781330; PMCID: PMC9545137.

Fichtner ML, Hoehn KB, Ford EE, Mane-Damas M, Oh S, Waters P, Payne AS, Smith ML, Watson CT, Losen M, Martinez-Martinez P, Nowak RJ, Kleinstein SH, O'Connor KC. Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy. Acta Neuropathol Commun. 2022 Oct 28;10(1):154. doi: 10.1186/s40478-022-01454-0. PMID: 36307868; PMCID: PMC9617453.

Ford M, Hari A, Rodriguez O, Xu J, Lack J, Oguz C, Zhang Y, Weber S, Magglioco M, Barnett J, Xirasagar S, Samuel S, Imberti L, Bonfanti P, Biondi A, Dalgard CL, Chanock S, Rosen L, Holland S, Su H, Notarangelo L; NIAID COVID Consortium; Vishkin U, Watson C, Sahinalp SC. ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data. bioRxiv [Preprint]. 2022 Feb 2:2022.01.31.478564. doi: 10.1101/2022.01.31.478564. Update in: Cell Syst. 2022 Oct 19;13(10):808-816.e5. PMID: 35132409; PMCID: PMC8820654.

Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. Cell Genom. 2022 Nov 30;2(12):100228. doi: 10.1016/j.xgen.2022.100228. PMID: 36778049; PMCID: PMC9903726.

Morrissey SM, Geller AE, Hu X, Tieri D, Ding C, Klaes CK, Cooke EA, Woeste MR, Martin ZC, Chen O, Bush SE, Zhang HG, Cavallazzi R, Clifford SP, Chen J, Ghare S, Barve SS, Cai L, Kong M, Rouchka EC, McLeish KR, Uriarte SM, Watson CT, Huang J, Yan J. A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients. JCI Insight. 2021 May 10;6(9):e148435. doi: 10.1172/jci.insight.148435. PMID: 33986193; PMCID: PMC8262329.

Kenter AL, Watson CT, Spille JH. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front Immunol. 2021 May 18;12:682589. doi: 10.3389/fimmu.2021.682589. PMID: 34084176; PMCID: PMC8167033.

Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, J�nsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT*, Karlsson Hedestam GB, Mangul S. Diversity in immunogenomics: the value and the challenge. Nat Methods. 2021 Jun;18(6):588-591. doi: 10.1038/s41592-021-01169-5. PMID: 34002093; PMCID: PMC8842483. (co-corresponding author)

Zhou M, Dascani P, Ding C, Kos JT, Tieri D, Lin X, Caster D, Powell D, Wen C, Watson CT, Yan J. Integrin CD11b Negatively Regulates B Cell Receptor Signaling to Shape Humoral Response during Immunization and Autoimmunity. J Immunol. 2021 Oct 1;207(7):1785-1797. doi: 10.4049/jimmunol.2100070. Epub 2021 Sep 1. PMID: 34470858; PMCID: PMC8455437.

Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor na�ve human B cells. NPJ Vaccines. 2021 Sep 6;6(1):113. doi: 10.1038/s41541-021-00376-7. PMID: 34489473; PMCID: PMC8421370.

Morrissey SM, Zhang F, Ding C, Montoya-Durango DE, Hu X, Yang C, Wang Z, Yuan F, Fox M, Zhang HG, Guo H, Tieri D, Kong M, Watson CT, Mitchell RA, Zhang X, McMasters KM, Huang J, Yan J. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through glycolytic dominant metabolic reprogramming. Cell Metab. 2021 Oct 5;33(10):2040-2058.e10. doi: 10.1016/j.cmet.2021.09.002. Epub 2021 Sep 23. PMID: 34559989; PMCID: PMC8506837.

Rodriguez OL, Sharp AJ, Watson CT. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One. 2021 Dec 13;16(12):e0261374. doi: 10.1371/journal.pone.0261374. PMID: 34898642; PMCID: PMC8668129.

Collins AM, Peres A, Corcoran MM, Watson CT, Yaari G, Lees WD, Ohlin M. Commentary on Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: relevance in infectious diseases and vaccination studies in human populations. Genes Immun. 2021 Dec;22(7-8):335-338. doi: 10.1038/s41435-021-00152-6. Epub 2021 Oct 19. PMID: 34667305; PMCID: PMC8674141

Snyder KE, Pittard CM, Fowler A, Watson CT. ï¿½Epic-Genetics�: An exploration of pre-service helping professionals� (mis)understanding of epigenetic influences on human development. Teaching and Learning Inquiry. 2020 March; 8:122-137.

Alsoussi WB, Turner JS, Case JB, Zhao H, Schmitz AJ, Zhou JQ, Chen RE, Lei T, Rizk AA, McIntire KM, Winkler ES, Fox JM, Kafai NM, Thackray LB, Hassan AO, Amanat F, Krammer F, Watson CT, Kleinstein SH, Fremont DH, Diamond MS, Ellebedy AH. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J Immunol. 2020 Aug 15;205(4):915-922. doi: 10.4049/jimmunol.2000583. Epub 2020 Jun 26. PMID: 32591393; PMCID: PMC7566074.

Ford M, Haghshenas E, Watson CT, Sahinalp SC. Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes Using Long Reads. iScience. 2020 Mar 27;23(3):100883. doi: 10.1016/j.isci.2020.100883. Epub 2020 Feb 4. Erratum in: iScience. 2020 Sep 4;23(9):101508. PMID: 32109676; PMCID: PMC7044747.

Do AN, Watson CT, Cohain AT, Griffin RS, Grishin A, Wood RA, Wesley Burks A, Jones SM, Scurlock A, Leung DYM, Sampson HA, Sicherer SH, Sharp AJ, Schadt EE, Bunyavanich S. Dual transcriptomic and epigenomic study of reaction severity in peanut-allergic children. J Allergy Clin Immunol. 2020 Apr;145(4):1219-1230. doi: 10.1016/j.jaci.2019.10.040. Epub 2019 Dec 12. PMID: 31838046; PMCID: PMC7192362.

Christley S, Aguiar A, Blanck G, Breden F, Bukhari SAC, Busse CE, Jaglale J, Harikrishnan SL, Laserson U, Peters B, Rocha A, Schramm CA, Taylor S, Vander Heiden JA, Zimonja B, Watson CT, Corrie B, Cowell LG. The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Front Big Data. 2020 Jun 17;3:22. doi: 10.3389/fdata.2020.00022. PMID: 33693395; PMCID: PMC7931935.

Alsoussi WB, Turner JS, Case JB, Zhao H, Schmitz AJ, Zhou JQ, Chen RE, Lei T, Rizk AA, McIntire KM, Winkler ES, Fox JM, Kafai NM, Thackray LB, Hassan AO, Amanat F, Krammer F, Watson CT, Kleinstein SH, Fremont DH, Diamond MS, Ellebedy AH. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J Immunol. 2020 Aug 15;205(4):915-922. doi: 10.4049/jimmunol.2000583. Epub 2020 Jun 26. PMID: 32591393; PMCID: PMC7566074.

Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol. 2020 Sep 23;11:2136. doi: 10.3389/fimmu.2020.02136. PMID: 33072076; PMCID: PMC7539625.

Waide ML, Polidoro R, Powell WL, Denny JE, Kos J, Tieri DA, Watson CT, Schmidt NW. Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections. Cell Rep. 2020 Dec 15;33(11):108503. doi: 10.1016/j.celrep.2020.108503. PMID: 33326773; PMCID: PMC7772993.

Collins AM, Yaari G, Shepherd AJ, Lees W, Watson CT. Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight? Curr Opin Syst Biol. 2020 Dec;24:100-108. doi: 10.1016/j.coisb.2020.10.011. Epub 2020 Oct 24. PMID: 37008538; PMCID: PMC10062056.

RPL Ding, Chuanlin (14)

Wu C, Zhong Q, Shrestha R, Wang J, Hu X, Li H, Rouchka EC, Yan J, Ding C. Reactive myelopoiesis and FX-expressing macrophages triggered by chemotherapy promote cancer lung metastasis. JCI Insight. 2023 Mar 28:e167499. doi: 10.1172/jci.insight.167499. Epub ahead of print. PMID: 36976637.

Ding C, Shrestha R, Zhu X, Geller AE, Wu S, Woeste MR, Li W, Wang H, Yuan F, Xu R, Chariker JH, Hu X, Li H, Tieri D, Zhang HG, Rouchka EC, Mitchell R, Siskind LJ, Zhang X, Xu XG, McMasters KM, Yu Y, Yan J. Inducing trained immunity in pro-metastatic macrophages to control tumor metastasis. Nat Immunol. 2023 Feb;24(2):239-254. doi: 10.1038/s41590-022-01388-8. Epub 2023 Jan 5. PMID: 36604547.

Noe JT, Ding C, Geller AE, Rendon BE, Yan J, Mitchell RA. A Tumor-admixture Model to Interrogate Immune Cell-dependent Tumorigenesis. Bio Protoc. 2023 Mar 5;13(5):e4630. doi: 10.21769/BioProtoc.4630. PMID: 36908637; PMCID: PMC9993080.

Woeste MR, Shrestha R, Geller AE, Li S, Montoya-Durango D, Ding C, Hu X, Li H, Puckett A, Mitchell RA, Hayat T, Tan M, Li Y, McMasters KM, Martin RCG, Yan J. Irreversible electroporation augments β-glucan induced trained innate immunity for the treatment of pancreatic ductal adenocarcinoma. J Immunother Cancer. 2023 Apr;11(4):e006221. doi: 10.1136/jitc-2022-006221. PMID: 37072351; PMCID: PMC10124260.

Wang Y, Qin H, Cai Y, Chen X, Li H, Montoya-Durango DE, Ding C, Hu X, Chariker JH, Sarojini H, Chien S, Rouchka EC, Zhang HG, Zheng J, Qiu F, Yan J. Natural γδT17 cell development and functional acquisition is governed by the mTORC2- c-Maf-controlled mitochondrial fission pathway. iScience. 2023 Apr 10;26(5):106630. doi: 10.1016/j.isci.2023.106630. PMID: 37192973

Wang L, Zhou M, Kong X, Wu S, Ding C, Hu X, Guo H, Yan J. Specific Targeting of STAT3 in B Cells Suppresses Progression of B Cell Lymphoma. Int J Mol Sci. 2023 Sep 4;24(17):13666. doi: 10.3390/ijms241713666. PMID: 37686472

Li M, Lee S, Zahedian M, Ding C, Yan J, Yu Y. Immobile ligands enhance FcγR-TLR2/1 crosstalk by promoting interface overlap of receptor clusters. Biophys J. 2022 Mar 15;121(6):966-976. doi: 10.1016/j.bpj.2022.02.010. Epub 2022 Feb 9. PMID: 35150619; PMCID: PMC8943811.

Geller AE, Shrestha R, Woeste MR, Guo H, Hu X, Ding C, Andreeva K, Chariker JH, Zhou M, Tieri D, Watson CT, Mitchell RA, Zhang HG, Li Y, Martin Ii RCG, Rouchka EC, Yan J. The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. Nat Commun. 2022 Feb 9;13(1):759. doi: 10.1038/s41467-02228407-4. PMID: 35140221; PMCID: PMC8828725.

Chen X, Cai Y, Hu X, Ding C, He L, Zhang X, Chen F, Yan J. Differential metabolic requirement governed by transcription factor c-Maf dictates innate γδT17 effector functionality in mice and humans. Sci Adv. 2022 May 27;8(21):eabm9120. doi: 10.1126/sciadv.abm9120. Epub 2022 May 25. PMID: 35613277; PMCID: PMC9132442.

Liu N, Qin H, Cai Y, Li X, Wang L, Xu Q, Xue F, Chen L, Ding C, Hu X, Tieri D, Rouchka EC, Yan J, Zheng J. Dynamic trafficking patterns of IL-17-producing γδ T cells are linked to the recurrence of skin inflammation in psoriasis-like dermatitis. EBioMedicine. 2022 Aug;82:104136. doi: 10.1016/j.ebiom.2022.104136. Epub 2022 Jul 1. PMID: 35785620; PMCID: PMC9256835.

Morrissey SM, Geller AE, Hu X, Tieri D, Ding C, Klaes CK, Cooke EA, Woeste MR, Martin ZC, Chen O, Bush SE, Zhang HG, Cavallazzi R, Clifford SP, Chen J, Ghare S, Barve SS, Cai L, Kong M, Rouchka EC, McLeish KR, Uriarte SM, Watson CT, Huang J, Yan J. A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients. JCI Insight. 2021 May 10;6(9):e148435. doi: 10.1172/jci.insight.148435. PMID: 33986193; PMCID: PMC8262329.

Zhou M, Dascani P, Ding C, Kos JT, Tieri D, Lin X, Caster D, Powell D, Wen C, Watson CT, Yan J. Integrin CD11b Negatively Regulates B Cell Receptor Signaling to Shape Humoral Response during Immunization and Autoimmunity. J Immunol. 2021 Oct 1;207(7):1785-1797. doi: 10.4049/jimmunol.2100070. Epub 2021 Sep 1. PMID: 34470858; PMCID: PMC8455437.

Morrissey SM, Zhang F, Ding C, Montoya-Durango DE, Hu X, Yang C, Wang Z, Yuan F, Fox M, Zhang HG, Guo H, Tieri D, Kong M, Watson CT, Mitchell RA, Zhang X, McMasters KM, Huang J, Yan J. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through glycolytic dominant metabolic reprogramming. Cell Metab. 2021 Oct 5;33(10):2040-2058.e10. doi: 10.1016/j.cmet.2021.09.002. Epub 2021 Sep 23. PMID: 34559989; PMCID: PMC8506837.

Liu M, Tong Z, Ding C*, Luo F, Wu S, Wu C, Albeituni S, He L, Hu X, Tieri D, Rouchka EC, Hamada M, Takahashi S, Gibb AA, Kloecker G, Zhang HG, Bousamra M 2nd, Hill BG, Zhang X, Yan J. Transcription factor c-Maf is a checkpoint that programs macrophages in lung cancer. J Clin Invest. 2020 Apr 1;130(4):2081-2096. doi: 10.1172/JCI131335. PMID: 31945018; PMCID: PMC7108920. (*co-first author)

RPL Li, Qingsheng (3)

Li Q, Goggin KE, Seo S, Warawa JM, Egilmez NK. Anti-PD-1 antibody-activated Tp7cells subvert re-invigoration of antitumor cytotoxic T-lymphocytes via myeloid cellderived COX2/PGE2. Cancer Immunol Immunother. 2023 Apr;72(4):1047-1058. doi: 10.1007/s00262-022-03285-3. PMID: 36074159.

Li Q, Ngo PT, Egilmez NK. Anti-PD-1 antibody-mediated activation of type 17 T-cells undermines checkpoint blockade therapy. Cancer Immunol Immunother. 2021 Jun;70(6):1789-1796. doi: 10.1007/s00262-020-02795-2. Epub 2020 Nov 27. PMID: 33245376.

Mandal RK, Denny JE, Waide ML, Li Q, Bhutiani N, Anderson CD, Baby BV, Jala VR, Egilmez NK, Schmidt NW. Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility. BMC Biol. 2020 Jul 3;18(1):83. doi: 10.1186/s12915-020-00810-7. PMID: 32620114; PMCID: PMC7334859.

Pilot Project Leader Li, Chi (5)

Meng S, Whitt AG, Stamp BF, Eaton JW, Li C, Yaddanapudi K. Exosome-based cancer vaccine for prevention of lung cancer. Stem Cell Investig. 2023 Jan 9;10:2. doi: 10.21037/sci-2022-030. PMID: 36742283; PMCID: PMC9892015.

Zhang Y, Do KK, Wang F, Lu X, Liu JY, Li C, Ceresa BP, Zhang L, Dean DC, Liu Y. Zeb1 facilitates corneal epithelial wound healing by maintaining corneal epithelial cell viability and mobility. Commun Biol. 2023 Apr 20;6(1):434. doi: 10.1038/s42003-023-04831-0. PMID: 37081200; PMCID: PMC10119281.

Whitt AG, Neely AM, Sarkar OS, Meng S, Arumugam S, Yaddanapudi K, Li C. Paraoxonase 2 (PON2) plays a limited role in murine lung tumorigenesis. Sci Rep. 2023 Jun 19;13(1):9929. doi: 10.1038/s41598-023-37146-5. PMID: 37337025

Sarkar OS, Donninger H, Al-Rayyan N, Chew LC, Stamp B, Zhang X, Whitt A, Li C, Hall M, Mitchell RA, Zippelius A, Eaton JW, Chesney JA, Yaddanapudi K. Monocytic MDSCs exhibit superior immune suppression via adenosine and depletion of adenosine improves efficacy of immunotherapy. Science Advances. 2023 Jun 30;9(26):eadg3736. doi: 10.1126/sciadv.adg3736. PMID: 37390211

Whitt AG, Meng S, Jin JZ, Conroy LR, McNally LA, Burlison JA, Hill BG, Clem BF, White C, Li C. PON2 mediates mitochondrial dysfunction in tracheal epithelial cells in response to a quorum sensing molecule N-(-3-oxododecanoyl)-l-homoserine lactone. Biochem J. 2022 Oct 14;479(19):2013-2034. doi: 10.1042/BCJ20220100. PMID: 36094147.

Pilot Project Leader Matoba, Nobuyuki (6)

Verjan Garcia N, Santisteban Celis IC, Dent M, Matoba N. Characterization and utility of two monoclonal antibodies to cholera toxin B subunit. Sci Rep. 2023 Mar 15;13(1):4305. doi: 10.1038/s41598-023-30834-2. PMID: 36922604

Franz�n Boger M, Benhach N, Hasselrot T, Brand RM, Rohan LC, Wang L, McGowan I, Edick S, Ho K, Meyn L, Matoba N, Palmer KE, Broliden K, Tjernlund A. A topical rectal douche product containing Q-Griffithsin does not disrupt the epithelial border or alter CD4⁺ cell distribution in the human rectal mucosa. Sci Rep. 2023 May 9;13(1):7547. doi: 10.1038/s41598-023-34107-w. PMID: 37161022

Verjan Garcia N, Hong KU, Matoba N. The Unfolded Protein Response and Its Implications for Novel Therapeutic Strategies in Inflammatory Bowel Disease. Biomedicines. 2023 Jul 23;11(7):2066. doi: 10.3390/biomedicines11072066. PMID: 37509705

Oh YJ, Dent MW, Freels AR, Zhou Q, Lebrilla CB, Merchant ML, Matoba N. Antitumor activity of a lectibody targeting cancer-associated high-mannose glycans. Mol Ther. 2022 Apr 6;30(4):1523-1535. doi: 10.1016/j.ymthe.2022.01.030. Epub 2022 Jan 22. PMID: 35077861; PMCID: PMC9077314.

Dent M, Mayer KL, Verjan Garcia N, Guo H, Kajiura H, Fujiyama K, Matoba N. Impact of glycoengineering and antidrug antibodies on the anticancer activity of a plant-made lectin-Fc fusion protein. Plant Biotechnol J. 2022 Nov;20(11):2217-2230. doi: 10.1111/pbi.13902. Epub 2022 Aug 19. PMID: 35900183; PMCID: PMC9616523.

Tus� D, Reeves M, Royal J, Hamorsky KT, Ng H, Arolfo M, Green C, Trigunaite A, Parman T, Lee G, Matoba N. Pharmacokinetics and Safety Studies in Rodent Models Support Development of EPICERTIN as a Novel Topical Wound-Healing Biologic for Ulcerative Colitis. J Pharmacol Exp Ther. 2022 Mar;380(3):162-170. doi: 10.1124/jpet.121.000904. Epub 2022 Jan 20. PMID: 35058349.

Pilot Project Leader Smith, Melissa (16)

Zhao J, Adiele N, Gomes D, Malovichko M, Conklin DJ, Ekuban A, Luo J, Gripshover T, Watson WH, Banerjee M, Smith ML, Rouchka EC, Xu R, Zhang X, Gondim DD, Cave MC, O'Toole TE. Obesogenic polystyrene microplastic exposures disrupt the gut-liver-adipose axis. Toxicol Sci. 2024 Mar 26;198(2):210-220. doi: 10.1093/toxsci/kfae013. PMID: 38291899

Gripshover TC, Wahlang B, Head KZ, Luo J, Bolatimi OE, Smith ML, Rouchka EC, Chariker JH, Xu J, Cai L, Cummins TD, Merchant ML, Zheng H, Kong M, Cave MC. Multiomics Analysis of PCB126's Effect on a Mouse Chronic-Binge Alcohol Feeding Model. Environ Health Perspect. 2024 Apr;132(4):47007. doi: 10.1289/EHP14132. Epub 2024 Apr 15. PMID: 38619879�

Watson CT, Rodriguez OL, Engelbrecht E, Safonova Y, Marasco WA, Smith ML. Genes Immun. Looking to the future of antibody genetics: resolving the roles of immunoglobulin diversity in gene regulation, function, and immunity. 2024 Feb;25(1):92-94. doi: 10.1038/s41435-023-00238-3. Epub 2023 Dec 14. PMID: 38097744

Kalbfleisch TS, Hussien AbouEl Ela NA, Li K, Brashear WA, Kochan KJ, Hillhouse AE, Zhu Y, Dhande IS, Kline EJ, Hudson EA, Murphy TD, Thibaud-Nissen F, Smith ML, Doris PA. The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat. Hypertension. 2023 Jan;80(1):138-146. doi: 10.1161/HYPERTENSIONAHA.122.20140. Epub 2022 Nov 4. PMID: 36330812; PMCID: PMC9814308.

Ford EE, Tieri D, Rodriguez OL, Francoeur NJ, Soto J, Kos JT, Peres A, Gibson WS, Silver CA, Deikus G, Hudson E, Woolley CR, Beckmann N, Charney A, Mitchell TC, Yaari G, Sebra RP, Watson CT, Smith ML. FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires. J Immunol. 2023 May 15;210(10):1607-1619. doi: 10.4049/jimmunol.2200825. PMID: 37027017; PMCID: PMC10152037

Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun. 2023 Jul 21;14(1):4419. doi: 10.1038/s41467-023-40070-x. PMID: 37479682

Gibson WS, Rodriguez OL, Shields K, Silver CA, Dorgham A, Emery M, Deikus G, Sebra R, Eichler EE, Bashir A, Smith ML, Watson CT. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun. 2023 Feb;24(1):21-31. doi: 10.1038/s41435-022-00188-2. Epub 2022 Dec 21. PMID: 36539592; PMCID: PMC10041605.

Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun. 2023 Oct 30;14(1):6902. doi: 10.1038/s41467-023-42558-y. PMID: 37903791

Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell. 2023 Dec 7;83(23):4255-4271.e9. doi: 10.1016/j.molcel.2023.10.036. Epub 2023 Nov 22. PMID: 37995687

Benner SE, Eby Y, Zhu X, Fernandez RE, Patel EU, Ruff JE, Habtehyimer F, Schmidt HA, Kirby CS, Hussain S, Ostrander D, Desai NM, Florman S, Rana MM, Friedman-Moraco R, Pereira MR, Mehta S, Stock P, Gilbert A, Morris MI, Stosor V, Mehta SA, Small CB, Ranganna K, Santos CA, Aslam S, Husson J, Malinis M, Elias N, Blumberg EA, Doby BL, Massie AB, Smith ML, Odim J, Quinn TC, Laird GM, Siliciano RF, Segev DL, Redd AD, Durand CM, Tobian AA. The effect of induction immunosuppression for kidney transplant on the latent HIV reservoir. JCI Insight. 2022 Nov 8;7(21):e162968. doi: 10.1172/jci.insight.162968. PMID: 36345940; PMCID: PMC9675561.

Dave A, Nekritz E, Charytonowicz D, Beaumont M, Smith M, Beaumont K, Silva J, Sebra R. Integration of Single-Cell Transcriptomics With a High Throughput Functional Screening Assay to Resolve Cell Type, Growth Kinetics, and Stemness Heterogeneity Within the Comma-1D Cell Line. Front Genet. 2022 Jun 14;13:894597. doi: 10.3389/fgene.2022.894597. PMID: 36630696; PMCID: PMC9237515.

Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. Cell Genom. 2022 Nov 30;2(12):100228. doi: 10.1016/j.xgen.2022.100228. PMID: 36778049; PMCID: PMC9903726.

de Jong TV, Chen H, Brashear WA, Kochan KJ, Hillhouse AE, Zhu Y, Dhande IS, Hudson EA, Sumlut MH, Smith ML, Kalbfleisch TS, Doris PA. mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly. Physiol Genomics. 2022 Jul 1;54(7):251-260. doi: 10.1152/physiolgenomics.00017.2022. Epub 2022 May 11. PMID: 35543507; PMCID: PMC9236863.

Fichtner ML, Hoehn KB, Ford EE, Mane-Damas M, Oh S, Waters P, Payne AS, Smith ML, Watson CT, Losen M, Martinez-Martinez P, Nowak RJ, Kleinstein SH, O'Connor KC. Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy. Acta Neuropathol Commun. 2022 Oct 28;10(1):154. doi: 10.1186/s40478-022-01454-0. PMID: 36307868; PMCID: PMC9617453.

Woolley CR, Chariker JH, Rouchka EC, Ford EE, Hudson EA, Waigel SJ, Smith ML, Mitchell TC. Reference long-read isoform-aware transcriptomes of 4 human peripheral blood lymphocyte subsets. G3 (Bethesda). 2022 Nov 4;12(11):jkac253. doi: 10.1093/g3journal/jkac253. PMID: 36161486; PMCID: PMC9635627.

Jackson KJL, Kos JT, Lees W, Gibson WS, Smith ML, Peres A, Yaari G, Corcoran M, Busse CE, Ohlin M, Watson CT, Collins AM. A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. Front Immunol. 2022 Jun 3;13:888555. doi: 10.3389/fimmu.2022.888555. PMID: 35720344; PMCID: PMC9205180.