Select Publications from SCI Faculty

  1.  Johnson MJ, DeFeo AP, Slipek NJ, Folsom TD, Henley T, Choudhry MS, Webber BR, Moriarity BS. Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates. J Vis Exp. 2025 May 9;(219). doi: 10.3791/68150. PMID: 40418657.
  2. Witte IP, Lampe GD, Eitzinger S, Miller SM, Berríos KN, McElroy AN, King RT, Stringham OG, Gelsinger DR, Vo PLH, Chen AT, Tolar J, Osborn MJ, Sternberg SH, Liu DR. Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase. Science. 2025 May
    15;388(6748):eadt5199. doi: 10.1126/science.adt5199. Epub 2025 May 15. PMID: 40373119.
  3. Garry DJ, Wolf E; XenExoCor consortium. Leducq-funded programme: engineering pig hearts for transplantation. Eur Heart J. 2025 May 29:ehaf270. doi: 10.1093/eurheartj/ehaf270. Epub ahead of print. PMID: 40439128.
  4. Chen K, Wei E, Mitanoska A, Gearhart MD, Kyba M, Bosnakovski D. Dux Is Dispensable for Skeletal Muscle Regeneration: A Study Inspired by a "Red Flagged" Publication and Editorial Oversight. Cells. 2025 May 12;14(10):695. doi: 10.3390/cells14100695. PMID: 40422198; PMCID: PMC12109671.
  5. Li J, Yu Y, Tranquillo RT. Computational construction and design optimization of a novel tri-tube heart valve. Biomech Model Mechanobiol. 2025 Jun;24(3):1103-1121. doi: 10.1007/s10237-025-01956-5. Epub 2025 May 26. PMID: 40418405.
  6. Lund TC, Gupta AO, Loes DJ, Nascene DR, Orchard PJ. Neurofilament light chain as a biomarker to indicate early activation of cerebral disease in boys with adrenoleukodystrophy. Commun Med (Lond). 2025 May 23;5(1):196. doi: 10.1038/s43856-025-00915-6. PMID: 40410561; PMCID: PMC12102243.
  7. Kuo HJ, Srinivasan P, Lin YC, Lu M, Rungkittikhun C, Zhang Q, Hu WS. Transcriptomic functional characterization of recombinant adeno-associated virus producing cell line adapted to suspension-growth. Biotechnol Prog. 2025 May 21:e70042. doi: 10.1002/btpr.70042. Epub ahead of print. PMID: 40396307.
  8. Borgatti A, Husbands BD, Sarver AL, Chacón JM, DeFor TE, Rendahl A, Henson MS, Modiano JF, et al. Younger Age Is Associated with Favorable Outcomes in Adult Dogs with Hemangiosarcoma Receiving Adjuvant Doxorubicin Chemotherapy: Results from the PRO-DOX Study. Res Sq [Preprint]. 2025 May 5:rs.3.rs-6573099. doi: 10.21203/rs.3.rs-6573099/v1. PMID: 40386412; PMCID: PMC12083661.
  9. Garry DJ, Garry MG, Nakauchi H, Masaki H, Sachs DH, Weiner JI, Reichart D, Wolf E. Allogeneic, Xenogeneic, and Exogenic Hearts for Transplantation. Methodist Debakey Cardiovasc J. 2025 May 15;21(3):92-99. doi: 10.14797/mdcvj.1590. PMID: 40384731; PMCID: PMC12082467.
  10. Umar S, Zhu W, Souza-Neto F, Bender I, Wu SC, Healy CL, O'Connell TD, van Berlo JH. RBFOX1 Regulates Calcium Signaling and Enhances SERCA2 Translation. Cells. 2025 May 1;14(9):664. doi: 10.3390/cells14090664. PMID: 40358188; PMCID: PMC12072054.
  11. Qian G, Zhang H, Liu Y, Shribak M, Eliceiri KW, Provenzano PP. Computationally Enabled Polychromatic Polarized Imaging Enables Mapping of Matrix Architectures that Promote Pancreatic Ductal Adenocarcinoma Dissemination. Am J Pathol. 2025 May 9:S0002-9440(25)00160-9. doi:
    10.1016/j.ajpath.2025.04.017. Epub ahead of print. PMID: 40350060.
  12. Knudsen C, Moriya A, Nakato E, Gulati R, Akiyama T, Nakato H. Chondroitin sulfate regulates proliferation of Drosophila intestinal stem cells. PLoS Genet. 2025 May 9;21(5):e1011686. doi: 10.1371/journal.pgen.1011686. PMID: 40343906; PMCID: PMC12063844.
  13. Wang M, Krueger JB, Gilkey AK, Stelljes EM, Kluesner MG, Pomeroy EJ, Skeate JG, Slipek NJ, Lahr WS, Claudio Vázquez PN, Zhao Y, Bell JB, Clement K, Eaton EJ, Laoharawee K, Chang JW, Webber BR, Moriarity BS. Precision enhancement of CAR-NK cells through non-viral engineering and highly multiplexed base editing. J Immunother Cancer. 2025 May 7;13(5):e009560. doi: 10.1136/jitc-2024-009560. PMID: 40341025; PMCID: PMC12067936.
  14. Vogt CD, Broomhead JR, Kunisaki KY, Teegarden JM, Frett KL, Pacello KQ, Vitale AH, Panoskaltsis-Mortari A. Efficient wet-spinning of pre-aligned
    microtissues for 3D bioprinting complex tissue alignment. Biofabrication. 2025 May 16;17(3):035008. doi: 10.1088/1758-5090/add37f. PMID: 40315901; PMCID: PMC12083473.
  15. Hao K, Nguyen T, Nakada Y, Walcott G, Wei Y, Wu Y, Garry DJ, Yao P, Zhang J. Newborn apical resection preserves the proliferative capacity of cardiomyocytes located throughout the left ventricle. Stem Cells. 2025 May 15;43(5):sxaf018. doi: 10.1093/stmcls/sxaf018. PMID: 40229986; PMCID: PMC12080357.
  16. Lou E, Choudhry MS, Starr TK, Folsom TD, Bell J, Rathmann B, DeFeo AP, Kim J, Slipek N, Jin Z, Sumstad D, Klebanoff CA, Ladner K, Sarkari A, McIvor RS, Murray TA, Miller JS, Rao M, Jensen E, Ankeny J, Khalifa MA, Chauhan A, Spilseth B, Dixit A, Provenzano PP, Pan W, Weber D, Byrne-Steele M, Henley T, McKenna DH, Johnson MJ, Webber BR, Moriarity BS. Targeting the intracellular immune checkpoint CISH with CRISPR-Cas9-edited T cells in patients with metastatic colorectal cancer: a first-in-human, single-centre, phase 1 trial. Lancet Oncol. 2025 May;26(5):559-570. doi: 10.1016/S1470-2045(25)00083-X. Epub 2025 Apr 29. Erratum in: Lancet Oncol. 2025 Jun;26(6):e298. doi: 10.1016/S1470-2045(25)00273-6. PMID: 40315882.
  17. Kalita B, Martinez-Cebrian G, McEvoy J, Allensworth M, Knight M, Magli A, Perlingeiro RCR, Dyer MA, Stewart E, Dynlacht BD. PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma. Cell. 2025 May 15;188(10):2757-2777.e22. doi: 10.1016/j.cell.2025.03.008. Epub 2025 Apr 3. PMID: 40185100; PMCID: PMC12085299.
  18. Osborn MJ, Panda S, Reineke TM, Tolar J, Nyström A. Progress in skin gene therapy: From the inside and out. Mol Ther. 2025 May 7;33(5):2065-2081. doi: 10.1016/j.ymthe.2025.03.017. Epub 2025 Mar 12. PMID: 40077969; PMCID: PMC12126782.
  19. Rolandsson Enes S, Dzneladze I, Hampton TH, Neff SL, Asarian L, Barua J, Tertel T, Giebel B, Pereyra N, McKenna DH, et al. Acute respiratory distress vs healthy lung environments differently affect mesenchymal stromal cell extracellular vesicle miRNAs. Cytotherapy. 2025 May;27(5):581-596. doi: 10.1016/j.jcyt.2025.01.006. Epub 2025 Jan 20. PMID: 39945694.
  20. Panda S, Eaton EJ, Muralikrishnan P, Stelljes EM, Seelig D, Leyden MC, Gilkey AK, Barnes JT, Morrissey DV, Sarupria S, Moriarity BS, Reineke TM. Machine Learning Reveals Amine Type in Polymer Micelles Determines mRNA Binding, In Vitro, and In Vivo Performance for Lung-Selective Delivery. JACS Au. 2025 Apr 14;5(4):1845-1861. doi: 10.1021/jacsau.5c00084. PMID: 40313817; PMCID: PMC12041957.
  21. Mallya AS, Burrows T, Hsieh J, Louwagie T, Dutton J, Ogle B, Hubel A. DMSO-free cryopreservation of hiPSC-derived cardiomyocytes: Low temperature characterization and protocol development. Res Sq [Preprint]. 2025 Apr 14:rs.3.rs-5183739. doi: 10.21203/rs.3.rs-5183739/v1. PMID: 40321769; PMCID: PMC12047977.
  22. Katoku-Kikyo N, Kawakami H, Cantor M, Kawakami Y, Kikyo N. METTL14 regulates chondrogenesis through the GDF5-RUNX-extracellular matrix gene axis during limb development. Nat Commun. 2025 Apr 30;16(1):4072. doi: 10.1038/s41467-025-59346-5. PMID: 40307229; PMCID: PMC12043825.
  23. Nakamura N, Sato-Dahlman M, Travis E, Jacobsen K, Yamamoto M. CDX2 Promoter-Controlled Oncolytic Adenovirus Suppresses Tumor Growth and Liver Metastasis of Colorectal Cancer. Cancer Sci. 2025 Apr 24. doi: 10.1111/cas.70063. Epub ahead of print. PMID: 40275626.
  24. Henry A, Mo X, Finan C, Chaffin MD, Speed D, Issa H, Denaxas S, Ware JS, Zheng SL, Malarstig A, Gratton J, Bond I, Roselli C, Miller D, Chopade S,
    Schmidt AF, Abner E, Adams L, Andersson C, Aragam KG, Ärnlöv J, Asselin G, Raja AA, Backman JD, Bartz TM, Biddinger KJ, Biggs ML, Bloom HL, Boersma E, Brandimarto J, Brown MR, Brunak S, Bruun MT, Buckbinder L, Bundgaard H, Carey DJ, Chasman DI, Chen X, Cook JP, Czuba T, de Denus S, Dehghan A, Delgado GE, Doney AS, Dörr M, Dowsett J, Dudley SC, et al; Genes & Health Research Team; Estonian Biobank Research Team; DBDS Genomic Consortium; Asselbergs FW, Cappola TP, Dubé MP, Dunn ME, Lang CC, Samani NJ, Shah S, Vasan RS, Smith JG, Holm H, Shah S, Ellinor PT, Hingorani AD, Wells Q, Lumbers RT; HERMES Consortium. Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes. Nat Genet. 2025 Apr;57(4):815-828. doi: 10.1038/s41588-024-02064-3. Epub 2025 Mar 4. PMID: 40038546; PMCID: PMC11985341.
  25. Asakura Y, Karthikeyan S, Asakura A. Three-Dimensional Analysis of Skeletal Muscle Stem Cell Niche Following Tissue Clearing. Methods Mol Biol. 2025 Apr 5. doi: 10.1007/7651_2025_618. Epub ahead of print. PMID: 40183843.
  26. Billington CJ Jr, Rayannavar A, Tryon R, Kaye T, Gupta A, Lund TC, Lteif A, Adriatico KL, Orchard PJ, Miller BS, Pillai NR. Prognostication and Biomarker Potential of C26:0 Lysophosphatidylcholine in Adrenoleukodystrophy. JAMA Pediatr. 2025 Apr 1;179(4):465-467. doi: 10.1001/jamapediatrics.2024.6774. PMID: 39928311; PMCID: PMC11811846.
  27. Hering BJ, Rickels MR, Bellin MD, Millman JR, Tomei AA, García AJ, Shirwan H, Stabler CL, Ma M, Yi P, Luo X, Tang Q, Ramachandran S, et al. Advances in Cell Replacement Therapies for Diabetes. Diabetes. 2025 Apr 24:db250037. doi: 10.2337/db25-0037. Epub ahead of print. PMID: 40272266.
  28. Piñeiro-Llanes J, Suzuki-Hatano S, Jain A, Venigalla S, Kamat M, Basso KB, Cade WT, Simmons CS, Pacak CA. Rescue of mitochondrial dysfunction through alteration of extracellular matrix composition in barth syndrome cardiac fibroblasts. Biomaterials. 2025 Apr;315:122922. doi:
    10.1016/j.biomaterials.2024.122922. Epub 2024 Oct 26. PMID: 39509858; PMCID: PMC11625619.
  29. Venkatachalapathy H, Dallon S, Yang Z, Azarin SM, Sarkar CA, Batchelor E. Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate. Mol Syst Biol. 2025 Apr;21(4):390-412. doi: 10.1038/s44320-025-00091-8. Epub 2025 Mar 3. PMID: 40033003; PMCID: PMC11965341.
  30. Saha R, Goyal A, Yuen J, Oh Y, Bloom RP, Benally OJ, Wu K, Netoff TI, Low WC, Bennet KE, Lee KH, Shin H, Wang JP. Micromagnetic stimulation (μMS) controls dopamine release: anin vivostudy using WINCSHarmoni. Biomed Phys Eng Express. 2025 Mar 17;11(2). doi: 10.1088/2057-1976/adbaf9. PMID: 40014877.
  31. Venkatesan G, Yang HQ, Chen H, Bigliardi P, Pastorin G. Enhancement of detoxification of xenobiotic aromatic amine dyes by N-acetyltransferase 1 (NAT1) enzyme on human keratinocytes cells through structural modification. Environ Toxicol Pharmacol. 2025 Mar;114:104622. doi: 10.1016/j.etap.2024.104622. Epub 2024 Dec 25. PMID: 39725341.
  32. Ferdjallah A, Long S, DeFor TE, Hoffmann C, Wagner JE, Jacobson P, MacMillan ML. CYP2B6 genetic variation in cyclophosphamide metabolism and hemorrhagic cystitis in Fanconi anemia patients undergoing allogeneic hematopoietic cell transplantation: A descriptive genetic association study. Medicine (Baltimore). 2025 Mar 21;104(12):e41937. doi: 10.1097/MD.0000000000041937. PMID: 40128086; PMCID: PMC11936550.
  33. Vouzas AE, Sasaki T, Rivera-Mulia JC, Turner JL, Brown AN, Alexander KE, Brueckner L, van Steensel B, Gilbert DM. Transcription can be sufficient, but is not necessary, to advance replication timing. bioRxiv [Preprint]. 2025 Feb 5:2025.02.04.636516. doi: 10.1101/2025.02.04.636516. PMID: 39975371; PMCID: PMC11838563.
  34. Ingolfsland EC, Molomjamts M, Foster A, Lee H, Roehrich H, Morikuni A, Qureishy H, Tran PV, McLoon LK, Georgieff MK. Phlebotomy-induced anemia reduces oxygen-induced retinopathy severity and dampens retinal developmental transcriptomic pathways in rats. Pediatr Res. 2025 Feb;97(3):1237-1245. doi: 10.1038/s41390-024-03477-w. Epub 2024 Oct 8. PMID: 39379628.
  35. Cedars MA, Root KM, Akhaphong B, Beetch M, Miles AE, Regal RR, Alejandro EU, Regal JF. Improved glucose handling in female rat offspring of a
    hypertensive pregnancy with intrauterine growth restriction. Physiol Rep. 2025 Feb;13(3):e70222. doi: 10.14814/phy2.70222. PMID: 39903552; PMCID: PMC11792987.
  36. Wilson H, Dhawan S, Do TH, Jones SH, Chen CC. The ClearPoint Prism® Laser Ablation System: A New Platform for Laser Interstitial Thermal Therapy (LITT) in Neuro-Oncology. Neurosurg Pract. 2024 Feb 21;5(1):e00084. doi: 10.1227/neuprac.0000000000000084. PMID: 39957854; PMCID: PMC11783675.
  37. Bigliardi E, Shetty AV, Low WC, Steer CJ. Interspecies Blastocyst Complementation and the Genesis of Chimeric Solid Human Organs. Genes
    (Basel). 2025 Feb 12;16(2):215. doi: 10.3390/genes16020215. PMID: 40004544; PMCID: PMC11854981.
  38. Choe YH, Das S, Ma X, Lee H, Sorensen JR, Hoffman DB, Jo CH, Johnson CP, Cassel N, Garry DJ, Greising SM, Garry MG. Porcine myogenesis in cloned wildtype and MYF5/MYOD/MYF6-null porcine embryo. Commun Biol. 2025 Feb 11;8(1):217. doi: 10.1038/s42003-025-07648-1. PMID: 39934347; PMCID: PMC11814088.
  39. Braun LM, Giesler S, Andrieux G, Riemer R, Talvard-Balland N, Duquesne S, Rückert T, Unger S, Kreutmair S, Zwick M, Follo M, Hartmann A, Osswald N, Melchinger W, Chapman S, Hutchinson JA, Haferkamp S, Torster L, Kött J, Gebhardt C, Hellwig D, Karantzelis N, Wallrabenstein T, Lowinus T, Yücel M, Brehm N, Rawluk J, Pfeifer D, Bronsert P, Rogg M, Mattern S, Heikenwälder M, Fusco S, Malek NP, Singer S, Schmitt-Graeff A, Ceteci F, Greten FR, Blazar BR, et al. Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Cancer Cell. 2025 Feb 10;43(2):269-291.e19. doi: 10.1016/j.ccell.2025.01.004. PMID: 39933899.
  40. Yamashita AMS, Garay BI, Kim H, Bosnakovski D, Abrahante JE, Azzag K, Abreu P, Ahlquist A, Perlingeiro RCR. Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cells. Stem Cell Reports. 2025 Feb 11;20(2):102396. doi: 10.1016/j.stemcr.2024.102396. Epub 2025 Jan 30. PMID: 39889709; PMCID: PMC11864150.
  41. Motallebnejad P, Lee Z, One JL, Cichocki F, Hu WS, Azarin SM. Integrated ATAC-seq and RNA-seq analysis identifies key regulatory elements in NK cells activated with feeder cells and IL-2. Bioeng Transl Med. 2025 Feb 26;10(3):e10747. doi: 10.1002/btm2.10747. PMID: 40385536; PMCID:
    PMC12079432.
  42. Sakurai H, Suzuki M, Asakura A. Editorial: Induced pluripotent stem cells (iPSCs) for skeletal muscle diseases. Front Cell Dev Biol. 2025 Jan 29;13:1556403. doi: 10.3389/fcell.2025.1556403. PMID: 39944085; PMCID: PMC11814464.
  43. Rathe SK, White JP, Sachs Z, Largaespada DA. DEAPR: Differential Expression and Pathway Ranking Tool Demonstrates NRASG12V and NRASG12D Mutations Have Differing Effects in THP-1 Cells. Cancers (Basel). 2025 Jan 30;17(3):467. doi:
    10.3390/cancers17030467. PMID: 39941834; PMCID: PMC11816133.
  44. Negm L, Chung J, Nobre L, Bennett J, Fernandez NR, Nunes NM, Liu ZA, Komosa M, Aronson M, Zhang C, Stengs L, Bianchi V, Edwards M, Doherty S, Ercan AB, Cardenas MF, Macias M, Lueder MR, Ku M, Johnson M, Chang Y, Dimayacyac JR, Kraya AA, Guo Y, Naky S, Keith J, Gao AF, Munoz DG, Nguyen L, Tsang DS, Lim-Fat MJ, Das S, Shlien A, Ramaswamy V, Huang A, Malkin D, Villani A, Ertl-Wagner B, Levine A, Robinson GW, Pollock BH, Spector LG, et al. The landscape of primary mismatch repair deficient gliomas in children, adolescents, and young adults: a multi-cohort study. Lancet Oncol. 2025 Jan;26(1):123-135. doi: 10.1016/S1470-2045(24)00640-5. Epub 2024 Dec 16. PMID: 39701117.
  45. Gustafson AL, Durbin AD, Artinger KB, Ford HL. Myogenesis gone awry: the role of developmental pathways in rhabdomyosarcoma. Front Cell Dev Biol. 2025 Jan 20;12:1521523. doi: 10.3389/fcell.2024.1521523. PMID: 39902277; PMCID: PMC11788348.
  46. Grattoni A, Korbutt G, Tomei AA, García AJ, Pepper AR, Stabler C, Brehm M, Papas K, Citro A, Shirwan H, Millman JR, Melero-Martin J, Graham M, Sefton M, Ma M, Kenyon N, Veiseh O, Desai TA, Nostro MC, Marinac M, Sykes M, Russ HA, Odorico J, Tang Q, Ricordi C, Latres E, Mamrak NE, Giraldo J, Poznansky MC, de Vos P. Harnessing cellular therapeutics for type 1 diabetes mellitus: progress, challenges, and the road ahead. Nat Rev Endocrinol. 2025 Jan;21(1):14-30. doi: 10.1038/s41574-024-01029-0. Epub 2024 Sep 3. PMID: 39227741; PMCID: PMC11938328.
  47. Wyllie MK, Morris CK, Moeller NH, Schares HAM, Moorthy R, Belica CA, Grillo MJ, Demir Ö, Ayoub AM, Carpenter MA, Aihara H, Harris RS, Amaro RE, Harki DA. The Impact of Sugar Conformation on the Single-Stranded DNA Selectivity of APOBEC3A and APOBEC3B Enzymes. ACS Chem Biol. 2025 Jan 17;20(1):117-127. doi: 10.1021/acschembio.4c00540. Epub 2024 Dec 16. PMID: 39680033.
  48. Komosa ER, Lin WH, Ogle BM. Toward robust and reproducible pluripotent stem cell expansion in bioprinted GelMA constructs. Int J Bioprint. 2025;11(1):363-381. doi: 10.36922/ijb.4633. Epub 2024 Dec 10. PMID: 40330989; PMCID: PMC12052315.
  49. Rathe SK, White JP, Sachs Z, Largaespada DA. DEAPR: Differential Expression and Pathway Ranking Tool Demonstrates NRASG12V and NRASG12D Mutations Have Differing Effects in THP-1 Cells. Cancers (Basel). 2025 Jan 30;17(3):467. doi: 10.3390/cancers17030467. PMID: 39941834; PMCID: PMC11816133.
  50. Var SR, Strell P, Shetty A, Roman A, Clark IH, Crane AT, Dunbar GL, Fink K, Grande AW, Parr AM, Rossignol J, Sanberg PR, Zhao LR, Zholudeva LV, Low WC; American Society for Neural Therapy and Repair Task Force. Research Guideline Recommendations for Research on Stem Cells, Human Embryos, and Gene Editing. Cell Transplant. 2025 Jan-Dec;34:9636897241312793. doi: 10.1177/09636897241312793. PMID: 40007211; PMCID: PMC11863228.