Cincinnati Children's Hospital Medical Center
Matt Kofron
3333 Burnet Avenue
Cincinnati, OH 45229-3026
https://www.cincinnatichildrens.org/research/cores/confocal-imaging
RRID: RRID:SCR_022628
1.) McCoy C, Dusing M, Jerow LG, Winstel GC, Zhan F, Rogers JL, Wesley M, Otten JB, Danzer SC, LaSarge CL (2025 Nov 3). Focal postnatal deletion of Tsc2 causes epilepsy Frontiers in Molecular Neuroscience, 18(), 1686023. . PMCID: 12620446.
2.) Peters AL, DePasquale EAK, Begum G, Roskin KM, Kotliar M, Barski A, Salomonis N, Shi T, Ranganathan S, Woodle ES, Hildeman DA (2025 Nov). Single-cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 25(11), 2345-2360. doi: 10.1016/j.ajt.2025.08.004. PMID: 40812614.
3.) Caldwell JT, Shi T, Burg AR, Koby A, Roskin KM, Peters AL, DePasquale EA, Woodle ES, Hildeman DA (2025 Oct 24). CO-STIMULATORY BLOCKADE PREVENTS INTRAGRAFT ACCRUAL OF CLASS-SWITCHED, ACTIVATED B CELLS DESPITE FAILING TO PREVENT T-CELL MEDIATED REJECTION bioRxiv, (), 2025.10.24.683156. . PMCID: 12633403.
4.) Yoo JJ, Serafin EK, Kofron JM, Baccei ML (2025 Oct 15). Early Life Injury Alters Spinal Astrocyte Development. The Journal of neuroscience : the official journal of the Society for Neuroscience, 45(42), . . PMID: 40935666.
5.) Edwards NA, Rankin SA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Kofron M, Shen Y, Chung WK, Zorn AM (2025 Sep 22). Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in Xenopus trachea-esophageal morphogenesis. Developmental cell, 60(18), 2487-2502.e4. . PMID: 40412385.
6.) Han SJY, Adani V, Farrow E, Parma B, Chang CF, Cochran K, Ramkissoon PJK, Esteban E, Elliott KH, Peterson KA, Gebelein BA, Garcia-Castro MI, Brugmann SA (2025 Aug 31). A dual role for GLI3 signaling in neural crest development. bioRxiv : the preprint server for biology, (), . . PMID: 40909740.
7.) Thakkar K, Yarlagadda S, Alkhudairy L, Potter A, Thorner K, Chaturvedi P, McCracken KW, Salomonis N, Kopan R, Schuh MP (2025 Aug 22). Bridging the gap of late-gestation nephrogenesis using a non-human primate model bioRxiv, (), 2025.08.18.670897. . PMCID: 12393440.
8.) Miao Y, Pek NM, Tan C, Jiang C, Yu Z, Iwasawa K, Shi M, Kechele DO, Sundaram N, Pastrana-Gomez V, Sinner DI, Liu X, Lin KC, Na CL, Kishimoto K, Yang MC, Maharjan S, Tchieu J, Whitsett JA, Zhang YS, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M (2025 Aug 7). Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids. Cell, 188(16), 4295-4313.e27. doi: 10.1016/j.cell.2025.05.041. PMID: 40592324.
9.) Clough CA, Cunningham C, Philbrook SY, Hueneman KM, Sampson AM, Choi K, Greis KD, Starczynowski D (2025 Aug). Characterization of E1 enzyme dependencies in mutant-UBA1 human cells reveals UBA6 as a novel therapeutic target in VEXAS syndrome. Leukemia, 39(8), 1997-2009. . PMID: 40588566.
10.) Canaday LM, Cox A, Feldman HA, Seelamneni H, Ali A, Tuazon JA, Botero Calderon L, Bennett SN, Yan A, Wilson M, Velu V, Waggoner SN (2025 Aug 1). Refined cell transfer model reveals roles for Ascl2 and Cxcr3 in splenic localization of mouse NK cells during virus infection. Journal of immunology (Baltimore, Md. : 1950), 214(8), 1917-1925. . PMID: 40694683.
11.) Shi M, Crouse B, Sundaram N, Pode Shakked N, Thorner K, King NM, Dutta P, Ester L, Zhang W, Govindarajah V, Kopan R, Cebrian C, Mayhew CN, Helmrath MA, Bonventre JV, McCracken KW (2025 Jul 3). Integrating collecting systems in human kidney organoids through fusion of distal nephron to ureteric bud. Cell stem cell, 32(7), 1055-1070.e8. . PMID: 40345193.
12.) Indugula S, Yarlagadda S, Drumgool L, Lindquist D, Fugate E, Walters S, Rudman-Melnick V, Charlton JR, VandenHeuvel K, Dudley J, Schuh MP (2025 Jul 1). Windows of susceptibility to neonatal acute kidney injury and nephron loss in a rabbit model. Scientific reports, 15(1), 21160. . PMID: 40596708.
13.) Ushuhuda EG, Nguyen JT, Pfaltzgraff NG, Kofron M, Mikedis MM (2025 Jun 15). MEIOC prevents continued mitotic cycling and promotes meiotic entry during mouse oogenesis bioRxiv, (), 2025.06.12.659330. . PMCID: 12258517.
14.) Iwasawa K, Koike H, Al Reza H, Milton Y, Kishimoto K, Thorner K, Granitto M, Saiki N, Santangelo C, Glaser K, Kimura M, Bondoc A, Lim HW, Morimoto M, Iwafuchi M, Wells JM, Zorn AM, Takebe T (2025 Jun 8). Primitive Hepatoblasts Driving Early Liver Development bioRxiv, (), 2025.06.08.658502. . PMCID: 12157602.
15.) Al Reza H, Santangelo C, Iwasawa K, Al Reza A, Sekiya S, Glaser K, Bondoc A, Merola J, Takebe T (2025 Apr 16). Multi-zonal liver organoids from human pluripotent stem cells Nature, 641(8065), 1258-1267. . PMCID: 12488051.
16.) Kinoshita Y, Kobayashi E, Matsui K, Inage Y, Morimoto K, Yamamoto S, Iwai S, Kitada K, Iwasawa K, Saito Y, Fujimoto T, Matsumoto K, Nagamori S, Nishiyama A, Kume H, Takebe T, Yokoo T, Yamanaka S (2025 Mar 22). Life-supporting functional kidney replacement by integration of embryonic metanephros-bladder composite tissue transplants Kidney international, 107(6), 1051-1063. . PMCID: 12521919.
17.) Liu B, Sajiki Y, Littlefield N, Hu Y, Stuart WD, Sridharan A, Cui X, Siefert ME, Araki K, Ziady AG, Shi D, Whitsett JA, Maeda Y (2025 Mar 5). PBAE-PEG-based lipid nanoparticles for lung cell-specific gene delivery. Molecular therapy : the journal of the American Society of Gene Therapy, 33(3), 1154-1165. . PMID: 39865654.
18.) Candor K, Ding L, Balchand S, Hammonds JE, Spearman P (2025 Mar). The CLIC/GEEC pathway regulates particle uptake and formation of the virus-containing compartment (VCC) in HIV-1-infected macrophages. PLoS pathogens, 21(3), e1012564. . PMID: 40067817.
19.) Walling I, Baumgartner S, Patel M, Crone SA (2025 Jan 22). Electrical stimulation of the sciatic nerve restores inspiratory diaphragm function in mice after spinal cord injury Frontiers in Neural Circuits, 18(), 1480291. . PMCID: 11794311.
20.) Halurkar MS, Inoue O, Singh A, Mukherjee R, Ginugu M, Ahn C, Bonatto Paese CL, Duszynski M, Brugmann SA, Lim HW, Sanchez-Gurmaches J (2025 Jan 17). The widely used Ucp1-Cre transgene elicits complex developmental and metabolic phenotypes. Nature communications, 16(1), 770. . PMID: 39824816.
21.) Tominaga K, Kechele DO, Sanchez JG, Vales S, Jurickova I, Roman L, Asai A, Enriquez JR, McCauley HA, Kishimoto K, Iwasawa K, Singh A, Horio Y, Múnera JO, Takebe T, Zorn AM, Helmrath MA, Denson LA, Wells JM (2024 Dec 17). Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells Cellular and Molecular Gastroenterology and Hepatology, 19(4), 101444. . PMCID: 11847122.
22.) Dai Q, Preusse K, Yu D, Kovall RA, Thorner K, Lin X, Kopan R (2024 Dec). Loss of Notch dimerization perturbs intestinal homeostasis by a mechanism involving HDAC activity. PLoS genetics, 20(12), e1011486. . PMID: 39666740.
23.) Shi M, Crouse B, Sundaram N, Pode Shakked N, Ester L, Zhang W, Janakiram V, Kopan R, Helmrath MA, Bonventre JV, McCracken KW (2024 Sep 20). Integrating collecting systems in kidney organoids through fusion of distal nephron to ureteric bud bioRxiv, (), 2024.09.19.613645. . PMCID: 11429897.
24.) Schrenk S, Bischoff LJ, Boscolo E (2024 Sep 20). Protocol for three-dimensional whole-mount imaging of the vascular network in the intestinal muscle. STAR protocols, 5(3), 103170. . PMID: 38968077.
25.) He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA (2024 Sep 16). PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function Nature Communications, 15(), 8112. . PMCID: 11405758.
26.) Sheth M, Sharma M, Lehn M, Reza H, Takebe T, Takiar V, Wise-Draper T, Esfandiari L (2024 Sep). Three-dimensional matrix stiffness modulates mechanosensitive and phenotypic alterations in oral squamous cell carcinoma spheroids. APL bioengineering, 8(3), 036106. . PMID: 39092008.
27.) Al Reza H, Santangelo C, Al Reza A, Iwasawa K, Sachiko S, Glaser K, Bondoc A, Merola J, Takebe T (2024 Aug 30). Self-Assembled Generation of Multi-zonal Liver Organoids from Human Pluripotent Stem Cells bioRxiv, (), 2024.08.30.610426. . PMCID: 11384014.
28.) Waggoner S, Cox A, Canaday L, Katko A, Feldman H, Warrick K, Tselikova A, Seelamneni H, Roskin K (2024 Aug 30). KLF2 determines the susceptibility of T cells to immunoregulatory NK cells Research Square, (), rs.3.rs-4921081. . PMCID: 11384801.
29.) Rochman M, Klinger AM, Caldwell JM, Sadovsky Y, Rothenberg ME (2024 Aug 27). Amniotic fluid modifies esophageal epithelium differentiation and inflammatory responses American Journal of Physiology - Gastrointestinal and Liver Physiology, 327(5), G629-G639. . PMCID: 11559652.
30.) DeVore SB, Schuetz M, Alvey L, Lujan H, Ochayon DE, Williams L, Chang WC, Filuta A, Ruff B, Kothari A, Hahn JM, Brandt E, Satish L, Roskin K, Herr AB, Biagini JM, Martin LJ, Cagdas D, Keles S, Milner JD, Supp DM, Khurana Hershey GK (2024 Aug 27). Regulation of MYC by CARD14 in human epithelium is a determinant of epidermal homeostasis and disease. Cell reports, 43(8), 114589. . PMID: 39110589.
31.) Pfaltzgraff NG, Liu B, de Rooij DG, Page DC, Mikedis MM (2024 Jul 15). Destabilization of mRNAs enhances competence to initiate meiosis in mouse spermatogenic cells. Development (Cambridge, England), 151(14), . . PMID: 38884383.
32.) Peters AL, DePasquale EAK, Begum G, Roskin KM, Woodle ES, Hildeman DA (2024 Feb 29). Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution. bioRxiv : the preprint server for biology, (), . . PMID: 38464256.
33.) Drake AW, Jerow LG, Ruksenas JV, McCoy C, Danzer SC (2024). Somatostatin interneuron fate-mapping and structure in a Pten knockout model of epilepsy. Frontiers in cellular neuroscience, 18(), 1474613. . PMID: 39497922.
34.) He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA (2023 Dec 20). PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function bioRxiv, (), 2023.12.20.570481. . PMCID: 10769259.
35.) Pode-Shakked N, Slack M, Sundaram N, Schreiber R, McCracken KW, Dekel B, Helmrath M, Kopan R (2023 Dec 9). RAAS-deficient organoids indicate delayed angiogenesis as a possible cause for autosomal recessive renal tubular dysgenesis. Nature communications, 14(1), 8159. . PMID: 38071212.
36.) Parkins EV, Brager DH, Rymer JK, Burwinkel JM, Rojas D, Tiwari D, Hu YC, Gross C (2023 Dec 8). Mir324 knockout regulates the structure of dendritic spines and impairs hippocampal long-term potentiation. Scientific reports, 13(1), 21919. . PMID: 38082035.
37.) LaSarge CL, McCoy C, Namboodiri DV, Hartings JA, Danzer SC, Batie MR, Skoch J (2023 Dec). Spatial and Temporal Comparisons of Calcium Channel and Intrinsic Signal Imaging During in Vivo Cortical Spreading Depolarizations in Healthy and Hypoxic Brains. Neurocritical care, 39(3), 655-668. doi: 10.1007/s12028-022-01660-7. PMID: 36539593.
38.) Edwards NA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Shen Y, Chung WK, Zorn AM (2023 Nov 21). Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. bioRxiv : the preprint server for biology, (), . . PMID: 37873300.
39.) Reza HA, Farooqui Z, Reza AA, Conroy C, Iwasawa K, Ogura Y, Okita K, Osafune K, Takebe T (2023 Nov 14). Synthetic augmentation of bilirubin metabolism in human pluripotent stem cell-derived liver organoids. Stem cell reports, 18(11), 2071-2083. . PMID: 37832542.
40.) Carpenter J, Yarlagadda S, VandenHeuvel KA, Ding L, Schuh MP (2023 Nov 4). Human Nephrogenesis can Persist Beyond 40 Postnatal Days in Preterm Infants Kidney International Reports, 9(2), 436-450. . PMCID: 10851065.
41.) Múnera JO, Kechele DO, Bouffi C, Qu N, Jing R, Maity P, Enriquez JR, Han L, Campbell I, Mahe MM, McCauley HA, Zhang X, Sundaram N, Hudson JR, Zarsozo-Lacoste A, Pradhan S, Tominaga K, Sanchez JG, Weiss AA, Chatuvedi P, Spence JR, Hachimi M, North T, Daley GQ, Mayhew CN, Hu YC, Takebe T, Helmrath MA, Wells JM (2023 Nov 2). Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon Cell stem cell, 30(11), 1434-1451.e9. . PMCID: 10913028.
42.) Parkins EV, Burwinkel JM, Ranatunga R, Yaser S, Hu YC, Tiwari D, Gross C (2023 Oct). Age-Dependent Regulation of Dendritic Spine Density and Protein Expression in Mir324 KO Mice. Journal of molecular neuroscience : MN, 73(9), 818-830. . PMID: 37773316.
43.) Mikedis MM, Liu B, de Rooij DG, Page DC (2023 Sep 22). Post-transcriptional repression of mRNA enhances competence to transit from mitosis to meiosis in mouse spermatogenic cells bioRxiv, (), 2023.09.20.557439. . PMCID: 10541148.
44.) Parkins EV, Burwinkel JM, Ranatunga R, Yaser S, Hu YC, Tiwari D, Gross C (2023 Aug 7). Age-dependent regulation of dendritic spine density and protein expression in Mir324 KO mice. Research square, (), . . PMID: 37609225.
45.) Witcher PC, Sun C, Millay DP (2023 May 1). Expression of Myomaker and Myomerger in myofibers causes muscle pathology Skeletal Muscle, 13(), 8. . PMCID: 10150476.
46.) Doll JR, Moreno-Fernandez ME, Stankiewicz TE, Wayland JL, Wilburn A, Weinhaus B, Chougnet CA, Giordano D, Cappelletti M, Presicce P, Kallapur SG, Salomonis N, Tilburgs T, Divanovic S (2023 Apr 25). BAFF and APRIL counterregulate susceptibility to inflammation-induced preterm birth. Cell reports, 42(4), 112352. . PMID: 37027297.
47.) Brooks EC, Han SJY, Bonatto Paese CL, Lewis AA, Aarnio-Peterson M, Brugmann SA (2024 Jul-Aug). The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning. Differentiation; research in biological diversity, 138(), 100782. . PMID: 38810379.
The Bio-Imaging and Analysis Facility at Cincinnati Children\'s Hospital Medical Center (CCHMC) provides access to and training on state-of-the-art optical microscopes and associated equipment. The facility and expertise are available to investigators at CCHMC and the University of Cincinnati College of Medicine. The BIAF is a Nikon Center of Excellence. This agreement combines the biological expertise of CCHMC with Nikon’s technical proficiency to further new developments in biomedical sciences to improve child health.
