Yongho Bae PhD

Yongho Bae

Yongho Bae
PhD

Assistant Professor

Department of Pathology and Anatomical Sciences

Jacobs School of Medicine & Biomedical Sciences


Specialty/Research Focus

Cell Cycle; Cell growth, differentiation and development; Cytoskeleton and cell motility; Gene Expression; Genomics and proteomics; Molecular and Cellular Biology; Molecular Basis of Disease; Signal Transduction

Contact Information
955 Main Street, Room 4262
Pathology and Anatomical Sciences
Buffalo, New York 14203-1121
Phone: 716-829-3523
Fax: 716-829-2911
yonghoba@buffalo.edu



Professional Summary:

I am a cell biologist and bioengineer, and my primary research focuses on the rapidly growing area of cell mechanics and mechanotransduction: the role that mechanical forces play in regulating cellular function from healthy to diseased phenotypes.

(1) Cardiovascular Biology, Mechanics and Disease:
Funding source: American Heart Association (7/1/2018–6/30/2022; PI)
Cardiovascular disease (CVD) is the main cause of death globally. Arterial stiffness is associated with many CVD. The molecular mechanisms governing arterial stiffening and the phenotypic changes in vascular smooth muscle cells (VSMCs) associated with the stiffening process are key areas in cardiovascular biology, mechanics and disease. Evidence suggests that arterial stiffening can drive aberrant migration and proliferation of VSMCs within the vessel wall. Yet, the underlying mechanisms regulating vascular stiffening and the molecular changes within VSMCs associated with the stiffening process remain unclear. While medications reduce hypertension, none specifically target pathways directly related to arterial stiffness.
The overall goal of work in my lab is to address this gap in our understanding by investigating how changes in arterial stiffness affect VSMC function and fundamentally contribute to the progression of CVD. This study also addresses an important concept in vascular tissue remodeling (the interaction between extracellular matrix stiffness and VSMC behavior). Methodologically, my lab use a novel approach to dissect the molecular mechanism in VSMCs: My lab combines methods for manipulating and measuring tissue and cell stiffness using atomic force microscopy and traction force microscopy for simultaneously modulating substrate stiffness and measuring contraction force by culturing cells on a compliant substrate that mimics in vivo mechanical environments of the VSMCs.

(2) Smooth Muscle Cell Heterogeneity:
Highly heterogeneous responses of VSMCs to arterial stiffness or CVD make it difficult to dissect underlying molecular mechanisms. To overcome this, my lab integrates Mechanobiology, Vascular Cell Biology, and Machine Learning to manipulate stiffness and assess responses with unique precision. Machine learning is used to deconvolve inter- and intracellular heterogeneity and identify specific subcellular traits that correlate with stiffness and VSMC behavior.

(3) Optogenetics and Biophotonics in Stem Cell Biology:
Funding source: National Science Foundation (8/1/2017–7/31/2021; co-PI)
National Science Foundation (2/1/2021–1/31/2024; co-PI)
Major breakthroughs in the field of genomics, embryonic stem cell biology, optogenetics and biophotonics are enabling the control and monitoring of biological processes through light. Additional research in my laboratory focuses on developing a nanophotonic platform able to activate/inactivate gene expression and, thus, control stem cell differentiation in neuronal cells, by means of light-controlled protein-protein interactions. More specifically, the light-controlled molecular toggle-switch based on Plant Phytochrome B and transcription factor Pif6 will be utilized to control the nuclear fibroblast growth factor receptor-1, which is a master regulator of stem cell differentiation.

Open Positions: The Bae lab is currently accepting graduate students through the Pathology and Biomedical Engineering Masters program as well as motivated undergraduates.

For Graduate Students: I am looking for one or two graduate (MS) students who understand my research interests, have read my previous publications, and have their own ideas as to where my research efforts should be directed. All graduate students are required to complete and submit internationally recognized Journal article(s) before graduation from my lab. A Masters thesis should generate at least one first author publication.

For Undergraduate Students: I encourage all UB undergraduates (with GPA 3.0 or higher) to get "hands on" experimental training in the sciences. An undergraduate research project tends to be part of a larger whole, but I make sure to include credit for students work in presentations and publications.

Education and Training:

  • PhD, Bioengineering, University of Pittsburgh (2010)
  • MS, Chemical and Biochemical Engineering, Rutgers University, The State University of New Jersey (2005)
  • BS, Biotechnology, AJou University (1998)

Employment:

  • Assistant Professor, Pathology and Anatomical Sciences, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2017-present)
  • Research Associate, Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine (2015–2016)
  • Post Doctoral Fellow, Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine (2010–2015)
  • American Heart Association Postdoctoral Fellow, Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine (2013–2014)

Awards and Honors:

  • Buffalo Blue Sky Silver Coin (2019)
  • American Heart Association Career Development Award (2018)
  • Eugene Mindell & Harold Brody Clinical Translational Research Award (2017)
  • Cell & Molecular Bioengineering Meeting: Fellow Travel Award (2015)
  • American Heart Association Postdoctoral Fellowship (2013)

Research Expertise:

  • Atomic Force Microscopy
  • Cell Mechanics and Mechanobiology
  • Cell, Vascular and Cancer Biology
  • Optogenetics and Optogenomics

Grants and Sponsored Research:

  • February 2021–January 2024
    Collaborative Research: Control of Information Processing and Learning in Neuronal Networks through Light-mediated Programming of Genomic Networks
    National Science Foundation
    Role: Co-Principal Investigator
    $366,284
  • August 2017–July 2022
    Networked Nanophotonic Devices for Stem Cell Regulation: From Optogenetics to Optogenomics
    National Science Foundation
    Role: Co-Principal Investigator
    $599,067
  • July 2018–June 2022
    Mechanotransduction in Vascular Smooth Muscle: Survivin as a Mediator of Stiffness-Induced Responses
    American Heart Association
    Role: Principal Investigator
    $266,000
  • January 2019–June 2020
    Non-invasive neuronal-vascular stimulation
    Buffalo Blue Sky Project, University at Buffalo
    Role: Co-Principal Investigator
    $30,000
  • January 2013–December 2014
    American Heart Association Postdoctoral Fellowship
    American Heart Association
    Role: Principal Investigator
    $93,000

Journal Articles:

  • Brazzo JA, Biber JC, Nimmer E, Heo Y, Ying L, Zhao R, Lee K, Krause M, Bae Y. (2021) Mechanosensitive expression of lamellipodin promotes intracellular stiffness, cyclin expression and cell proliferation. Journal of cell science (Jun), 134(12)
  • Xia B, Kim DH, Bansal S, Bae Y, Mauck RL, Heo SJ. (2021) Development of a decellularized meniscus matrix-based nanofibrous scaffold for meniscus tissue engineering. Acta biomaterialia (Apr)
  • Vaidyanathan K, Wang C, Krajnik A, Yu Y, Choi M, Lin B, Heo SJ, Kolega J, Lee K, Bae Y. (2020) Machine learning reveals heterogeneous responses to FAK, Rac, Rho, and Cdc42 inhibition on vascular smooth muscle cell spheroid formation and morphology. bioRxiv (Sep)
  • Krajnik A, Brazzo JA, Vaidyanathan K, Das T, Redondo-Muñoz J, Bae Y. (2020) Phosphoinositide Signaling and Mechanotransduction in Cardiovascular Biology and Disease. Frontiers in cell and developmental biology (Jan), 8: 595849. doi:10.3389/fcell.2020.595849
  • Jornet JM*, Bae Y*, Handelmann CR, Decker B, Balcerak A, Sangwan A, Miao P, Desai A, Feng L*, Stachowiak EK, Stachowiak MK*. (2019) Optogenomic Interfaces: Bridging Biological Networks With the Electronic Digital World. Proceedings of the IEEE (Jul), 107(7): 1387-1401.
  • Wirdatmadja S, Johari P, Desai A, Bae Y, Stachowiak E, Stachowiak M, Jornet JM, Balasubramaniam S. (2019) Analysis of Light Propagation on Physiological Properties of Neurons for Nanoscale Optogenetics. IEEE Transactions on Neural Systems & Rehabilitation Engineering (Feb), 27(2): 108-117.
  • Liu SL, Bajpai A, Hawthorne EA, Bae Y, Castagnino P, Monslow J, Puré E, Spiller KL, Assoian RK. (2019) Cardiovascular protection in females linked to estrogen-dependent inhibition of arterial stiffening and macrophage MMP12. JCI Insight (Jan), 4(1).
  • Wang C, Choi HJ, Kim SJ, Desai A, Lee N, Kim D, Bae Y, Lee K. (2018) Deconvolution of subcellular protrusion heterogeneity and the underlying actin regulator dynamics from live cell imaging. Nature communications (Apr), 9(1): 1688. doi:10.1038/s41467-018-04030-0
  • Courtenay JC, Deneke C, Lanzoni EM, Costa CA, Bae Y, Scott JL, Sharma RI. (2018) Modulating cell response on cellulose surfaces; tunable attachment and scaffold mechanics. Cellulose (London, England) (Jan), 25(2): 925-940. doi:10.1007/s10570-017-1612-3
  • Mui KM, Bae YH, Gao L, Liu S, Xu T, Radice GL, Chen CS, and Assoian RK. (2015) N-Cadherin Induction by ECM Stiffness and FAK Overrides the Spreading Requirement for Proliferation of Vascular Smooth Muscle Cells. Cell Reports (Mar), 10(9).
  • Bae YH¶, Mui KL, Hsu BY, Liu SL, Cretu A, Razinia Z, Xu T, Puré E, Assoian RK¶. Featured cover article; ¶corresponding author). (2014) A FAK-Cas-Rac-Lamellipodin Signaling Module Transduces Extracellular Matrix Stiffness into Mechanosensitive Cell Cycling. Science Signaling (Jun), 7(330).
  • Kothapalli D, Liu SL, Bae YH, Monslow J, Xu T, Hawthorne EA, Byfield FJ, Castagnino P, Rao S, Rader DJ, Puré E, Phillips MC, Lund-Katz S, Janmey PA, Assoian RK. (2012) Cardiovascular protection by ApoE and ApoE-HDL linked to suppression of ECM gene expression and arterial stiffening. Cell Reports (Nov), 2(5).
  • Choi HJ, Wang C, Pan X, Jang J, Cao M, Brazzo J, Bae Y, Lee K. (2021) Emerging machine learning approaches to phenotyping cellular motility and morphodynamics. Physical biology (May)
  • Decker B, Liput M, Abdellatif H, Yergeau D, Bae Y, Jornet JM, Stachowiak EK, Stachowiak MK. (2020) Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1-The Genome Archipelago Model. International journal of molecular sciences (Dec), 22(1) doi:10.3390/ijms22010347
  • Johns MA, Bae Y, Guimarães FEG, Lanzoni EM, Costa CAR, Murray PM, Deneke C, Galembeck F, Scott JL, Sharma RI. (2018) Predicting Ligand-Free Cell Attachment on Next-Generation Cellulose-Chitosan Hydrogels. ACS omega (Jan), 3(1): 937-945. doi:10.1021/acsomega.7b01583
  • Bae YH¶, Liu SL, Byfield FJ, Janmey PA, Assoian RK. (¶ corresponding author). (2016) Measuring the Stiffness of Ex Vivo Mouse Aortas Using Atomic Force Microscopy. Journal of Visualized Experiments (Oct), 116.
  • Liu SL, Bae YH, Yu C, Monslow J, Hawthorne E, Castagnino P, Branchetti E, Ferrari G, Damrauer SM, Puré E, Assoian RK. (2015) Matrix metalloproteinase-12 is an essential mediator of acute and chronic arterial stiffening. Scientific Reports (Nov), 5(17189).
  • Hsu B*, Bae YH*¶, Mui KL, Liu SL, and Assoian RK (*co-first & ¶ corresponding author). (2015) Apolipoprotein E3 inhibits Rho to regulate the mechanosensitive expression of Cox2. PLoS ONE (Jun), 10(6).
  • Ding Z, Bae YH, Roy P. (2012) Molecular insights on context-specific role of profilin-1 in cell migration. Cell Adhesion & Migration (Sep), 6(5).
  • Bae YH, Ding Z, Das T, Wells A, Gertler F, Roy P. (2010) Profilin1 regulates PI(3,4)P2 and lamellipodin accumulation at the leading edge thus influencing motility of MDA-MB-231 cells. Proceedings of the National Academy of Sciences (Dec), 107(50).
  • Leloup L, Shao H, Bae YH, Deasy B, Stolz D, Roy P, Wells A. (2010) m-Calpain activation is regulated by its membrane localization and by its binding to phosphatidylinositol 4,5-bisphosphate. Journal of Biological Chemistry (Oct), 285(43).
  • Bae YH, Ding Z, Zou L, Wells A, Gertler F, Roy P. (2009) Loss of profilin-1 expression enhances breast cancer cell motility by Ena/VASP proteins. Journal of Cellular Physiology (May), 219(2).
  • Das T, Bae YH, Wells A, Roy P. (2009) Profilin-1 overexpression upregulates PTEN and suppresses AKT activation in breast cancer cells. Journal of Cellular Physiology (Feb), 218(2).
  • Bae YH, Johnson PA, Florek CA, Kohn J, Moghe PV. (2006) Minute changes in composition of polymer substrates produce amplified differences in cell adhesion and motility via optimal ligand conditioning. Acta Biomaterialia (Sep), 2(5).
See all (14 more)

Books and Book Chapters:

  • Chuye LB, Dimitri A, Desai A, Handelmann C, Bae Y, Johari P, Jornet JM, Stachowiak MK, Stachowiak EK. (2018) Series: Results and Problems in Cell Differentiation. In: Brain Organoids – expanding our understanding of human development and disease. In "Human Neural Stem Cells: From Generation to Differentiation and Application” L. Buzanska (Ed).
  • Roy P, Jaramillo M, Bae YH, Das T. (2008) In: Actin cytoskeleton and cancer. In The motile actin system in health and disease. (C. Ampe and A. Lambrechts, eds.).

Professional Memberships:

  • Cellular and Molecular Bioengineering (2014–present)
  • American Heart Association (2012–present)
  • Biomedical Engineering Society (2008–present)
  • American Society for Cell Biology (2007–present)

Service Activities:

  • University at Buffalo; Member, UB Faculty Senate (2021–present)
  • Faculty Search Committee, Department of Pathology and Anatomical Sciences, UB; Faculty Search Committee Member (2021–present)
  • Frontiers in Cardiovascular Medicine; Topic co-editor of "Lipids in Mechanobiology" (2021–present)
  • Life by MDPI; Topical Advisory Panel Members (2020–present)
  • Ph.D. Program in Biomedical Science Admissions Committee, Jacobs School of Medicine and Biomedical Sciences; Secondary Member (2019–2020)
  • M.D./Ph.D. Admission Interview/Research Discussion, Jacobs School of Medicine and Biomedical Sciences; Interviewer (2019–present)
  • Department of Pathology and Anatomical Sciences; Research office representative (2019–present)
  • M.D./Ph.D. Admission Interview/Research Discussion, Jacobs School of Medicine and Biomedical Sciences; Interviewer (2019–present)
  • Ph.D. Program in Biomedical Science Admissions Committee, Jacobs School of Medicine and Biomedical Sciences; Primary Member (2017–2018)
  • PPBS Recruitment Day Departmental Poster Session; Faculty Representative (2017–present)
  • PPBS Recruitment Day Departmental Poster Session; Faculty Representative (2017–present)
  • Journal of Microbiology and Pathology; Editorial Board Member (2017–present)
  • Graduate Admissions Committee, Department of Pathology and Anatomical Sciences, UB; Graduate Admissions Committee (2017–present)
  • Journal of Biomedical Engineering and Informatics; Editorial Board Member (2015–present)
  • Departmental equipment negotiating and purchasing: NX12 atomic force microscope (Park Systems), BIO-X 3D Bioprinters (CELLINK), Ultramicrotome EM UC7 (Leica), and Optical Tweezer (ThorLabs)
  • 6/2021. NIH- Intercellular Interactions Study Section; Ad Hoc reviewer
  • 2019: Israel Science Foundation; Ad Hoc reviewer for a grant proposal
  • 2019 & 2020 PPBS Admission Interview Day; Faculty Interviewer
  • • Peer reviewer for Cancer Research, Journal of Vascular Research, Cell Cycle, Scientific Reports, PLoS One, Integrative Biology, Cellular and Molecular Bioengineering, BioEssays, Cellulose, Current Biotechnology, Journal of Tissue Engineering, Journal of the Mechanical Behavior of Biomedical Materials, and Journal of Imaging; Peer Reviewer
  • 2019: 6th ACM International Conference on Nanoscale Computing and Communication; Technical program committee member

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Contact Information

955 Main Street, Room 4262
Pathology and Anatomical Sciences
Buffalo, New York 14203-1121
Phone: 716-829-3523
Fax: 716-829-2911
yonghoba@buffalo.edu