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 (7/1/2018–6/30/2021; 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 (and Cancer 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 intra-cellular heterogeneity and identify specific subcellular traits that correlate with stiffness and VSMC behavior.
My lab also applies Machine Learning approaches to identify specific breast cancer cell behaviors that respond to different stiffness conditions.

(3) Optogenetics and Biophotonics in Stem Cell Biology:
Funding source: National Science Foundation (8/1/2017–7/31/2021; 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 Masters program (or other programs) 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 deas 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:

  • 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 2021
    Networked Nanophotonic Devices for Stem Cell Regulation: From Optogenetics to Optogenomics
    National Science Foundation
    Role: Co-Principal Investigator
    $599,067
  • July 2018–June 2021
    Mechanotransduction in Vascular Smooth Muscle: Survivin as a Mediator of Stiffness-Induced Responses
    American Heart Association
    Role: Principal Investigator
    $231,000
  • 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:

  • Krajnik A, Brazzo JA, Vaidyanathan K, Das T, Redondo-Muñoz J, Bae Y. (2020) Phosphoinositide Signaling and Mechanotransduction in Cardiovascular Biology and Disease. Front Cell Dev Biol (Dec), 8: 595849-595849.
  • 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).
  • 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.
  • 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).
  • Wang C, Choi HJ, Kim S, 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(1688).
  • 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).
  • 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).
  • Brazzo III JA, Lee K, Bae Y. (2020) Mechanosensitive Expression of Lamellipodin Governs Cell Cycle Progression and Intracellular Stiffness. bioRxiv (Oct).
  • Courtenay JC, Deneke C, Lanzoni EM, Costa CA, Bae Y, Scott JL, Sharma RI. (2018) Modulating cell response on cellulose surfaces; tuneable attachment and scaffold mechanics. Cellulose (Feb), 25(2).
  • 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.
  • 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).
  • 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).
  • 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.
  • 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, 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).
  • 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).
  • 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).
  • Johns MA, Bae Y, Guimarães F,Lanzoni EM, Costa C, 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).
  • 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, 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).
See all (11 more)

Books and Book Chapters:

  • 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.).
  • 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).

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)

Presentations:

  • "Lamellipodin links Rac to intracellular stiffening and mechanosensitive cell cycling" Cell Bio Virtual 2020; American Society of Cell Biology and European Molecular Biology Organization (2020)
  • "Machine learning reveals heterogeneous responses to FAK, Rac, Rho, and Cdc42 inhibition on vascular smooth muscle cell spheroid formation and morphology" Vascular Biology 2020 Annual Meeting; North American Vascular Biology Organization (2020)
  • "The effect of methylcellulose treatment on vascular smooth muscle cell spheroid formation, stiffness, and extracellular matrix production" Biomedical Engineering Society (2020)
  • "Survivin is a mechanosensitive regulator of vascular smooth muscle cell proliferation" Annual Meeting of the Biophysical Society (2020)
  • "Optogenomic Interfaces: Applications, Proof of Concept and Enabling Technologies" Optogenetic Technologies and Applications; American Institute of Chemical Engineers (2019)
  • "Machine learning analysis of vascular spheroid formation: Heterogeneous effect of FAK inhibition" Biomedical Engineering Society (2019)
  • "Breast cancer cell invasiveness is stimulated by loss of membrane interaction of actin-binding protein profilin1 via altered phosphoinositide metabolism" Experimental Biology (2019)
  • "Integrated Genome Regulation of Brain Development: Targeting Ontogenomic Networks in Schizophrenia via Nanomachine-Genome Optical Communications" Nanoscale Computing and Communication; ACM/IEEE International Conference (2018)
  • "Deconvolution of Subcellular Protrusion Heterogeneity by Machine Learning-Based Live Cell Analysis" Quantitative Biology Meeting (2018)
  • "Nanophotonics and Optogenetics- A Novel Combination towards Precise Stem Cell Regulation" American Society for Cell Biology/EMBO (2017)
  • "Apolipoprotein E interrupts a positive feedback loop that links collagen-I synthesis to intracellular stiffness" Biomedical Engineering Society; ; Cellular and Molecular Bioengineering (2015)
  • "A FAK-Cas-Rac-Lamellipodin Signaling Module Transduces Extracellular Matrix Stiffness into Mechanosensitive Cell Cycling" Gordon Research Conference; ; Signal Transduction by Engineered Extracellular Matrices (2014)
  • "Matrix metalloproteinase-12 controls arterial stiffness in vascular remodeling" American Heart Association; ; Scientific Session (2012)
  • "The FAK/Src/p130Cas pathway controls stiffness-dependent Rac activation and cell cycling" Gordon Research Conference; ; Signaling by Adhesion Receptors (2012)
  • "A Novel Actin-independent Anti-migratory Function of Profilin1 in Breast Cancer Cells" American Society for Cell Biology (2010)
  • "Membrane phosphoinositide availability, regulated by profilin-1, determines breast cancer cell motility secondary to binding of lamellipodin" American Society for Cell Biology (2009)
  • "Turning Profilin-1 to an anti-migratory molecule in breast cancer cells - molecular dissection" Biomedical Engineering Society (2009)
  • "Loss of Profilin-1 expression leads to hypermotile phenotype of breast cancer cell via lamellipodial targeting of Ena/VASP" American Society for Cell Biology (2008)
  • "Profilin is a negative regulator of mammary carcinoma aggressiveness" American Association for Cancer Research (2007)
  • "Evaluation of the effect of the chemistry of biodegradable polycarbonate polymers containing iodine and PEG on cellular response of vascular cell lines" American Institute of Chemical Engineers (2005)
See all (10 more)

Service Activities:

  • Admissions Committee; Member (2018–present)
  • Editorial Board Journal of Microbiology and Pathology; Editorial Board Member (2017–present)
  • Editorial Review Board Journal of Biomedical Engineering and Informatics; Editorial Board Member (2015–present)
  • Reviewer for Journal Articles Cancer Research, PLoS One, Integrative Biology, Current Biotechnology, Journal of Tissue Engineering, Journal of the Mechanical Behavior of Biomedical Materials, Journal of Vascular Research and Cellulose; Peer Reviewer

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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