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

Patents:

  • Mechanosensitive lamellipodin pathway as a target to reduce the vascular stiffening process A new technology disclosure was submitted to the Technology Transfer office at the University at Buffalo (2021)

Journal Articles:

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.).

Abstracts:

  • Krajnik A, Nimmer E, Bae Y. (2022) A novel role of survivin modulation on extracellular matrix production and intracellular stiffness of vascular smooth muscle cells. Biophysical Society Annual Meeting. San Francisco, California (Feb)
  • Sullivan A, Biber J, Brazzo III JA, Krajnik A, Heo SJ, Bae Y. (2021) Uncovering the Role of Survivin as a Stiffness-Sensitive Mediator of Cell Cycling and Proliferation in Vascular Smooth Muscle Cells. Cell Bio Virtual 2021, American Society of Cell Biology and European Molecular Biology Organization Meeting. Virtual Conference, (Dec) Poster
  • Brazzo III JA, Biber JC, Nimmer E, Heo Y, Lee K, Krause M, Bae Y. (2021) Role of Lamellipodin in Cellular Mechanotransduction. American Society for Matrix Biology. St. Louis, Missouri (Sep) Oral
  • Brazzo J, Bae Y. (2020) Lamellipodin links Rac to intracellular stiffening and mechanosensitive cell cycling. Cell Bio Virtual 2020, American Society of Cell Biology and European Molecular Biology Organization Meeting. Virtual Conference, (Dec) Poster
  • Nimmer E, Biber J, Vaidyanathan K, Krajnik A, Bae Y. (2020) The effect of methylcellulose treatment on vascular smooth muscle cell spheroid formation, stiffness, and extracellular matrix production. Biomedical Engineering Society. Virtual Conference, (Oct) Poster
  • Vaidyanathan K, Wang C, Krajnik A, Yu Y, Choi M, Lin B, Heo S, 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. Vascular Biology 2020 Annual Meeting, North American Vascular Biology Organization. Virtual Conference, (Oct) Poster
  • Biber J, Badalamenti B, Kolega J, Bae Y. (2020) Survivin is a mechanosensitive regulator of vascular smooth muscle cell proliferation. Annual Meeting of the Biophysical Society. SAN DIEGO, California (Feb) Poster
  • Sangwan A, Jornet JM, Bae Y, Handelmann C, Decker B, Balcerak A, Miao P, Desai A, Feng L, Stachowiak EK, Stachowiak MK. (2019) Optogenomic Interfaces: Applications, Proof of Concept and Enabling Technologies. American Institute of Chemical Engineers. Boston, Massachusetts (Nov) Poster
  • Vaidyanathan K, Yu Y, Desai A, Kolega J, Lee K, Bae Y. (2019) Machine learning analysis of vascular spheroid formation: Heterogeneous effect of FAK inhibition. Biomedical Engineering Society. Philadelphia, Pennsylvania (Oct) Oral
  • Gau D, Bae Y, Roy P. (2019) Breast cancer cell invasiveness is stimulated by loss of membrane interaction of actin-binding protein profilin1 via altered phosphoinositide metabolism. Experimental Biology. Orlando, Florida (Apr) Poster
  • Wang C, Choi HJ, Kim S, Desai A, Bae Y, Lee K. (2018) Deconvolution of Subcellular Protrusion Heterogeneity by Machine Learning-Based Live Cell Analysis. Quantitative Biology Meeting. Wailea, Hawaii (Nov) Oral
  • Desai A, Handelmann C, Harikrishnan K, Decker B, Miao P, Sangwan A, Stachowiak MK, Jornet JM, Feng L, Bae Y. (2017) Nanophotonics and Optogenetics - A Novel Combination towards Precise Stem Cell Regulation. American Society of Cell Biology-European Molecular Biology Organization Meeting. Philadelphia, Pennsylvania (Dec) Poster
  • Wang C, Choi HJ, Kim S, Bae Y, Lee K. (2017) Deconvolution of subcellular protrusion heterogeneity reveals the role of VASP in accelerating cell protrusion. American Society of Cell Biology-European Molecular Biology Organization. Philadelphia, Pennsylvania (Dec) Poster
  • Johns MA, Bae Y, Guimarães F, Lanzoni EM, Costa CA, Deneke C, Galembeck F, Scott JL, Sharma RI. (2017) Predicting ligand-free cell attachment on next generation cellulose-chitosan hydrogels. The Engineering and Science for a Sustainable Future Conference 2017. Poster Presentation (Nottingham, England). Nottingham, (Jun) Poster
  • Bae Y, Hsu BY, Mui KL, Liu SL, Assoian RK. (2015) Apolipoprotein E interrupts a positive feedback loop that links collagen-I synthesis to intracellular stiffness. Biomedical Engineering Society- Cellular and Molecular Bioengineering. St. Thomas, (Jan) Oral
  • Bae Y, Mui KL, Hsu BY, Liu SL, Cretu A, Razinia Z, Xu T, Puré E, Assoian RK. (2014) A FAK-Cas-Rac-Lamellipodin Signaling Module Transduces Extracellular Matrix Stiffness into Mechanosensitive Cell Cycling. Signal Transduction by Engineered Extracellular Matrices 2014, Gordon Research Conference. Waltham, Massachusetts (Jul) Poster
  • Liu SL, Bae Y, Xu T, Hawthorne E, Assoian RK. (2013) Matrix metalloproteinase-12 controls arterial stiffness in vascular remodeling. Translating the Biology of Atherosclerosis, Gordon Research Conference. Stowe, Vermont (Jun) Poster
  • Liu SL, Bae Y, Klein E, Hawthorne E, Xu T, Assoian RK. (2012) Matrix metalloproteinase-12 controls arterial stiffness in vascular remodeling. American Heart Association Scientific Session. Los Angeles, California (Nov) Poster
  • Bae Y, Assoian RK. (2012) The FAK/Src/p130Cas pathway controls stiffness-dependent Rac activation and cell cycling. Signaling by Adhesion Receptors 2012, Gordon Research Conference. Waterville, Maine (Jun) Poster
  • Mui KM, Gao L, Bae Y, Xu T, Chen CS, Assoian RK. (2012) Stiffness-induced expression of N-cadherin is essential for FAK-mediated cell cycling. Signaling by Adhesion Receptors 2012, Gordon Research Conference. Waterville, Maine (Jun) Poster
  • Ding Z*, Bae Y*, Das T, Wells A, Gertler F, Roy P. (2010) A Novel Actin-independent Anti-migratory Function of Profilin1 in Breast Cancer Cells. American Society of Cell Biology. Philadelphia, Pennsylvania (Dec) Poster
  • Bae Y, Das T, Ding Z, Wells A, Gertler F, Roy P. (2009) Membrane phosphoinositide availability, regulated by profilin-1, determines breast cancer cell motility secondary to binding of lamellipodin. American Society of Cell Biology. SAN DIEGO, California (Dec) Poster
  • Bae Y, Ding Z, Das T, and Roy P. (2009) Turning Profilin-1 to an anti-migratory molecule in breast cancer cells - molecular dissection. Biomedical Engineering Society. Pittsburgh, Pennsylvania (Oct) Oral
  • Krishna P, Lu X, Bae Y, Wells A. (2009) The effects of decorin and biglycan on the human vocal fold fibroblast. Wound Healing Society. Dallas, Texas (Apr) Poster
  • Bae Y, Zou L, Wells A, Gertler F, Roy P. (2008) Loss of Profilin-1 expression leads to hypermotile phenotype of breast cancer cell via lamellipodial targeting of Ena/VASP. American Society of Cell Biology. San Francisco, California (Dec) Poster
  • Roy P, Bae Y, Das T, Jaramillo M, Zou L. (2008) Profilin-1 as a suppressor of breast cancer cell motility: Molecular insights. Biomedical Engineering Society. St. Louis, Missouri (Oct) Poster
  • Leloup L, Hanshuang S, Bae Y, Stolz D, Roy P, Wells A. (2008) The signal transduction-related intracellular protease calpain2 (m-calpain) is differentially localized and activated in response to growth factors and CXCR3 chemokines CXCL10 and CXCL11 in human fibroblasts and endothelial cells. 17th Annual Growth Factor and Signal Transduction Symposium. Ames, Indiana (Sep) Poster
  • Zou L, Das T, Bae Y, Wells A, Roy P. (2008) Profilin-1 modulates proliferation and survival of breast cancer cells. American Association for Cancer Research. SAN DIEGO, California (Apr) Poster
  • Bae Y, Wells A, Roy P. (2007) Profilin is a negative regulator of mammary carcinoma aggressiveness. American Association for Cancer Research. Los Angeles, California (Apr) Poster
  • Johnson PA, Bae Y, Dubin R, Kohn J, Moghe PV. (2005) 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. Cincinnati, Ohio (Oct) Poster
See all (20 more)

Professional Memberships:

  • North American Vascular Biology Organization (2020–present)
  • Biophysical Society (2019–present)
  • American Heart Association (2010–present)
  • Biomedical Engineering Society (2009–present)
  • American Society for Cell Biology (2008–present)

Presentations:

  • "Sensing and transducing ECM stiffness into vascular smooth muscle cell function" Grand Round, Department of Pathology and Anatomical Sciences (2021)
  • "Mechanotransduction in vascular smooth muscle: FAK-Rac-ATF3 as mediators of stiffness-induced responses" Special Seminar Series, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine (2018)
  • "Mechanotransduction in vascular smooth muscle: FAK-Rac-ATF3 as mediators of stiffness-induced responses" Special Seminar Series, School of Life Sciences, Ulsan National Institute of Science and Technology (2018)
  • "Vascular cell mechanotransduction: the role that mechanical forces play in regulating vascular cell function from healthy to diseased phenotypes" Special Seminar Series, School of Dentistry, Pusan National University (2018)
  • "Mechanotransduction in vascular smooth muscle: FAK-Rac-ATF3 as mediators of stiffness-induced responses" Special Seminar Series, Department of Dental Medicine and Life Sciences, Seoul National University (2018)
  • "Mechanotransduction in vascular smooth muscle" Mechanisms and new Theory of Ontogeny Lecture Series, Stem Cell Bioengineering Unit, Polish Academy of Sciences (via Skype) (2018)
  • "Mechanotransduction in vascular smooth muscle: FAK-Rac as mediators of stiffness-induced responses" Graduate Seminar Series, Department of Bioengineering, University of Pittsburgh (2018)
  • "Effect of extracellular matrix stiffness on cellular mechanotransduction" Department Seminar, Department of Pathology and Anatomical Sciences, University of at Buffalo (2016)
  • "Effect of extracellular matrix stiffness on cellular mechanotransduction" Department Seminar, Department of Physiology and Biophysics, University of Illinois at Chicago (2016)
  • "Cell signaling by extracellular matrix stiffness" BME Seminar Series, Department of Biomedical Engineering, University of Wisconsin-Madison (2015)
  • "Cell signaling by extracellular matrix stiffness" Seminar, Wellcome Trust Centre for Cell-Matrix Research, University of Manchester (2015)
  • "Cell signaling by extracellular matrix stiffness" Seminar, Department of Biomedical Engineering, University of Texas at San Antonio (2014)
  • "A FAK-Cas-Rac signaling module transduces ECM stiffness into cell stiffness and mechanosensitive cell proliferation" Department Seminar, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (2013)
  • "A FAK-Cas-Rac signaling module transduces ECM stiffness into cell stiffness and mechanosensitive cell proliferation" Department Seminar, Department of Biochemistry and Medical Center, Chungbuk National University College of Medicine (2013)
  • "Profilin-1 regulation of breast cancer cell aggressiveness" Seminar, Department of Pharmacology, University of Pennsylvania (2009)
  • "Profilin-1 regulation of breast cancer cell aggressiveness" Seminar, Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University (2009)
See all (6 more)

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)
  • Experiential Learning Network (mentored 1 undergraduate student); Faculty mentor (2021–present)
  • Life by MDPI; Topical Advisory Panel Members (2020–present)
  • Experiential Learning Network (mentored 1 undergraduate student); Faculty mentor (2020–2021)
  • 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)
  • Experiential Learning Network (mentored 1 undergraduate student); Faculty Mentor (2019–2020)
  • 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)
  • Center for Undergraduate Research and Creative Activities (mentored 4 undergraduate students); Faculty Mentor (2018–2019)
  • 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)
  • 6/2021. NIH- Intercellular Interactions Study Section; Ad Hoc reviewer
  • Departmental equipment negotiating and purchasing: NX12 atomic force microscope (Park Systems), BIO-X 3D Bioprinters (CELLINK), Ultramicrotome EM UC7 (Leica), and Optical Tweezer (ThorLabs)
  • 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