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Eight Subcellular Pathologies driving Chronic Metabolic Diseases – Methods for Mapping Bioelectronic Adjustable Measurements as potential new Therapeutics: Impact on Pharmaceuticals in Use

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Eight Subcellular Pathologies driving Chronic Metabolic Diseases – Methods for Mapping Bioelectronic Adjustable Measurements as potential new Therapeutics: Impact on Pharmaceuticals in Use

Curators:

Cardiovascular Expertise – Dr. Justin D. Pearlman, MD, PhD, FACC
Pharmacology and Oncology Expertise – Dr. Stephen J. Williams, PhD
Principal Investigator, initiator of the project – Aviva Lev-Ari, PhD, RN

THE VOICE of Aviva Lev-Ari, PhD, RN

In this curation we wish to present two breaking through goals:

Goal 1:

Exposition of a new direction of research leading to a more comprehensive understanding of Metabolic Dysfunctional Diseases that are implicated in effecting the emergence of the two leading causes of human mortality in the World in 2023: (a) Cardiovascular Diseases, and (b) Cancer

Goal 2:

Development of Methods for Mapping Bioelectronic Adjustable Measurements as potential new Therapeutics for these eight subcellular causes of chronic metabolic diseases. It is anticipated that it will have a potential impact on the future of Pharmaceuticals to be used, a change from the present time current treatment protocols for Metabolic Dysfunctional Diseases.

According to Dr. Robert Lustig, M.D, an American pediatric endocrinologist. He is Professor emeritus of Pediatrics in the Division of Endocrinology at the University of California, San Francisco, where he specialized in neuroendocrinology and childhood obesity, there are eight subcellular pathologies that drive chronic metabolic diseases.

These eight subcellular pathologies can’t be measured at present time.

In this curation we will attempt to explore methods of measurement for each of these eight pathologies by harnessing the promise of the emerging field known as Bioelectronics.

Unmeasurable eight subcellular pathologies that drive chronic metabolic diseases

Glycation
Oxidative Stress
Mitochondrial dysfunction [beta-oxidation Ac CoA malonyl fatty acid]
Insulin resistance/sensitive [more important than BMI], known as a driver to cancer development
Membrane instability
Inflammation in the gut [mucin layer and tight junctions]
Epigenetics/Methylation
Autophagy [AMPKbeta1 improvement in health span]

Diseases that are not Diseases: no drugs for them, only diet modification will help

Image source

Robert Lustig, M.D. on the Subcellular Processes That Belie Chronic Disease

https://www.youtube.com/watch?v=Ee_uoxuQo0I

Exercise will not undo Unhealthy Diet

Image source

Robert Lustig, M.D. on the Subcellular Processes That Belie Chronic Disease

https://www.youtube.com/watch?v=Ee_uoxuQo0I

These eight Subcellular Pathologies driving Chronic Metabolic Diseases are becoming our focus for exploration of the promise of Bioelectronics for two pursuits:

Will Bioelectronics be deemed helpful in measurement of each of the eight pathological processes that underlie and that drive the chronic metabolic syndrome(s) and disease(s)?
IF we will be able to suggest new measurements to currently unmeasurable health harming processes THEN we will attempt to conceptualize new therapeutic targets and new modalities for therapeutics delivery – WE ARE HOPEFUL

In the Bioelecronics domain we are inspired by the work of the following three research sources:

Biological and Biomedical Electrical Engineering (B2E2) at Cornell University, School of Engineering https://www.engineering.cornell.edu/bio-electrical-engineering-0
Bioelectronics Group at MIT https://bioelectronics.mit.edu/
The work of Michael Levin @Tufts, The Levin Lab

Michael Levin is an American developmental and synthetic biologist at Tufts University, where he is the Vannevar Bush Distinguished Professor. Levin is a director of the Allen Discovery Center at Tufts University and Tufts Center for Regenerative and Developmental Biology. Wikipedia

Born: 1969 (age 54 years), Moscow, Russia

Education: Harvard University (1992–1996), Tufts University (1988–1992)

Affiliation: University of Cape Town

Research interests: Allergy, Immunology, Cross Cultural Communication

Awards: Cozzarelli prize (2020)

Doctoral advisor: Clifford Tabin

Fields: Developmental biology, synthetic biology

SOURCE

https://www.google.com/search?q=Michael+Levin+%40Tufts&oq=Michael+Levin+%40Tufts&aqs=chrome..69i57j69i58.894128314j0j15&sourceid=chrome&ie=UTF-8

Most recent 20 Publications by Michael Levin, PhD

SOURCE

https://facultyprofiles.tufts.edu/michael-levin-1/publications

SCHOLARLY ARTICLE

The nonlinearity of regulation in biological networks

1 Dec 2023npj Systems Biology and Applications9(1)

Co-authorsManicka S, Johnson K, Levin M…

VIEW PDF

10.1038/S41540-023-00273-W

SCHOLARLY ARTICLE

Toward an ethics of autopoietic technology: Stress, care, and intelligence

1 Sep 2023BioSystems231

Co-authorsWitkowski O, Doctor T, Solomonova E…

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10.1016/J.BIOSYSTEMS.2023.104964

SCHOLARLY ARTICLE

Closing the Loop on Morphogenesis: A Mathematical Model of Morphogenesis by Closed-Loop Reaction-Diffusion

14 Aug 2023Frontiers in Cell and Developmental Biology11:1087650

Co-authorsGrodstein J, McMillen P, Levin M

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10.3389/FCELL.2023.1087650

SCHOLARLY ARTICLE

Correcting instructive electric potential patterns in multicellular systems: External actions and endogenous processes.

30 Jul 2023Biochim Biophys Acta Gen Subj1867(10):130440

Co-authorsCervera J, Levin M, Mafe S

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10.1016/J.BBAGEN.2023.130440

SCHOLARLY ARTICLE

Regulative development as a model for origin of life and artificial life studies

1 Jul 2023BioSystems229

Co-authorsFields C, Levin M

10.1016/J.BIOSYSTEMS.2023.104927

SCHOLARLY ARTICLE

The Yin and Yang of Breast Cancer: Ion Channels as Determinants of Left–Right Functional Differences

1 Jul 2023International Journal of Molecular Sciences24(13)

Co-authorsMasuelli S, Real S, McMillen P…

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10.3390/IJMS241311121

SCHOLARLY ARTICLE

Bioelectricidad en agregados multicelulares de células no excitables- modelos biofísicos

Jun 2023Revista Española de Física32(2)

Co-authorsCervera J, Levin M, Mafé S

SCHOLARLY ARTICLE

Bioelectricity: A Multifaceted Discipline, and a Multifaceted Issue!

1 Jun 2023Bioelectricity5(2):75

Co-authorsDjamgoz MBA, Levin M

10.1089/BIOE.2023.0022.EDITORIAL

SCHOLARLY ARTICLE

Control Flow in Active Inference Systems – Part I: Classical and Quantum Formulations of Active Inference

1 Jun 2023IEEE Transactions on Molecular, Biological, and Multi-Scale Communications9(2):235-245

Co-authorsFields C, Fabrocini F, Friston K…

10.1109/TMBMC.2023.3272150

SCHOLARLY ARTICLE

Control Flow in Active Inference Systems – Part II: Tensor Networks as General Models of Control Flow

1 Jun 2023IEEE Transactions on Molecular, Biological, and Multi-Scale Communications9(2):246-256

Co-authorsFields C, Fabrocini F, Friston K…

10.1109/TMBMC.2023.3272158

SCHOLARLY ARTICLE

Darwin’s agential materials: evolutionary implications of multiscale competency in developmental biology

1 Jun 2023Cellular and Molecular Life Sciences80(6)

Co-authorsLevin M

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10.1007/S00018-023-04790-Z

SCHOLARLY ARTICLE

Morphoceuticals: Perspectives for discovery of drugs targeting anatomical control mechanisms in regenerative medicine, cancer and aging

1 Jun 2023Drug Discovery Today28(6)

Co-authorsPio-Lopez L, Levin M

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10.1016/J.DRUDIS.2023.103585

SCHOLARLY ARTICLE

Morphoceuticals: Perspectives for discovery of drugs targeting anatomical control mechanisms in regenerative medicine, cancer and aging

Jun 2023DRUG DISCOVERY TODAY28(6):1-13

Co-authorsPio-Lopez L, Levin M

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10.1016/J.DRUDIS.2023.103585THIS

SCHOLARLY ARTICLE

Cellular signaling pathways as plastic, proto-cognitive systems: Implications for biomedicine

12 May 2023Patterns4(5)

Co-authorsMathews J, Chang A, Devlin L…

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10.1016/J.PATTER.2023.100737

SCHOLARLY ARTICLE

Making and breaking symmetries in mind and life

14 Apr 2023Interface Focus13(3)

Co-authorsSafron A, Sakthivadivel DAR, Sheikhbahaee Z…

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10.1098/RSFS.2023.0015

SCHOLARLY ARTICLE

The scaling of goals from cellular to anatomical homeostasis: an evolutionary simulation, experiment and analysis

14 Apr 2023Interface Focus13(3)

Co-authorsPio-Lopez L, Bischof J, LaPalme JV…

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10.1098/RSFS.2022.0072

SCHOLARLY ARTICLE

The collective intelligence of evolution and development

Apr 2023Collective Intelligence2(2):263391372311683SAGE Publications

Co-authorsWatson R, Levin M

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10.1177/26339137231168355

SCHOLARLY ARTICLE

Bioelectricity of non-excitable cells and multicellular pattern memories: Biophysical modeling

13 Mar 2023Physics Reports1004:1-31

Co-authorsCervera J, Levin M, Mafe S

10.1016/J.PHYSREP.2022.12.003

SCHOLARLY ARTICLE

There’s Plenty of Room Right Here: Biological Systems as Evolved, Overloaded, Multi-Scale Machines

1 Mar 2023Biomimetics8(1)

Co-authorsBongard J, Levin M

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10.3390/BIOMIMETICS8010110

SCHOLARLY ARTICLE

Transplantation of fragments from different planaria: A bioelectrical model for head regeneration

7 Feb 2023Journal of Theoretical Biology558

Co-authorsCervera J, Manzanares JA, Levin M…

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10.1016/J.JTBI.2022.111356

SCHOLARLY ARTICLE

Bioelectric networks: the cognitive glue enabling evolutionary scaling from physiology to mind

1 Jan 2023Animal Cognition

Co-authorsLevin M

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10.1007/S10071-023-01780-3

SCHOLARLY ARTICLE

Biological Robots: Perspectives on an Emerging Interdisciplinary Field

1 Jan 2023Soft Robotics

Co-authorsBlackiston D, Kriegman S, Bongard J…

10.1089/SORO.2022.0142

SCHOLARLY ARTICLE

Cellular Competency during Development Alters Evolutionary Dynamics in an Artificial Embryogeny Model

1 Jan 2023Entropy25(1)

Co-authorsShreesha L, Levin M

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10.3390/E25010131

SCHOLARLY ARTICLE

Endless forms most beautiful 2.0: teleonomy and the bioengineering of chimaeric and synthetic organisms (July, blac073, 2022)

1 Jan 2023BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY138(1):141

Co-authorsClawson WP, Levin M

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VIEW MORE INFO

10.1093/BIOLINNEAN/BLAC116

SCHOLARLY ARTICLE

Future medicine: from molecular pathways to the collective intelligence of the body

1 Jan 2023Trends in Molecular Medicine

Co-authorsLagasse E, Levin M

10.1016/J.MOLMED.2023.06.007

THE VOICE of Dr. Justin D. Pearlman, MD, PhD, FACC

PENDING

THE VOICE of Stephen J. Williams, PhD

Ten TakeAway Points of Dr. Lustig’s talk on role of diet on the incidence of Type II Diabetes

25% of US children have fatty liver
Type II diabetes can be manifested from fatty live with 151 million people worldwide affected moving up to 568 million in 7 years
A common myth is diabetes due to overweight condition driving the metabolic disease
There is a trend of ‘lean’ diabetes or diabetes in lean people, therefore body mass index not a reliable biomarker for risk for diabetes
Thirty percent of ‘obese’ people just have high subcutaneous fat. the visceral fat is more problematic
there are people who are ‘fat’ but insulin sensitive while have growth hormone receptor defects. Points to other issues related to metabolic state other than insulin and potentially the insulin like growth factors
At any BMI some patients are insulin sensitive while some resistant
Visceral fat accumulation may be more due to chronic stress condition
Fructose can decrease liver mitochondrial function
A methionine and choline deficient diet can lead to rapid NASH development

Read Full Post »

Use of 3D Bioprinting for Development of Toxicity Prediction Models

Posted in 3D Plotting Scaffolds, 3D Printing for Medical Application, Bio-MEMS, BioBanking, Bioengineering & reverse engineering design, BioInks, Biological Engineering, Biological Networks, BioPrinting in Regenerative Medicine, CANCER BIOLOGY & Innovations in Cancer Therapy, Cell Biology, Cell Level, Disease Biology, Drug Development using MultiOrgan Chip, Drug Development/Formulation using 3D Printing, Drug Toxicity, MEMS, MicroEngineering Cell-Tissue & Systems, Organoids, Pharmaceutical Analytics, Pharmaceutical Discovery, Pharmaceutical Drug Discovery, Pharmacologic toxicities, Tissue Engineering and Regenerative Medicine, Tissue Microenvironment, Translational Research, tagged 3-D printed liver tissue, 3D bioprinting, 3D tissue, Amnion Foundation, bioprinting, Brigham & Women's Hospital, drug induced liver injury, ECM, Harvard Medical School, hepatoxicity, Liver Tissue Engineeering, National Institutes of Health (NIH) ’s Common Fund, organova, Tissue engineering, toxicology on April 27, 2019| Leave a Comment »

Use of 3D Bioprinting for Development of Toxicity Prediction Models

Curator: Stephen J. Williams, PhD

SOT FDA Colloquium on 3D Bioprinted Tissue Models: Tuesday, April 9, 2019

The Society of Toxicology (SOT) and the U.S. Food and Drug Administration (FDA) will hold a workshop on “Alternative Methods for Predictive Safety Testing: 3D Bioprinted Tissue Models” on Tuesday, April 9, at the FDA Center for Food Safety and Applied Nutrition in College Park, Maryland. This workshop is the latest in the series, “SOT FDA Colloquia on Emerging Toxicological Science: Challenges in Food and Ingredient Safety.”

Human 3D bioprinted tissues represent a valuable in vitro approach for chemical, personal care product, cosmetic, and preclinical toxicity/safety testing. Bioprinting of skin, liver, and kidney is already appearing in toxicity testing applications for chemical exposures and disease modeling. The use of 3D bioprinted tissues and organs may provide future alternative approaches for testing that may more closely resemble and simulate intact human tissues to more accurately predict human responses to chemical and drug exposures.

A synopsis of the schedule and related works from the speakers is given below:

8:40 AM–9:20 AM	Overview and Challenges of Bioprinting Sharon Presnell, Amnion Foundation, Winston-Salem, NC
9:20 AM–10:00 AM	Putting 3D Bioprinting to the Use of Tissue Model Fabrication Y. Shrike Zhang, Brigham and Women’s Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, Boston, MA
10:00 AM–10:20 AM	Break
10:20 AM–11:00 AM	Uses of Bioprinted Liver Tissue in Drug Development Jean-Louis Klein, GlaxoSmithKline, Collegeville, PA
11:00 AM–11:40 AM	Biofabrication of 3D Tissue Models for Disease Modeling and Chemical Screening Marc Ferrer, National Center for Advancing Translational Sciences, NIH, Rockville, MD

Sharon Presnell, Ph.D. President, Amnion Foundation

Dr. Sharon Presnell was most recently the Chief Scientific Officer at Organovo, Inc., and the President of their wholly-owned subsidiary, Samsara Sciences. She received a Ph.D. in Cell & Molecular Pathology from the Medical College of Virginia and completed her undergraduate degree in biology at NC State. In addition to her most recent roles, Presnell has served as the director of cell biology R&D at Becton Dickinson’s corporate research center in RTP, and as the SVP of R&D at Tengion. Her roles have always involved the commercial and clinical translation of basic research and early development in the cell biology space. She serves on the board of the Coulter Foundation at the University of Virginia and is a member of the College of Life Sciences Foundation Board at NC State. In January 2019, Dr. Presnell will begin a new role as President of the Amnion Foundation, a non-profit organization in Winston-Salem.

A few of her relevant publications:

Bioprinted liver provides early insight into the role of Kupffer cells in TGF-β1 and methotrexate-induced fibrogenesis

Integrating Kupffer cells into a 3D bioprinted model of human liver recapitulates fibrotic responses of certain toxicants in a time and context dependent manner. This work establishes that the presence of Kupffer cells or macrophages are important mediators in fibrotic responses to certain hepatotoxins and both should be incorporated into bioprinted human liver models for toxicology testing.

Bioprinted 3D Primary Liver Tissues Allow Assessment of Organ-Level Response to Clinical Drug Induced Toxicity In Vitro

Abstract: Modeling clinically relevant tissue responses using cell models poses a significant challenge for drug development, in particular for drug induced liver injury (DILI). This is mainly because existing liver models lack longevity and tissue-level complexity which limits their utility in predictive toxicology. In this study, we established and characterized novel bioprinted human liver tissue mimetics comprised of patient-derived hepatocytes and non-parenchymal cells in a defined architecture. Scaffold-free assembly of different cell types in an in vivo-relevant architecture allowed for histologic analysis that revealed distinct intercellular hepatocyte junctions, CD31+ endothelial networks, and desmin positive, smooth muscle actin negative quiescent stellates. Unlike what was seen in 2D hepatocyte cultures, the tissues maintained levels of ATP, Albumin as well as expression and drug-induced enzyme activity of Cytochrome P450s over 4 weeks in culture. To assess the ability of the 3D liver cultures to model tissue-level DILI, dose responses of Trovafloxacin, a drug whose hepatotoxic potential could not be assessed by standard pre-clinical models, were compared to the structurally related non-toxic drug Levofloxacin. Trovafloxacin induced significant, dose-dependent toxicity at clinically relevant doses (≤ 4uM). Interestingly, Trovafloxacin toxicity was observed without lipopolysaccharide stimulation and in the absence of resident macrophages in contrast to earlier reports. Together, these results demonstrate that 3D bioprinted liver tissues can both effectively model DILI and distinguish between highly related compounds with differential profile. Thus, the combination of patient-derived primary cells with bioprinting technology here for the first time demonstrates superior performance in terms of mimicking human drug response in a known target organ at the tissue level.

A great interview with Dr. Presnell and the 3D Models 2017 Symposium is located here:

Please click here for Web based and PDF version of interview

Some highlights of the interview include

Exciting advances in field showing we can model complex tissue-level disease-state phenotypes that develop in response to chronic long term injury or exposure
Sees the field developing a means to converge both the biology and physiology of tissues, namely modeling the connectivity between tissues such as fluid flow
Future work will need to be dedicated to develop comprehensive analytics for 3D tissue analysis. As she states “we are very conditioned to get information in a simple way from biochemical readouts in two dimension, monocellular systems” however how we address the complexity of various cellular responses in a 3D multicellular environment will be pertinent.
Additional challenges include the scalability of such systems and making such system accessible in a larger way

Shrike Zhang, Brigham and Women’s Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology

Dr. Zhang currently holds an Assistant Professor position at Harvard Medical School and is an Associate Bioengineer at Brigham and Women’s Hospital. His research interests include organ-on-a-chip, 3D bioprinting, biomaterials, regenerative engineering, biomedical imaging, biosensing, nanomedicine, and developmental biology. His scientific contributions have been recognized by >40 international, national, and regional awards. He has been invited to deliver >70 lectures worldwide, and has served as reviewer for >400 manuscripts for >30 journals. He is serving as Editor-in-Chief for Microphysiological Systems, and Associate Editor for Bio-Design and Manufacturing. He is also on Editorial Board of Bioprinting, Heliyon, BMC Materials, and Essays in Biochemistry, and on Advisory Panel of Nanotechnology.

Some relevant references from Dr. Zhang

Multi-tissue interactions in an integrated three-tissue organ-on-a-chip platform.

Skardal A, Murphy SV, Devarasetty M, Mead I, Kang HW, Seol YJ, Shrike Zhang Y, Shin SR, Zhao L, Aleman J, Hall AR, Shupe TD, Kleensang A, Dokmeci MR, Jin Lee S, Jackson JD, Yoo JJ, Hartung T, Khademhosseini A, Soker S, Bishop CE, Atala A.

Sci Rep. 2017 Aug 18;7(1):8837. doi: 10.1038/s41598-017-08879-x.

Reconstruction of Large-scale Defects with a Novel Hybrid Scaffold Made from Poly(L-lactic acid)/Nanohydroxyapatite/Alendronate-loaded Chitosan Microsphere: in vitro and in vivo Studies.

Wu H, Lei P, Liu G, Shrike Zhang Y, Yang J, Zhang L, Xie J, Niu W, Liu H, Ruan J, Hu Y, Zhang C.

Sci Rep. 2017 Mar 23;7(1):359. doi: 10.1038/s41598-017-00506-z.

A liver-on-a-chip platform with bioprinted hepatic spheroids.

Bhise NS, Manoharan V, Massa S, Tamayol A, Ghaderi M, Miscuglio M, Lang Q, Shrike Zhang Y, Shin SR, Calzone G, Annabi N, Shupe TD, Bishop CE, Atala A, Dokmeci MR, Khademhosseini A.

Biofabrication. 2016 Jan 12;8(1):014101. doi: 10.1088/1758-5090/8/1/014101.

Marc Ferrer, National Center for Advancing Translational Sciences, NIH

Marc Ferrer is a team leader in the NCATS Chemical Genomics Center, which was part of the National Human Genome Research Institute when Ferrer began working there in 2010. He has extensive experience in drug discovery, both in the pharmaceutical industry and academic research. Before joining NIH, he was director of assay development and screening at Merck Research Laboratories. For 10 years at Merck, Ferrer led the development of assays for high-throughput screening of small molecules and small interfering RNA (siRNA) to support programs for lead and target identification across all disease areas.

At NCATS, Ferrer leads the implementation of probe development programs, discovery of drug combinations and development of innovative assay paradigms for more effective drug discovery. He advises collaborators on strategies for discovering small molecule therapeutics, including assays for screening and lead identification and optimization. Ferrer has experience implementing high-throughput screens for a broad range of disease areas with a wide array of assay technologies. He has led and managed highly productive teams by setting clear research strategies and goals and by establishing effective collaborations between scientists from diverse disciplines within industry, academia and technology providers.

Ferrer has a Ph.D. in biological chemistry from the University of Minnesota, Twin Cities, and completed postdoctoral training at Harvard University’s Department of Molecular and Cellular Biology. He received a B.Sc. degree in organic chemistry from the University of Barcelona in Spain.

Some relevant references for Dr. Ferrer

Fully 3D Bioprinted Skin Equivalent Constructs with Validated Morphology and Barrier Function.

Derr K, Zou J, Luo K, Song MJ, Sittampalam GS, Zhou C, Michael S, Ferrer M, Derr P.

Tissue Eng Part C Methods. 2019 Apr 22. doi: 10.1089/ten.TEC.2018.0318. [Epub ahead of print]

Determination of the Elasticity Modulus of 3D-Printed Octet-Truss Structures for Use in Porous Prosthesis Implants.

Bagheri A, Buj-Corral I, Ferrer M, Pastor MM, Roure F.

Materials (Basel). 2018 Nov 29;11(12). pii: E2420. doi: 10.3390/ma11122420.

Mutation Profiles in Glioblastoma 3D Oncospheres Modulate Drug Efficacy.

Wilson KM, Mathews-Griner LA, Williamson T, Guha R, Chen L, Shinn P, McKnight C, Michael S, Klumpp-Thomas C, Binder ZA, Ferrer M, Gallia GL, Thomas CJ, Riggins GJ.

SLAS Technol. 2019 Feb;24(1):28-40. doi: 10.1177/2472630318803749. Epub 2018 Oct 5.

A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models.

Boutin ME, Voss TC, Titus SA, Cruz-Gutierrez K, Michael S, Ferrer M.

Sci Rep. 2018 Jul 24;8(1):11135. doi: 10.1038/s41598-018-29169-0.

A High-Throughput Screening Model of the Tumor Microenvironment for Ovarian Cancer Cell Growth.

Lal-Nag M, McGee L, Guha R, Lengyel E, Kenny HA, Ferrer M.

SLAS Discov. 2017 Jun;22(5):494-506. doi: 10.1177/2472555216687082. Epub 2017 Jan 31.

Exploring Drug Dosing Regimens In Vitro Using Real-Time 3D Spheroid Tumor Growth Assays.

Lal-Nag M, McGee L, Titus SA, Brimacombe K, Michael S, Sittampalam G, Ferrer M.

SLAS Discov. 2017 Jun;22(5):537-546. doi: 10.1177/2472555217698818. Epub 2017 Mar 15.

RNAi High-Throughput Screening of Single- and Multi-Cell-Type Tumor Spheroids: A Comprehensive Analysis in Two and Three Dimensions.

Fu J, Fernandez D, Ferrer M, Titus SA, Buehler E, Lal-Nag MA.

SLAS Discov. 2017 Jun;22(5):525-536. doi: 10.1177/2472555217696796. Epub 2017 Mar 9.

Lesson 5 Cell Signaling And Motility: Cytoskeleton & Actin: Curations and Articles of reference as supplemental information: #TUBiol3373

Posted in Alzheimer's Disease, Biological Networks, Ca2+ triggered activation, Calcium, Calcium Signaling, Cancer - General, Curation, Cytoskeleton, Metastasis Process, Neurological Diseases, Scientific Publishing, Tissue Engineering and Regenerative Medicine, Tissue Microenvironment, tagged #TUBiol3373, actin, actin filaments, Alzheimer Disease, Cell Motility, cell physiology, Cytoskeleton, cytoskeleton transport, Microtubule Affinity‐Regulating Kinase, microtubules, Parkinsons disease, Synaptic vesicle on March 13, 2019| Leave a Comment »

Lesson 5 Cell Signaling And Motility: Cytoskeleton & Actin: Curations and Articles of reference as supplemental information: #TUBiol3373

Curator: Stephen J. Williams, Ph.D.

Cell motility or migration is an essential cellular process for a variety of biological events. In embryonic development, cells migrate to appropriate locations for the morphogenesis of tissues and organs. Cells need to migrate to heal the wound in repairing damaged tissue. Vascular endothelial cells (ECs) migrate to form new capillaries during angiogenesis. White blood cells migrate to the sites of inflammation to kill bacteria. Cancer cell metastasis involves their migration through the blood vessel wall to invade surrounding tissues.

Please Click on the Following Powerpoint Presentation for Lesson 4 on the Cytoskeleton, Actin, and Filaments

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cell signaling 5 lesson

This post will be updated with further information when we get into Lesson 6 and complete our discussion on the Cytoskeleton

Please see the following articles on Actin and the Cytoskeleton in Cellular Signaling

Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

This article, constitutes a broad, but not complete review of the emerging discoveries of the critical role of calcium signaling on cell motility and, by extension, embryonic development, cancer metastasis, changes in vascular compliance at the junction between the endothelium and the underlying interstitial layer. The effect of calcium signaling on the heart in arrhtmogenesis and heart failure will be a third in this series, while the binding of calcium to troponin C in the synchronous contraction of the myocardium had been discussed by Dr. Lev-Ari in Part I.

Universal MOTIFs essential to skeletal muscle, smooth muscle, cardiac syncytial muscle, endothelium, neovascularization, atherosclerosis and hypertension, cell division, embryogenesis, and cancer metastasis. The discussion will be presented in several parts:

1. Biochemical and signaling cascades in cell motility

2. Extracellular matrix and cell-ECM adhesions

3. Actin dynamics in cell-cell adhesion

4. Effect of intracellular Ca++ action on cell motility

5. Regulation of the cytoskeleton

6. Role of thymosin in actin-sequestration

7. T-lymphocyte signaling and the actin cytoskeleton

Identification of Biomarkers that are Related to the Actin Cytoskeleton

In this article the Dr. Larry Bernstein covers two types of biomarker on the function of actin in cytoskeleton mobility in situ.

First, is an application in developing the actin or other component, for a biotarget and then, to be able to follow it as

(a) a biomarker either for diagnosis, or

(b) for the potential treatment prediction of disease free survival.

Second, is mostly in the context of MI, for which there is an abundance of work to reference, and a substantial body of knowledge about

(a) treatment and long term effects of diet, exercise, and

(b) underlying effects of therapeutic drugs.

Microtubule-Associated Protein Assembled on Polymerized Microtubules

(This article has a great 3D visualization of a microtuble structure as well as description of genetic diseases which result from mutations in tubulin and effects on intracellular trafficking of proteins.

A latticework of tiny tubes called microtubules gives your cells their shape and also acts like a railroad track that essential proteins travel on. But if there is a glitch in the connection between train and track, diseases can occur. In the November 24, 2015 issue of PNAS, Tatyana Polenova, Ph.D., Professor of Chemistry and Biochemistry, and her team at the University of Delaware (UD), together with John C. Williams, Ph.D., Associate Professor at the Beckman Research Institute of City of Hope in Duarte, California, reveal for the first time — atom by atom — the structure of a protein bound to a microtubule. The protein of focus, CAP-Gly, short for “cytoskeleton-associated protein-glycine-rich domains,” is a component of dynactin, which binds with the motor protein dynein to move cargoes of essential proteins along the microtubule tracks. Mutations in CAP-Gly have been linked to such neurological diseases and disorders as Perry syndrome and distal spinal bulbar muscular dystrophy.

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LIVE – OCTOBER 16 – DAY 1- Koch Institute Immune Engineering Symposium 2017, MIT, Kresge Auditorium

Posted in Adaptive Immune Response to Biomaterials and Tissue Repair, Biological Engineering, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer-Immune Interactions, combination immunotherapies., Conference Coverage with Social Media, Drug Carrier Design, Efficacy of Anti-Tumor T Cells, Engineering Better T Cells, Engineering Enhanced Cancer Vaccines, Human Antibody Response, Human Naive B Cell Repertoire, Inflammatory Pathophysiology, Synthetic Immunology: Hacking Immune Cells, Systemic Inflammatory Response Related Disorders, Tissue Microenvironment, tumor microenvironment on October 14, 2017| Leave a Comment »

LIVE – OCTOBER 16 – DAY 1- Koch Institute Immune Engineering Symposium 2017, MIT, Kresge Auditorium

Reporter: Aviva Lev-Ari, PhD, RN

Image Source:Koch Institute

Koch Institute

The Immune System, Stress Signaling, Infectious Diseases and Therapeutic Implications: VOLUME 2: Infectious Diseases and Therapeutics and VOLUME 3: The Immune System and Therapeutics (Series D: BioMedicine & Immunology) Kindle Edition – on Amazon.com since September 4, 2017

https://www.amazon.com/dp/B075CXHY1B

SYMPOSIUM SCHEDULE

OCTOBER 16 – DAY 1

7:00 – 8:15 Registration

8:15 – 8:30Introductory Remarks
Darrell Irvine | MIT, Koch Institute; HHMI

Stimulating the Immune system not only sustaining it for therapies

K. Dane Wittrup | MIT, Koch Institute

8:30 – 9:45Session I
Moderator: Douglas Lauffenburger | MIT, Biological Engineering and Koch Institute

Garry P. Nolan – Stanford University School of Medicine
Pathology from the Molecular Scale on Up

Intracellular molecules,
how molecules are organized to create tissue
Meaning from data Heterogeneity is an illusion: Order in Data ?? Cancer is heterogeneous, Cells in suspension – number of molecules
System-wide changes during Immune Response (IR)
Untreated, Ineffective therapy, effective therapy
Days 3-8 Tumor, Lymph node…
Variation is a Feature – not a bug: Effective therapy vs Ineffective – intercellular modules – virtual neighborhoods
ordered by connectivity: very high – CD4 T-cells, CD8 T-cels, moderate, not connected
Landmark nodes, Increase in responders
CODEX: Multiples epitome detection
Adaptable to proteins & mRNA
Rendering antibody staining via removal to neighborhood mapping
Human tonsil – 42 parameters: CD7, CD45, CD86,
Automated Annotations of tissues: F, P, V,
Normal BALBs
Marker expression defined by the niche: B220 vs CD79
Marker expression defines the niche
Learn neighborhoods and Trees
Improving Tissue Classification and staining – Ce3D – Tissue and Immune Cells in 3D
Molecular level cancer imaging
Proteomic Profiles: multi slice combine
Theory is formed to explain 3D nuclear images of cells – Composite Ion Image, DNA replication
Replication loci visualization on DNA backbone – nascent transcriptome – bar code of isotopes – 3D 600 slices
use CRISPR Cas9 for Epigenetics

Susan Napier Thomas – Georgia Institute of Technology
Transport Barriers in the Tumor Microenvironment: Drug Carrier Design for Therapeutic Delivery to Sentinel Lymph Nodes

Lymph Nodes important therapeutics target tissue
Lymphatic flow support passive and active antigen transport to lymph nodes
clearance of biomolecules and drug formulations: Interstitial transport barriers influence clearance: Arteriole to Venule –
Molecular tracers to analyze in vivo clearance mechanisms and vascular transport function
quantifying molecular clearance and biodistribution
Lymphatic transport increases tracer concentrations within dLN by orders of magnitude
Melanoma growth results in remodeled tumor vasculature
passive transport via lymphatic to dLN sustained in advanced tumors despite abrogated cell trafficking
Engineered biomaterial drug carriers to enhance sentinel lymph node-drug delivery: facilitated by exploiting lymphatic transport
TLR9 ligand therapeutic tumor in situ vaccination – Lymphatic-draining CpG-NP enhanced
Sturcutral and Cellular barriers: transport of particles is restriced by
Current drug delivery technology: lymph-node are undrugable
Multistage delivery platform to overcome barriers to lymphatic uptake and LN targeting
nano particles – OND – Oxanorbornade OND Time sensitive Linker synthesized large cargo – NP improve payload
OND release rate from nanoparticles changes retention in lymph nodes – Axilliary-Brachial delivery
Two-stage OND-NP delivery and release system dramatically – OND acumulate in lymphocyte
delivers payload to previously undraggable lymphe tissue
improved drug bioactivity – OND-NP eliminate LN LYMPHOMAS
Engineered Biomaterials

Douglas Lauffenburger – MIT, Biological Engineering and Koch Institute
Integrative Multi-Omic Analysis of Tissue Microenvironment in Inflammatory Pathophysiology

How to intervene, in predictive manner, in immunesystem-associated complex diseases
Understand cell communication beteen immune cells and other cells, i.e., tumor cells
Multi-Variate in Vivo – System Approach: Integrative Experiment & COmputational Analysis
Cell COmmunication & Signaling in CHronic inflammation – T-cell transfer model for colitis
COmparison of diffrential Regulation (Tcell transfer-elicited vs control) anong data types – relying solely on mRNA can be misleading
Diparities in differential responses to T cell transfer across data types yield insights concerning broader multi-organ interactions
T cell transfer can be ascertained and validated by successful experimental test
Cell COmmunication in Tumor MIcro-Environment — integration of single-cell transcriptomic data and protein interaction
Standard Cluster Elucidation – Classification of cell population on Full gene expression Profiles using Training sets: Decision Tree for Cell Classification
Wuantification of Pairwise Cell-Cell Receptor/Ligand Interactions: Cell type Pairs vs Receptor/Ligand Interaction
Pairwise Cell-Cell Receptor/Ligand Interactions
Calculate strength of interaction and its statistical significance
How the interaction is related to Phenotypic Behaviors – tumor growth rate, MDSC levels,
Correlated the Interactions translated to Phynotypic behavior for Therapeutic interventions (AXL via macrophage and fibroblasts)
Mouth model translation to Humans – New machine learning approach
Pathways, false negative, tumor negative expression
Molecular vs Phynotypical expression
Categories of inter-species translation
Semi-supervised Learning ALgorithms on Transcriptomic Data can ascertain Key Pathways/Processes in Human IBD from mapping mouse IBD

9:45 – 10:15 Break

10:15 – 11:30Session II
Moderator: Tyler Jacks | MIT, Koch Institute; HHMI

Tyler Jacks – MIT, Koch Institute; HHMI
Using Genetically Engineered Mouse Models to Probe Cancer-Immune Interactions

Utility of genetically-engineered mouse models of Cancer:

Immune Response (IR),
Tumor0immune microenvironment

Lung adenocarcinoma – KRAS mutation: Genetically-engineered model, applications: CRISPR, genetic interactions
Minimal Immune response to KP lung tumors: H&E, T cells (CD3), Bcells (B220) for Lenti-x 8 weeks
Exosome sequencing : Modeling loss-and gain-of-function mutations in Lung Cancer by CRISPR-Cas9 – germline – tolerance in mice, In vivo CRISPR-induced knockout of Msh2
Signatures of MMR deficient
Mutation burden and response to Immunotherapy (IT)
Programmed neoantigen expression – robust infiltration of T cells (evidence of IR)
Immunosuppression – T cell rendered ineffective
Lymphoid infiltration: Acute Treg depletion results in T cell infiltration — this depletion causes autoimmune response
Lung Treg from KP tumor-bearing mice have a distinct transcriptional heterogeneity through single cell mRNA sequencing
KP, FOXP3+, CD4
Treg from no existent to existance, Treg cells increase 20 fold =>>> Treg activation and effectiveness
Single cells cluster by tissue and cell type: Treg, CD4+, CD8+, Tetramer-CD4+
ILrl1/II-33r unregulated in Treg at late time point
Treg-specific deletion of IL-33r results in fewer effector Tregs in Tumor-bearing lungs
CD8+ T cell infiltration
Tetramer-positive T cells cluster according to time point: All Lung CD8+ T cells
IR is not uniform functional differences – Clones show distinct transcriptional profiles
Different phynotypes Exhaustive signature
CRISPR-mediated modulation of CD8 T cell regulatory genes
Genetic dissection of the tumor-immune microenvironment
Single cell analysis, CRISPR – CRISPRa,i, – Drug development

Wendell Lim – University of California, San Francisco

Synthetic Immunology: Hacking Immune Cells

Precision Cell therapies – engineered by synthetic biology
Anti CD19 – drug approved
CAR-T cells still face major problems

success limited to B cells cancers = blood vs solid tumors
adverse effects
OFF-TUMOR effects

Cell engineering for Cancer Therapy: User remote control (drug) – user control safety
Cell Engineering for TX

new sensors – decision making for
tumor recognition – safety,
Cancer is a recognition issue

How do we avoid cross-reaction with bystader tissue (OFF TISSUE effect)
Tumor recognition: More receptors & integration
User Control
synthetic NOTCH receptors (different flavors of synNotch) – New Universal platform for cell-to -cell recognition: Target molecule: Extracellular antigen –>> transciptional instruction to cell
nextgen T cell: Engineer T cell recognition circuit that integrates multiple inputs: Two receptors – two antigen priming circuit
UNARMED: If antigen A THEN receptor A activates CAR
“Bystander” cell single antigen vs “tumor” drug antigen
Selective clearance of combinatorial tumor – Boulian formulation, canonical response
Cell response: Priming –>> Killing: Spatial & Temporal choreographed cell
CAR expression while removed from primed cells deminished
Solid Tumor: suppress cell microenvironment: Selected response vs non-natural response
Immune stimulator IR IL2, IL12, flagellin in the payload — Ourcome: Immune enhancement “vaccination”
Immune suppression – block
Envision ideal situation: Unarmed cells
FUTURE: identify disease signatures and vulnerabilities – Precision Medicine using Synthetic Biology

Darrell Irvine – MIT, Koch Institute; HHMI
Engineering Enhanced Cancer Vaccines to Drive Combination Immunotherapies

Vaccine to drive IT
Intervening in the cancer-immunity cycle – Peptide Vaccines
poor physiology of solute transport to tissue
endogenous albumin affinity – Lymphe Node dying
Designing Albumin-hitchhiking vaccines
Amphiphile-vaccine enhance uptake in lymph nodes in small and large animal models
soluble vaccine vs Amphiphile-vaccine
DIRECTING Vaccines to the Lymph nodes
amph-peptide antigen: Prime, booster, tetramer
albimin-mediated LN-targeting of both antigen and adjuvant maximizes IR
Immuno-supressed microenvironment will not be overcome by vaccines
Replacing adoptive T cell transfer with potent vaccine
exploiting albumin biology for mucosal vaccine delivery by amph-vaccines
Amph-peptides and -adjuvants show enhanced uptake/retention in lung tissue
Enhancing adoptive T cell therapy: loss of T cell functionality, expand in vivo
boost in vivo enhanced adoptive T cell therapy
CAR-T cells: Enable T cells to target any cell surface protein
“Adaptor”-targeting CAR-T cells to deal with tumor cell heterogeneity
Lymph node-targeting Amph as CAR T booster vaccine: prining, production of cytokines
Boosting CAR T with amph-caccines: anti FITC CAR-T by DSPE=PEG-FITC coated
Targeting FITC to lymph node antigen presenting cells
Modulatory Macrophages
Amph-FITC expands FITC-CAR T cells in vivo – Adjuvant is needed
Hijacking albumin’s natural trafficking pathway

11:30 – 1:00 Lunch Break

1:00 – 2:15Session III
Moderator: Darrell Irvine | MIT, Koch Institute; HHMI

Nicholas P. Restifo – National Cancer Institute
Extracellular Potassium Regulates Epigenetics and Efficacy of Anti-Tumor T Cells

Why T cell do not kill Cancer cells?

co-inhibition
hostile tumor microenvironment

CAR T – does not treat solid tumors

Somatic mutation

resistence of T cell based IT due to loss of function mutations
Can other genes be lost?

CRISPR Cas9 – used to identify agents – GeCKOv2 Human library

Two cell-type (2CT) CRISPR assay system for genome-wide mutagenesis

work flow for genome-scale SRISPR mutagenesis profiling of genes essential for T cell mediate cytosis
sgRNA enrichment at the individual gene level by multiple methods:

subunits of the MHC Class I complex
CRISPR mutagenesis cut germline

Measutring the generalizability of resistance mechanism and mice in vivo validation
Validation of top gene candidates using libraries: MART-1
Checkpoint blockade: cells LOF causes tumor growth and immune escape
Weird genesL Large Ribisomal Subunit Proteins are nor all essential for cell survival
Bias in enrichment of 60S vs 40S
Novel elements of MHC class I antigen processing and presentation
Association of top CRISPR hits with response rates to IT – antiCTLA-4
CRISPR help identify novel regulators of T cells
Analyzed sgRNA – second rarest sgRNA for gene BIRC2 – encoded the Baculoviral Inhibitor
Drugs that inhibit BIRC2
How T cells can kill tumor cells more efficiently
p38kiaseas target for adoptive immunotherapy
FACS-based – Mapk14
Potent targets p38 – Blockade PD-1 or p38 ??
p38 signaling: Inhibition augments expansion and memory-marked human PBMC and TIL cells, N. P. Restifo
Tumor killing capacity of human CD19-specific, gene engineered T cells

Jennifer Elisseeff – Johns Hopkins University
The Adaptive Immune Response to Biomaterials and Tissue Repair

design scafolds, tissue-specific microenvironment
clinical translation of biosynthetic implants for soft tissue reconstruction
Local environment affects biomaterials: Epidermis, dermis
CD4+ T cells
Immune system – first reponders to materials: Natural or Synthetic
Biological (ECM) scaffolds to repair muscle injury
Which immune cells enter the WOUND?
ECM alters Macrophages: CD86, CD206
Adaptive system impact on Macrophages: CD86
mTOR signaling pathway M2 depend on Th2 Cells in regeneration of cell healing of surgical wounds
Systemic Immunological changes
Is the response antigen specific? – IL-4 expression in ILN,
Tissue reconstruction Clinical Trial: FDA ask to look at what cells infiltrate the scaffold
Trauma/biomaterial response – Injury induction of Senescence, anti apoptosis
Injury to skin or muscle
Is pro-regenerative environment (Th2/M2) pro-tumorigenic?
SYNTHETIC Materials for scafolds
Biomaterials and Immunology

Immune response to bioscafolds
environment modulate the immune system

Regenerative Immunetherapy

Marcela Maus – Massachusetts General Hospital

Engineering Better T Cells

Comparing CD19 CARs for Leukemia – anti-CD19- directed CAR T cells with r/r B-cell ALL – age 3-25 – FDA approved Novartis tisagenlecleucel – for pediatric r/r/ ALL
Phase II in diffuse large B cell lymphoma. Using T cells – increases prospects for cure
Vector retroviral – 30 day expression
measuring cytokines release syndrome: Common toxicity with CAR 19
neurological toxicity, B-cell aplagia
CART issues with heme malignancies

decrease cytokine release
avoid neurological toxicity – homing
new targets address antigene escape variants – Resistance, CD19 is shaded, another target needed
B Cell Maturation Antigen (BCMA) Target
Bluebird Bio: Response duratio up to 54 weeks – Active dose cohort
natural ligand CAR based on April
activated in response to TACI+ target cells – APRIL-based CARs but not BCMA-CAR is able to kill TACI+ target cells

Hurdles for Solid Tumors

Specific antigen targets
tumor heterogeneity
inhibitory microenvironment

CART in Glioblastoma

rationale for EGFRvIII as therapeutic target
Preclinical Studies & Phase 1: CAR t engraft, not as highly as CD19
Upregulation of immunosuppression and Treg infiltrate in CART EGFRvIII as therapeutic target, Marcela Maus

What to do differently?

2:15 – 2:45 Break

2:45 – 4:00 Session IV
Moderator: Arup K. Chakraborty | MIT, IMES

Laura Walker – Adimab, LLC
Molecular Dissection of the Human Antibody Response to Respiratory Syncytial Virus

prophylactic antibody is available
Barriers for development of Vaccine
Prefusion and Postfusion RSV structures
Six major antigenic sites on RSV F
Blood samples Infants less 6 month of age and over 6 month: High abundance RSV F -specific memory B Cells are group less 6 month

Arup K. Chakraborty – MIT, Institute for Medical Engineering & Science
How to Hit HIV Where it Hurts

antibody – Model IN SILICO
Check affinity of each Ab for the Seaman panel of strain
Breadth of coverage
immmunize with cocktail of variant antigens
Mutations on Affinity Maturation: Molecular dynamics
bnAb eveolution: Hypothesis – mutations evolution make the antigen binding region more flexible,
Tested hypothesisi: carrying out affinity maturation – LOW GERMLINE AFFINITY TO CONSERVE RESIDUES IN 10,000 trials, acquire the mutation (generation 300)

William Schief – The Scripps Research Institute
HIV Vaccine Design Targeting the Human Naive B Cell Repertoire

HIV Envelope Trimer Glycan): the Target of neutralizing Antibodies (bnAbs)
Proof of principle for germline-targeting: VRC)!-class bnAbs
design of a nanoparticle
can germline -targeting innumogens prime low frequency precursors?
Day 14 day 42 vaccinate
Precursor frequency and affinity are limiting for germline center (GC) entry at day 8
Germline-targeting immunogens can elicit robust, high quality SHM under physiological conditions of precursor frequency and affinity at day 8, 16, 36
Germline-targeting immunogens can lead to production of memory B cells