designing and constructing a set of fundamental cell models: application to cardiac disease

20jun01: http://nsr.bioeng.washington.edu Silico.6.01

Designing and Constructing a Set of Fundamental Cell Models:

Application to Cardiac Disease

James B.Bassingthwaighte

University of Washington

Seattle


Engineering and reverse engineering the route from Genome to Function:

(Integrating Biological Systems Knowledge)

Genes

HealthOrganism

Organ

Tissue

Cell

Molecule

The Physiome Projecthttp://www.physiome.org

Structure and Function:• Biomedical Problem Formulation• Quantitative Approaches• Engineering Methods• Mechanistic System Modeling• Databasing & Dissemination


The Physiome and the Physiome Project

• The “Physiome”, like the Genome, is a quantitative description of the functional behavior of the physiological state of an individual of a species. In its fullest form it should define relationships from organism to genome and vice versa.

• The “Physiome Project” is a concerted effort to define the Physiome through databasing and through the development of a sequence of model types: schema of interactions, descriptions of structure and function, logical prediction, and integrative quantitative modeling for critical projections.


Physiome and Physiome Project

• The models of genomic, metabolic, or integrative systems should, via iteration with carefully designed experiments, resolve contradictions amongst prior observations and interpretations.

• Reasonably comprehensive and accurate models will demonstrate emergent properties. This is the “reverse engineering” of biology. Some of these will be applied to clinical diagnosis and the evaluation of care.

• Databases, concepts, descriptions, and models are to be put in the public domain, an open system.


Structure with FunctionStructure with Function• The Genome, and the Transcriptome. THE PHYSIOME:• The physico-chemical status.• Descriptions of the Proteome, of solutes, bilayers,

organelles, organs, organisms. • Quantitative measures of structural components,

e.g. protein and solute levels in cells and organelles, volumes, surface areas, material properties, etc. (The Morphome)

• Schema of interactions between the components. Regulatory apparatus for gene expression and metabolism. (The Metabolome)

• Computational models (genes +milieu organism).


Three Incentives for Developing the Physiome

• To develop understanding of a mechanism or a phenomenom: basic science.

• To determine the most effective targets for therapy, either pharmaceutic or genomic.

• To design artificial or tissue-engineered, biocompatible implants.


An example: LBBBLeft Bundle Branch Block of the Cardiac

Conduction System

Auscultation: Reverse splitting of the second heart sound

ECG: Wide QRS complex and often late T wave X-ray: Moderate cardiac enlargementThallium scan: Low flow in the septumPET scan: Decreased septal glucose uptake,

but normal septal fatty acid uptake.

The imaging gave three clues to the physiology.

How can the observations be explained?


Electrical activation of the normal heart

bundle branches

His bundle

AV node

sinus node

Purkinje fibers

right ventricle

left atrium

Prinzen et al., 2000


RV apex pacing left bundle branch block

Schematics of electrical activation

X

Prinzen et al., 2000


Explaining what is observed in Left Bundle Branch Block

ECG: Wide QRS complex and often late T wave

The RBB is activated normally, and excitation proceeds

normally over the RV, but since the left branch of the bundle of

His is blocked the spread of

activation into the left ventricular

muscle is delayed 50 to 100 ms,

broadening the QRS complex,

and delaying the repolarization

phase (late T wave)


ECG

Tagging pulse Delay = 50 ms Delay = 90 ms Delay = 130 ms

50ms 90ms 130ms

...

...

Pacingspike

Gx

RF

Presat.pulse

MRI tagging of Cardiac Contraction

(Prinzen, Hunter, Zerhouni,1999)


Explaining what is observed in Left Bundle Branch Block

Auscultation: Reversed splitting of S2 (second heart sound)

The RBB is activated normally, but activation of the left ventricle is delayed 50 to 100 ms, so that aortic valve closing is delayed and is later than pulmonic closing, rather than earlier. During inspiration increased RV filling, delaying pulmonic valve closure, shortens (rather than lengthening) the interval between pulmonic and aortic valve closure: reversed respiratory influence on second sound splitting interval.

Normally, Insp longer A2–P2 , but here Insp shorter P2–A2


Effect of RV apex pacing on regional LV epicardial fiber strain

atrialpacing

ventricularpacing

site A site B

ejection phase

early-activated late-activated

Prinzen et al, Am. J. Physiol, 1990

S

egm

ent l

engt

h


Atrial pacing RV apex pacing LV free wall pacing

.

Fiber length

.

Fiber length

.

Fiber length

apex

base anterior

posterior

sep

tum

Prinzen et al, J Am Coll Cardiol, 1999

**

0

(mJ/g) 8

Distribution of external work in the LV wall

0


To explain what is seen in LBBB:Thallium scans: Decreased septal blood flow relative to rest of LV because local demand is reduced. Decreased septal mass due to local atrophy.

PET Glucose Uptake: Decreased septal uptake due to shift away from glucose with diminished demand relative to supply. PET data show normal FA uptake. Regional FA uptake is matched to local flow.

X-ray: LV hypertrophy: Hypertrophic free wall due to increased workload and low contractile efficiency. This is partially attributable to increased wall tension with LV cavity volume increase: T=PxR.


Cardiac fiber structuring:

LV base

LV near the apex

From Torrent-Guasp, 1998


Rabbit Heart: Epicardial fibers – blue Subendocardial fibers - yellow

From Vetter and McCulloch, UCSD


Integration by Computation: The Cardiome

• Transport:• UW: Flows, uptake (O2, fats)

• Cardiac Mechanics:• Auckland Univ: P.Hunter• UCSD: McCulloch • Maastricht: Arts, Prinzen, Reneman• JHU: W.Hunter

• Action Potentials:• Oxford U: D. Noble• Johns Hopkins: Winslow• Case-Western: Rudy

• Cardiac excitatory spread:• CWRU: Rudy et al.• Johns Hopkins: Winslow• Syracuse: Jalife• UCSD: McCulloch

N.Smith, P. Hunter,et al. 1998


What are the mechanisms for the responses in

Left Bundle Branch Block?

Thallium scans: How is local flow regulated?

PET Glucose Uptake: How is glycolysis regulated?

MR Strain Patterns: How do structure, excitation, and contraction combine to produce these?

X-ray LV hypertrophy: What regulates actin and myosin expression?


Excitation-Contraction Coupling

• Cooperativity • Mechanical Feedback


The Motor Units


ffSTRONGSTRONG

g +g Vg +g V

Energy Use depends on shortening velocity:

WEAK

ADPADPATPATP00 11

ADPADP

Weak-Strong vs. Attached-DetachedWeak-Strong vs. Attached-Detached

ATPATP

Mechanical FeedbackMechanical Feedback Landesberg/Sideman, 1998


The Conservative Phys-chem cell(no protein synthesis or proteolyis)

• Balances mass, charge, volume, energy, reducing equivalents, concentrations

• Serves as a primitive for expanded models• RBC, prokaryote, eukaryote, myocyte, B-cell• Serve as entry to databases• Component of healthy and diseased tissues• Basis for multicellular integrated systems models• Understanding via metabolic control analysis of networks

• Test bed for mechanistic pharmacodynamic models and selection for drug design and for genomic intervention


The glycolytic conservative cell (with eternal proteins)

Na+

Ca2

Ca

Ca2+

3Na+

ATP

3Na+

ATP

Na+

Substrates

Glycolysis

pH balance~P balancePurine balanceOsmotic balanceWater balance

Charge neutrality

Redox state Free Energy

RBC

e.g. arep.med.harvard.edu,Edwards, Palsson,Church et al.

Metabolites


The conservative cell with eternal proteins

Na+ Na+

INaK

Ca2+

Ip(Ca)

Ca2+

INaCa

Na+

Endoplasmic reticulum

ATP

ATP

ATP

Na+

Substrates

Glycolysis,fatty acid

pH~P balancePurine balanceOsmotic balanceWater balance

Charge neutrality

Redox state Free Energy

TCAOxPhosph


The sustainable metabolic muscle cell

Na+ Na+ Na+

K+

K+

K+

K+

Ca2+

Ip(Ca)ICa,K

K+Ca2+

ICa,b

Ca2+ TRPN

T-tubuleCa2+

Na+

Sarcoplasmic reticulum

ICa

Ca2+

Ca2+

subspace

calseq

calmodulincalmodulin

RyR

Ca2+

Ca2+

ATP

ATP

ATP

K+

K+

H+

Na+

TCA

OxPhosphSubstrates

ATP regulation

pH, P &Charge neutrality

Leak


The cardiac muscle cell

Na+ Na+ Na+

K+

K+

K+

K+

Kp

NaK Na INa,b

Ca2+

Ip(Ca)ICa,K

K+Ca2+

ICa,b

T-tubuleCa2+

aCa

Na+

Sarcoplasmic reticulum

ICa

Ca2+

Ca2+

subspace

calseq

calmodulin

RyR

Ca2+

Ca2+

ATP

ATP

ATP

K+Ks

K+to1

H+

Na+

Substrates

Leak

(building from Luo-Rudy 1994-2001and Winslow et al. 1999)

OxPhosph

TCA

Glycolysis


Conclusions:

• Conservative cell models provide a basis for a host of specific applications.

• Their behavior is innately complex and highly dependent on the conditions.

• Computability is a major issue if models are to be used are practical aids to thinking.

• Even now they provide short-term prediction of the consequences of intervention.


END

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designing and constructing a set of fundamental cell models: application to cardiac disease

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