Refresher Course:
Integrating Genomics Into Physiology Courses: A New
Paradigm or Just More Information?
Incorporating physiological genomics into
an undergraduate physiology course.
Sergey Kasparov
University of Bristol, UK.
[email protected]
What is Physiological Genomics-1?
Griffiths et al – Introduction to Genetic Analysis 8th ed.
Chapter 12 – Genomics.
“… Indeed the knowledge of entire genomes has revolutionized not only genetics but most fields of
biological research. … this exciting new field broadly called genomics - the study of genomes
in their entirety. “
“Functional Genomics uses various automated procedures to delineate networks of interacting
genes active during some developmental process.”
W.F. Boron & EL Boulpaep “Medical Physiology” 2003
Pg 4…>
“Physiological Genomics is the Link Between the Organ and the Gene.
Physiological genomics (or functional genomics) is a new branch of
physiology devoted to understanding the roles of genes play in physiology.
Traditionally physiologists have moved in reductionistic direction from organ to cell to molecule to
gene. One of the most fascinating aspects of physiological genomics is that it has closed the circle
and linked organ physiology directly with molecular biology…. In order to grasp the function of a
gene product the physiologist must retrace his steps back up the reductionistic road and achieve an
integrated understanding of that gene’s function at the level of cells, organs, and the whole body.”
What is Physiological Genomics-2 ?
Lodish et al. Molecular Cell Biology
Starting from Pg 380
9.4 Genomics: Genome-wide Analysis of Gene Structure and Expression
Key concepts:
-The function of an unknown protein may be predicted based on the aminoacid similarity to
the known ones…
- BLAST searches protein databases for similarities with the known proteins…
- Functional motifs may be identified…
- A protein family may be identified within a range of available genomes…
- Computer programmes search for open reading frames (> 100 codons)…
- Microarrays… cluster analysis and so on…
Journal of Physiology – a special issue in 2003 contained a set of
papers all about Physiological Genomics
A.W.Cowley Jr, The chief editor of the “Physiological Genomics” wrote an editorial
called “Physiological Genomics: tools and concepts”.
”Physiological genomics is an emerging field that brings together
disciplines of genomics and cell, organ and whole animal systems
integrative physiology in an effort to attach function to the DNA
sequences of complex living systems”.
What is Physiological Genomics-3 ?
This meeting:
Symposium: Discovery of Genes for Polycystic Kidney Disease
Symposium: Genomics of Circadian Clocks
Symposium: Genomics of Transport and Sensory Functions
Symposium: Imprinting, Development and the Programming of Adult Health
Featured Topic: Complex Pathway of Function and Disease Deduced from the
Whole Genome Perspective
Featured Topic: Genetic Basis of Cardiopulmonary Disorders
Symposium: Functional Genomics of Macromolecular Damage Responses and
Environmental Stress Adaptation
Featured Topic: Epithelial Genomics, Proteomics and Genetic Models
Symposium: Genetic Determinants of Obesity and Metabolic Disease
Symposium: Comparative Genomics of Blood Pressure Control: Genetic Maps
in Humans, Rats and Mice
Symposium: Comparative Genomics of the Lung
Teaching Physiological Genomics to the Physiology
Students in Bristol
Our cohort of students:
-NOT specialised in molecular biology or biochemistry… Some examples
of the topics covered in Y1 and 2
-Physiological Genomics is one of the two Elements they do in Y3
-Class size in Y 2005 = 18
-Many of our students DO NOT continue as scientists, but take jobs
related to biomedicine, for example with the scientific publishers or ???
Teaching Physiological Genomics to the Physiology
Students in Bristol…
A dream course…
1. Revision of the structure of genes, gene expression and basics of
genetics
2. Bioinformatics and approaches to genome annotation and gene discovery
3. Comparative genomics and model organisms
4. Molecular high throughput systems for studies of gene function
5. Methods of Gene Expression analysis (high throughput vs high fidelity),
microarrays.
6. Gene expression and genetic plasticity
7. Polymorphisms in experimental science and medicine
8. Epigenetics
9. Transgenic animals (including knockouts)
10.Other approaches to gene suppression (antisense, decoys, siRNA etc)
and gene “loss-of-function” experiments (dominant negatives and similar
approaches).
11.Somatic gene transfer (viral vectors) – application for physiological
studies
12.Gene therapy
13.Safety and legal aspects of GM experimentation
Module learning objectives
On completion of the module, students will:Be able to describe a range of current molecular approaches used
to investigate physiological functions at different levels of
organisation, from single cell to whole body.
Be familiar with the advantages of cross-species analysis for
studies of gene function.
Be aware of the rationales for the use of different molecular
approaches, and the advantages and disadvantages of individual
techniques.
Be familiar of the application of the Functional Genomics to studies
of the origins of human diseases.
Be able to give examples of the recent publications where methods
of physiological genomics have been successfully used.
Understand and be able to explain molecular strategies used in
drug development and rational drug design.
Be able to compare gene therapy with conventional biomedical
approaches to the treatment of diseases, and give examples of
recent advances in gene therapy.
The overall structure of our course (Element)
STAR
T
FINIS
H
SESSIO
N
10/01/2
005
14:00
15:20
LECT
Element 3B: Introduction to Physiological Genomics
SEK
stuff
10/01/2
005
15:40
17:00
LECT
Element 3B: Model organisms 1
PBM
stuff
12/01/2
005
09:00
10:20
LECT/
PA
Element 3B: Model organisms 2
PBM
stuff
12/01/2
005
10:40
12:00
LECT
Element 3B: Microarrays
DaM
17/01/2
005
14:00
15:20
LECT
Element 3B: Somatic gene transfer 1
SEK
17/01/2
005
15:40
17:00
LECT
Element 3B: Somatic gene transfer 2
JFP
19/01/2
005
09:00
10:20
LECT
Element 3B:Germline transgenesis
DaM
guest
19/01/2
005
10:40
12:00
LECT
Element 3B: Gene suppression
SW
guest
24/01/2
005
14:00
15:20
LECT
Element 3B: GM Legislation
SJ
24/01/2
005
15:40
17:00
LECT
Element 3B: Genetic Plasticity
DaM
26/01/2
005
09:00
10:20
LECT
Element 3B: Gene Therapy
AB
26/01/2
005
10:40
12:00
LECT/
PA
Element 3B: Genomic tools and rational drug design
HJW
stuff
31/01/2
005
15:40
17:00
LECT/
PA
Element 3B:Gene therapy vs chemicals & drugs?
HJW
stuff
02/02/2
005
09:00
10:20
Element 3B: From Genome to Therapy Paper
Analysis1
SEK
stuff
02/02/2
005
10:40
12:00
PA
PA
Element 3B: From Genome to Therapy Paper
Analysis2
SEK
DATE
TITLE
STAFF
guest
stuff
stuff
guest
guest
guest
stuff
EXAMPLES from lectures
S. Kasparov
Teaching using Paper Analysis
Beginning of the Element:
Introduced the paper and explained
the process of orphan receptors
discovery.
Students
were
given
their
assignments (to prepare talks to
explain various experiments which
were included in that study).
During the Element:
Students were reading the paper and
preparing their presentations using
(some of the) information they were
taught.
Last two sessions of the Element:
Students made their presentations
and answered questions. The
teacher had to step in from time to
time.
Citric acid cycle intermediates as ligands for orphan G-proteincoupled receptors
Weihai He1*, Frederick J.-P. Miao1, Daniel C.-H. Lin1, Ralf T.
Schwandner1,2, Zhulun Wang1, Jinhai Gao1*, Jin-Long Chen1, Hui
Tian1 & Lei Ling1
NATURE, VOL 429, 13 MAY 2004, 188
A handout to assist paper analysis:
I. First steps. Proof of the physiological activity of the putative receptors, identification of the ligands and crossspecies analysis.
1.
Identification of putative GPCRs by analysis of ESTs and genome-wide screening (based on
Wittenberg et al (2001) paper. Initial assumptions based on sequence homology. Questions which were
unanswered:
a) do these sequences really encode for functional GPCRs?
b) where are these GPCRs present in mammalian organisms?
c) what are their endogenous ligands
d) what are their physiological roles)
2. Development of an assay which could be used to identify the ligand(s): Stables 1997 paper
3. Identification of the ligand for GPR91: a) basic chemistry of that ligand b) Mass spec analysis = at charge one,
mol mass is ~ 120 c) NMR for 1H = in highly ionised form only one type of H atoms and 13C = presence of C=O
and CH2. What could it be? Succinate! Comparison with synthetic chemical proved the guess.
4. Inter-species analysis of GPR91 in aequorin essay.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5. Generation of a stable cell line with human GPR91 (the same was done for GPR99)– a way to screen for any
other ligand or a drug lead compound.
6. Cracking the GPR99: structurally very close to GPR91. Hypothesised that the ligands might be similar.
Screened in aequorin assay (but the number of suspects was relatively small) and identified it to be ketoglutarate, another intermediate of the same cycle.
NOW NEED to find out how they work in order to get an idea of what they might be doing…
II. Analysis of G-protein signalling mechanism and the molecular structure of the receptor.
7. 7a: hGPR91 couples to PTX-sensitive Gio to inhibit forskolin-induced cAMP accumulation and to Gq to trigger
IP (MUST BE IP3!) accumulation (Figs 2e,f,g).. 7b: GPR99 couples via Gq only (Figs 2g&supplementary info)
8. Internalisation – Fig 2h
9. Generation of a computer model of the binding site and site-directed mutagenesis – Fig 3 a,b,c,d. WHY THIS
MIGHT BE NECESSARY???
EXAMPLES from lectures
EXAMPLES of STUDENTS
PRESENTATIONS
The outcomes in Y2005
Average scores Phys Genom 2005 (n=12)
5
4.5
4
3.5
3
2.5
2
1.5
1
0.5
0
Usefulness of the
element
Was your background
sufficient for this
element?
Did you like paper
analysis as a method
of teaching?
Did you like the
selection of topics and
speakers?
Successful and unsuccessful teaching?
Correlation between the Overall Interest and
Understanding and Student’s Background Level
(Teacher 2)
Correlation between the Overall Interest and
Understanding and Student’s Background Level
(Teacher 1)
12
16
10
14
12
8
10
6
8
6
4
4
2
2
0
0
0
1
2
3
4
5
6
0
1
2
3
4
Correlation between the Overall Interest and
Understanding and Student’s Background Level
(Teacher 3)
16
14
Overall Interest=
Clarity+
Interest+
“Can remember”
12
10
8
6
4
2
0
0
1
2
3
4
5
6
5
6
What is still missing:
Bioinformatics (could be a bit problematic because of the need of
good background in mol biology and also maths)
Polymorphisms and their potential roles in human diseases
Epigenetics…???
A fundamental problem – wider and deeper teaching of
biochemistry and general molecular biology during the initial part
of training.
However, this is slightly at odds with the overall ambition of this
Department to be seen as a knowledge base for systems and in
vivo physiology.
Conclusions
1.Our view, consistent with (A.W.Cowley Jr), is that
”Physiological genomics… brings together disciplines of genomics
and cell, organ and whole animal systems integrative physiology in
an effort to attach function to the DNA sequences of complex
living systems”
2.Combination of traditional lectures and paper analysis seems to
work best
3. Students seem to be more interested in application of genomic
tools to physiological and medical problems than in “hard-core”
molecular genetics
4. Background knowledge is a problem and needs to be looked at.
5.Several important areas have not been covered in sufficient
detail, but this also depends on the time allocated in the
curriculum.
6.Finally, we have successfully run an “element” of “Physiological
Genomics” to a non-specialist class of 3Y Physiology Students