5th NIGMS Workshop on Pluripotent Stem Cell Research: Recent Progress and Future Directions of NIGMS Grantees

March 10-11, 2014

Workshop Summary

NIGMS-supported research on the basic biology on human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC) was the focus of this recent workshop, which brought together members of three program projects for basic research on human embryonic stem cells and three program projects on the basic biology of pluripotency and reprogramming. The meeting was an opportunity to share recent advances, discuss technologies and analytical tools, and consider the future of this exciting and fast-moving research area.

The talks and posters focused on several broad areas of hESC and iPSC research: pluripotency and self-renewal, exiting pluripotency and differentiation, reprogramming and cell fate conversions, and genomics and genome architecture. Following one-and-a-half days of scientific presentations, the workshop concluded with a discussion of future directions and challenges. Topics ranged from the challenges of computationally modeling cell state dynamics for predicting complex cell behaviors to the opportunities for using iPSC models to identify causative mutations among the large number of variants found by whole genome sequencing.

The full agenda and list of registered participants are below.

Agenda

Monday, March 10, 2014
Natcher Conference Center Room D

9:00 – 9:15 AM Welcome and Introduction
Jon Lorsch and Susan Haynes
 
9:15 – 10:30 AM Session I: Pluripotency and self-renewal
Chair: Stephen Dalton
 
9:15 – 9:40 AM Metabolomics of naive human embryonic stem cells
Hannele Ruohola-Baker
   
9:40 – 10:05 AM A quantitative perspective of transcription in pluripotent
and differentiated cells
Stephen Smale
 
10:05 – 10:30 AM X-chromosome dynamics in female pluripotent cells
Kevin Eggan
   
10:30 – 10:45 AM Discussion/Break
   
10:45 – 12:00 PM Session II: Exiting pluripotency
Chair: Kathrin Plath
   
10:45 – 11:10 AM Cell cycle-regulated mechanisms linking replication to cell fate transitions
David Gilbert
   
11:10 – 11:35 AM       Regulatory dynamics during the exit from pluripotency
Alex Meissner
   
11:35 – 12:00 PM Coordination of cell fate decisions with the cell cycle
Stephen Dalton
   
12:00 – 1:00 PM Lunch and informal discussions
   
1:00 – 3:00 PM Poster Session
Natcher Conference Center Atrium
   
3:00 – 4:15 PM Session III: Differentiation
Chair: Kevin Eggan
   
3:00 – 3:25 PM Molecular pathways to human cardiogenesis
Chuck Murry
   
3:25 – 3:50 PM Human fetal tissue is necessary to instruct hESC differentiation
Amander Clark
   
3:50 – 4:15 PM Identification of novel regulators of let-7 activity
Bill Lowry
   
4:15 – 4:30 PM Discussion/Break
   
4:30 – 5:20 PM Session IV: Genome architecture
Chair: Alex Meissner
   
4:30 – 4:55 PM Role of architectural proteins in nuclear organization and gene expression
Victor Corces
   
4:55 – 5:20 PM           Connecting genome organization to function
Kathrin Plath

 

Tuesday, March 11, 2014
Natcher Conference Center Room D


8:30 – 10:10 AM Session V: Functional genomics and RNAs
Chair: Mike Snyder
        
8:30 – 8:55 AM     Computational methods for analyzing high dimensional chromatin data
Matteo Pellegrini
   
8:55 – 9:20 AM           Dissection of cis-regulatory elements
Tarjei Mikkelsen
   
9:20 – 9:45 AM Bias in RNA-seq data
Larry Ruzzo
   
9:45 – 10:10 AM Essential roles for non-coding RNAs in development
John Rinn
   
10:10 – 10:30 AM Discussion/Break
   
10:30 – 11:45 AM Session VI: Pluripotency states and cell fate conversions
Chair: Stephen Smale
   
10:30 – 10:55 AM       Mechanisms underlying cell type conversion
Ken Zaret
   
10:55 – 11:20 AM Mechanisms of naive and primed pluripotency
Joanna Wysocka
   
11:20 – 11:45 PM Aging and reprogramming – how "young" are aged donor-derived iPSCs?
Salah Mahmoudi (Brunet lab)
   
11:45 – 12:45 PM      Lunch and informal discussions
   
12:45 – 1:35 PM Session VII: Reprogramming
Chair: Bill Lowry
   
12:45 – 1:10 PM Mechanisms of reprogramming
In-huyn Park
   
1:10 – 1:35 PM Transcriptional change during somatic cell reprogramming
Jared Churko (Wu lab)
 
1:35 – 1:50 PM Break/Discussion
   
1:50 – 3:20 PM Session VIII: Future Directions and Challenges
Chair: Susan Haynes
   
1:50 – 2:05 PM Commentary 1 – Stem cells, developmental biology, and translation
Ken Zaret
   
2:05 – 2:35 PM Open discussion
   
2:35 – 2:50 PM Commentary 2 – Comprehensive genomes, methylomes and transcriptomes
Mike Snyder
   
2:50 – 3:20 PM Open discussion
   
  Closing Remarks
Susan Haynes

 

Registered Participants

Justin Becker
Graduate Student
Cell and Developmental Biology
University of Pennsylvania School of Medicine
3400 Civic Center Blvd., Rm. 9-167
Smilow Center for Translational Research, Bldg. 42
Philadelphia, PA 19104
E-mail: justinbe@mail.med.upenn.edu

Kaytlyn Beres
Graduate Student
Bioengineering
University of Washington
Center for Cardiovascular Biology
850 Republican Street
Room 454
Seattle, WA 98109
E-mail: kaberes@uw.edu

Davide Cacchiarelli
Stem Cell and Regenerative Biology
Harvard University
7 Divinity Avenue
Cambridge, MA 02138
E-mail: davide.kun@gmail.com

James Chappell
Graduate Student
University of Georgia
180 Normal Avenue
Athens, GA 30606
E-mail: jchap14@gmail.com

Konstantinos Chronis
Postdoctoral Fellow
Biological Chemistry
UCLA
BSRB
354
Los Angeles, CA 90095
E-mail: k1chronis@gmail.com

Tim Cliff
Graduate Student
Biochemistry and Molecular Biology
University of Georgia
500 D.W. Brooks Drive
Athens, GA 30605
E-mail: clifftim@uga.edu

Victor Corces
Professor
Emory University
1510 Clifton Road
Rollins Research Center, Room 1071B
Atlanta, GA 30322
E-mail: vcorces@emory.edu

Stephen Dalton
Department of Biochemistry and Molecular Biology
University of Georgia
500 D.W. Brooks Drive
Athens, GA 30602
E-mail: sdalton@uga.edu

Miguel Edwards
UCLA
675 Charles E. Young Drive South
Los Angeles, CA 90095
E-mail: migs54@gmail.com

Kevin Eggan
Professor
Stem Cell and Regenerative Biology
Harvard University
7 Divinity Avenue, SF #258
Cambridge, MA 02138
E-mail: eggan@mcb.harvard.edu

Meilin Fernandez
Graduate Student
Biochemistry and Molecular Biophysics
University of Pennsylvania
Smilow Center for Translational Research
3400 Civic Center Blvd., Rm. #9-166
Philadelphia, PA 19104
E-mail: meilinfe@mail.med.upenn.edu

Xavier Gaeta
Graduate Student
UCLA
621 Charles E. Young Drive
Biological Sciences Research Building 457
Los Angeles, CA 90095
E-mail: xgaeta@ucla.edu

Igal Germanguz
Postdoctoral Fellow
MCDB/UCLA
1431 S. Shenandoah Street #10
Los Angeles, CA 90035
E-mail: germanguz@ucla.edu

David Gilbert
Florida State University
319 Stadium Drive
Tallahassee, FL 32306-4295
E-mail: gilbert@bio.fsu.edu

Susan Haynes
Program Director
NIGMS
45 Center Drive
Bethesda, MD 20892
E-mail: sh494m@nih.gov

Kavitha Kuppusamy
University of Washington
850 Republican Street
Seattle, WA 98109
E-mail: kavithak@uw.edu

Anna La Torre
Postdoctoral Fellow
Biological Structure, University of Washington
1959 Pacific Street NE
Seattle, WA 98195
E-mail: annalt@uw.edu

Justin Langerman
UCLA
Los Angeles, CA 90066
E-mail: ikari999@ucla.edu

Li Li
Biostatistics and Bioinformatics
Emory University
1518 Clifton Road NE
Room 327
Atlanta, GA 30322
E-mail: lilisysbio@gmail.com

Jing Liao
Postdoctoral Fellow
Stem Cell and Regenerative Biology
Harvard University
7 Divinity Avenue
Bauer 208
Cambridge, MA 02138
E-mail: jing_liao@harvard.edu

Jon Lorsch
Director, NIGMS
Bldg. 45, Rm. 3AN.44
45 Center Drive
Bethesda, MD 20892
E-mail: jon.lorsch@nih.gov

William Lowry
UCLA
621 Charles Young Drive
Los Angeles, CA 90077
E-mail: blowry@ucla.edu

Alexander Meissner
Harvard University
7 Divinity Avenue
Cambridge, MA 02138
E-mail: alexander_meissner@harvard.edu

Florian Merkle
Stem Cell and Regenerative Biology
Harvard University
7 Divinity Avenue
SF 216
Cambridge, MA 02138
E-mail: fmerkle@fas.harvard.edu

Tarjei Mikkelsen
Broad Technology Labs
Broad Institute
320 Charles Street, Room 2265
Cambridge, MA 02142
E-mail: tarjei@broadinstitute.org

Charles Murry
University of Washington
850 Republican Street
Brotman Building, Room 454
Seattle, WA 98109
E-mail: murry@uw.edu

Nathan Palpant
Postdoctoral Fellow
Pathology
University of Washington
850 Republican Street
Seattle, WA 98109
E-mail: npalpant@uw.edu

Kathrin Plath
Associate Professor
Department of Biological Chemistry
UCLA School of Medicine
615 Charles E. Young Drive South
BSRB 390D
Los Angeles, CA 90095
E-mail: kplath@mednet.ucla.edu

Steve Qin
Emory University
GCR338, 1518 Clifton Road NE
Department of Biostatistics and Bioinformatics
Atlanta, GA 30322
E-mail: zhaohui.qin@emory.edu

John Rinn
Associate Professor
Harvard University
7 Divinity Avenue, Room 305
Cambridge, MA 02138
E-mail: john_rinn@harvard.edu

Juan Carlos Rivera-Mulia
Postdoctoral Fellow
Biological Science, Florida State University
319 Stadium Drive
Tallahassee, FL 32306-4295
E-mail: riveramjc@bio.fsu.edu

Walter Ruzzo
Professor
University of Washington
Box 352350
Seattle, WA 98195
E-mail: ruzzo@uw.edu

Amar Singh
Postdoctoral Associate
Biochemistry and Molecular Biology
University of Georgia
500 D.W. Brooks Drive
Paul D. Coverdell Center
Athens, GA 30602
E-mail: singha@uga.edu

Stephen Smale
Professor
Microbiology, Immunology, and Molecular Genetics
UCLA, 1602B MSB, UCLA
Los Angeles, CA 90095
E-mail: smale@mednet.ucla.edu

Michael Snyder
Professor and Chair
Genetics
Stanford University
300 Pasteur Drive M344
Stanford, CA 94305
E-mail: mpsnyder@stanford.edu

Abdenour Soufi
Postdoctoral Associate
University of Pennsylvania
Perelman School of Medicine, CDB Department
Smilow Center for Translational Research, Bldg. 21
Room 166, 3400 Civic Center Boulevard
Philadelphia, PA 19104-5157
E-mail: asoufi@upenn.edu

Rajini Srinivasan
Research Assistant
Stanford University
265 Campus Drive
SIM1 Lokey Building
Room G3065
Stanford, CA 94305
E-mail: rajinis@stanford.edu

Yuhua Sun
University of Georgia
245# Coverdell Center, UGA
Athens, GA 30602
E-mail: yhsun@uga.edu

Alex Tsankov
Postdoctoral Fellow
Stem Cell and Regenerative Biology
Harvard University
7 Divinity Avenue
Bauer 208
Cambridge, MA 02138
E-mail: atsankov@broadinstitute.org

Guangwen Wang
Director, Stem Cell Core
Stanford University
265 Campus Drive West
SIM1 G1165A
Stanford, CA 94305
E-mail: gavin.wang@stanford.edu

Korey Wilson
Florida State University
319 Stadium Drive
Tallahassee, FL 32306
E-mail: kwilson@bio.fsu.edu

Yuan Xie
Ph.D. Candidate
MCDB
UCLA
Los Angeles, CA 90034
E-mail: xieyuanmail@gmail.com

Chenhuan Xu
Emory University
1510 Clifton Road
Rollins Research Building, Room 1071B
Atlanta, GA 30322
E-mail: chenhuan.xu@emory.edu

Ken Zaret
Professor
University of Pennsylvania
Institute for Regenerative Medicine
Department of Cell and Developmental Biology
3400 Civic Center Boulevard, Building 421
Philadelphia, PA 19104
E-mail: zaret@upenn.edu