Sperm Molecular Alterations are Biomarkers of Testicular Injury and Dysfunction By Sara Ellen ...

279 Pages·2012·3.15 MB·English

by  Sara Pacheco

!Sperm Molecular Alterations are Biomarkers of Testicular Injury and Dysfunction

By
Sara Ellen Pacheco
B.S., University of Massachusetts, Amherst, 2007

Dissertation
Submitted in partial fulfillment of the requirements for the
Degree of Doctor of Philosophy in Biology and Medicine at Brown University

PROVIDENCE, RHODE ISLAND
MAY 2012
© Copyright 2012 by Sara Ellen Pacheco
This dissertation by Sara Ellen Pacheco is accepted in its present form by the
Department of Biology and Medicine as satisfying the dissertation requirement
for the degree of Doctor of Philosophy.

Date______________ ________________________________
Kim Boekelheide, M.D., Ph.D., Advisor

Recommended to the Graduate Council
Date______________ ________________________________
Mary Hixon, Ph.D., Reader
Date______________ ________________________________
Karl T. Kelsey, M.D., M.O.H., Reader
Date______________ ________________________________
Mark Sigman, M.D., Reader
Date______________ ________________________________
Robert Chapin, Ph.D., Outside Reader

Approved by the Graduate Council
Date______________ ________________________________
Peter M. Weber, Ph.D., Dean of the
Graduate School

iii
CURRICULUM VITAE
Sara Ellen Pacheco
Education
2007-2012 Brown University Providence, RI
Ph.D. in Medical Science, Pathobiology Graduate Program
Mentor: Kim Boekelheide, M.D., Ph.D.

2003-2007 University of Massachusetts Amherst, MA
B.S. in Microbiology, Commonwealth College Scholar
Departmental Honors, Summa Cum Laude

Publications
1. Sara E. Pacheco, Edward Dere, and Kim Boekelheide
Rat sperm microRNA profiling identifies microRNAs important for reproductive
function and embryonic development. Manuscript in preparation.

2. Sara E. Pacheco, Linnea M. Anderson, Moses A. Sandrof, Marguerite M.
Vantangoli, Susan J. Hall, Kim Boekelheide
Sperm mRNA transcripts are biomarkers of sub-chronic low dose Sertoli cell
injury in the rat. Manuscript in preparation.

3. Sara E. Pacheco, Linnea M. Anderson, and Kim Boekelheide
Optimization of a filter-lysis protocol to purify rat testicular homogenates for
automated spermatid counting. J Androl. 2012 Jan 12. [Epub ahead of print]

iv
4. Sara E. Pacheco, E. Andres Houseman, Brock C. Christensen, Carmen J.
Marsit, Karl T. Kelsey, Mark Sigman, and Kim Boekelheide
Integrative DNA methylation and gene expression analyses identify DNA
packaging and epigenetic regulatory genes associated with low motility sperm.
PLoS One. 2011;6(6):e20280. Epub 2011 Jun 2.

5. Sarah N. Campion, Natasha Catlin, Nicholas Heger, Elizabeth V. McDonnell,
Sara E. Pacheco, Camelia Saffarini, Moses A. Sandrof, and Kim
Boekelheide
Male reprotoxicity and endrocrine disruption. Molecular, Clinical and
Environmental Toxicology, Volume 3: Environmental Toxicology. Birkhäuser
Publishing, Basel, Switzerland. In press.

Awards and Accolades
 Superfund Research Trainee-Highlight (Spring 2012)
 Rhode Island Hospital’s 19th Annual Research Celebration’s New Investigator
Award (Clinical Research), Finalist (Fall 2011)
 Northeast Society of Toxicology, Poster Competition, 3rd Place (Fall 2011)
 Northeast Society of Toxicology, Oral Presentation Finalist (Fall 2011)
 Pathobiology Program Retreat Poster Competition, 3rd Place (Fall 2010)
 Levy Pre-doctoral Travel Award for Ph.D. Students in BioMed (2009)
 Sheridan Center Program 1 Teaching Certificate (2009)
 UMass Amherst Alumni Association: 5 under 25 (2009)
 Graduate Training Grant: “Training in Environmental Pathology” #ES007272 (Fall
2008-Fall 2011)
 Jr. Fellows Program (Fall 2006-Spring 2007)
v
 CBR-REU Intern (Summer 2006)
 William Field Alumni Scholar (Spring 2006)
 Golden Key International Honor Society (Fall 2005)
 Alpha Lambda Delta National Honor Society (Spring 2004)
 Dean’s List (Fall 2003-Spring 2007)

Invited Lectures
 American Society of Andrology 2012 Basic Science Workshop “Diagnosing Male
Reproductive Capacity in the Laboratory”, Tuscon, AZ (04/21/12). “Tools for
detecting testicular injury in rodent models”
 Superfund Research Program Student Roundup, Brown University, Providence,
RI (03/21/12). “Sperm mRNA transcripts as biomarkers of low dose testicular
injury in the rat”
 Pathobiology Admissions Weekend, Brown University, Providence, RI (02/11/12).
“Hidden messages: sperm mRNA transcripts as biomarkers of low dose testicular
injury in the rat”
 2012 Pathobiology Seminar Series, Brown University, Providence, RI (01/26/12).
“Sperm molecular signatures: reading and writing the paternal transcriptome and
epigenome”
 Brown BioMed Office of Graduate and Postdoctoral Studies Summer Graduate
Student Research Series, Brown University, Providence, RI (07/21/11).
“Integrating clinical semen parameters with sperm molecular biomarkers”

vi
Conferences and Abstracts
 American Society of Andrology Annual Meeting
o Poster – 2012, 2011, 2010, and 2009
o Podium – 2012 and 2011
 Rhode Island Hospital’s 19th Annual Research Celebration
o Poster – 2011
 Northeast Society of Toxicology Regional Chapter Meeting
o Poster and Podium – 2011
 American Society of Andrology Testis Workshop
o Poster – 2011 and 2009
 American Association for Cancer Research Annual Meeting
o Poster – 2007
 Massachusetts Annual Undergraduate Research Conference
o Poster – 2007 and 2004

Teaching and Leadership Experience
 Peer Reviewer, Journal of Andrology
 Trainee-Representative Elect, American Society of Andrology Council
 Member, American Society of Andrology Trainee Affairs Committee
 Special Lecturer of Biology, Providence College
 Graduate Student Educator, Advancing RI Science Education
 Guest Lecturer, Brown University
 Graduate Student Mentor, Brown University Pathobiology Program
 Member, Pathobiology Graduate Student Steering Committee, Brown University

vii
ACKNOWLEDGEMENTS
The work highlighted in this dissertation could not have come to fruition
without the support and encouragement from a number of people. I would like to
take this opportunity to express my gratitude to the following individuals:
 Kim Boekelheide – Thank you for being my mentor and providing the
environment necessary for me to succeed. You had high expectations for my
work from day one and that really motivated me to push myself harder than I
probably would have on my own. You cultivated my research and critical
thinking skills by allowing me to ask questions and speak my mind. I have
learned so much during these past 5 years – I really couldn’t have asked for a
better experience.

 Karl Kelsey, Mark Sigman, and Bob Chapin – Thank you for being part of my
thesis brain-trust. I really value all of your guidance and feedback.

 Mary Hixon – Thank you for being you. I truly believe that you are the reason
that I am where I am today. You are my guardian angel and your
benevolence will never be forgotten. You have had a profound impact on my
life and when I think about the kind of teacher that I would like to be someday,
I think of you.

 Team Testis – Thank you all for everything. Sue, thank you for always
listening to me, especially when things were difficult for me both in and out of
viii
lab. I couldn’t have made it through without your endless support. Moses,
thank you for being my work-husband – one of my favorite parts of graduate
school was being your bay-mate. Camelia, you have been a true friend for all
these years. Thank you for consistently picking me back up whenever I was
down. I am really going to miss our heart-to-hearts. Nick, grad school would
not have been the same without you. I am glad we got to navigate through
this process together. Maggie, I could not have asked for a better
replacement bay-mate! You are the little sister I never had and I know we will
keep in touch. Thanks for editing this beast. Natasha and Linnea, I still think
you are both nuts, but I think I am “half” crazy, too. Thank you for encouraging
me to do the unthinkable and accomplish one of the greatest feats of my
lifetime. Liz, thank you for being an extra set of hands when I needed them.
You were always willing to help me and I really appreciate it. Ed, you are a
computer genius. Thank you for making all of my figures aesthetically
pleasing and educating me about all of the intricacies of Microsoft Word. The
thesis writing process would not have gone as smoothly without you. Dan,
I’ve really enjoyed our conversations about random facts. They were a much-
needed distraction from all of this writing.

 Jodie Pietruska – I am so grateful that fate put us in the same place at the
same time. You will always be more than just my work-wife and I look forward
to continuing our friendship after we leave the 5th floor.

ix
 My wolf pack – Thank you for all of the laughs. I am going to miss our daily
doses of coffee and gossip.

 My family – Nick, Mom, and Dad, I could not have done this without the love
and support from all three of you. Nick, you are an amazing person and I
could not have chosen a better life partner. You stuck by me when things got
tough and never let me give up. I am a better person because you are in my
life. Mom and Dad, I am so lucky that you are my parents. You have never
stopped believing in me. You say I can do anything that I set my mind to, but
everything I have accomplished is a direct result of your unconditional love
and support. I would never have made it this far without you.
x