Institute  for  Systems  Genomics  Networking  Workshop  

Tuesday,  June  7,  2016  

 

Institute  for  Systems  Genomics  Networking  Workshop  

Tuesday,  June  7,  2016  

The  Jackson  Laboratory  for  Genomic  Medicine  Auditorium  10  Discovery  Drive,  Farmington,  Connecticut  

9:00  AM   Registration  

9:30  AM   Opening  Remarks    Charles  Lee    Director  and  Professor,  The  Jackson  Laboratory  for  Genomic  Medicine  

9:40  AM   “Drosophila  melanogaster  gut  microbiota:  emergent  and  dependent  properties”  Nichole  Broderick,  Ph.D.,  University  of  Connecticut  

9:55  AM   “The  Human  Skin  Microbiome:  Metagenomes  to  Therapeutics”  Julia  Oh,  Ph.D,  The  Jackson  Laboratory  for  Genomic  Medicine  

10:10  AM   “Roadmap  to  identifying  craniofacial  enhanceropathies”  Justin  Cotney,  Ph.D,  University  of  Connecticut  School  of  Medicine  

10:25  AM   “Leveraging  Diverse  Biomedical  Data  to  Elucidate  Complex  Diseases  via  Statistical  Learning”  Yuping  Zhang,  Ph.D.,  University  of  Connecticut  

10:40  AM    “Casilio:  A  multitasking  CRISPR-­‐OS  for  the  genome”  Albert  Cheng,  Ph.D.,  The  Jackson  Laboratory  of  Genomic  Medicine  

10:55  AM   BREAK  

11:10  AM   “Identify  candidate  anti-­‐cancer  drug  resistant  biomarkers  by  integrating  genomics  data”  Sheida  Nabavi,  Ph.D.,  University  of  Connecticut  

11:25  AM   “Regulatory  Riddles  on  &  beyond  the  X  chromosome”  Stefan  Pinter,  Ph.D,  University  of  Connecticut  School  of  Medicine  

11:40  AM   “The  Present  and  Future  of  Genomic  Technologies:  from  Genome  Structure  to  Regulatory  Function”  Chia-­‐Lin  Wei,  Ph.D.,  The  Jackson  Laboratory  for  Genomic  Medicine  

11:55  AM   “Uconn  Microbial  Analysis,  Resources,  and  Services  Facility”  Kendra  Maas,  Ph.D.,  University  of  Connecticut  

12:10  PM   “PITCH:  Program  in  Innovative  Therapeutics  for  Connecticut  Health”  Dennis  Wright,  Ph.D.,  University  of  Connecticut  

Sandra  Weller,  Ph.D.,  University  of  Connecticut  School  of  Medicine  

12:25  PM   Closing  Remarks  Marc  Lalande,  Ph.D.  Director,  Institute  for  Systems  Genomics  

12:30  PM   Lunch  

1:30  PM   Workshop  Adjourns  

 

ABSTRACTS  

Nichole  Broderick,  Ph.D.  Assistant  Professor,  Department  of  Molecular  and  Cell  Biology  University  of  Connecticut  

The  animal  gut  is  the  primary  site  of  interaction  between  a  host  and  many  microorganisms,  both  beneficial  and  invasive.  The  indigenous  gut  microbiota  has  diverse  effects  on  host  physiology,  including  mucosal  immune  responses  and  proper  epithelium  development.  In  general,  gut  microbiota  are  perceived  as  beneficial,  by  supplying  essential  nutrients,  metabolizing  indigestible  compounds,  or  preventing  colonization  by  invasive  bacteria.  Invasive  bacteria,  in  contrast,  are  often  deleterious  to  the  host  by  inducing  inflammatory  states  that  ultimately  disrupt  gut  homeostasis,  leading  to  pathogenesis.  However,  this  simple  dichotomy  only  partially  reflects  the  dynamic  interactions  of  microbiota  with  their  host.  To  gain  insights  into  the  complex  relationships  among  gut  microbiota,  bacterial  pathogens,  and  host  responses,  I  have  used  the  genetically  tractable  model  Drosophila  melanogaster.  Compared  to  the  complexity  of  the  mammalian  gut  microbiota,  the  microbiota  of  D.  melanogaster  is  simple  in  composition  and  diversity.  However,  this  simple  consortium  has  important  impacts  on  the  host.  I  will  describe  the  gut  microbiota  associated  with  D.  melanogaster  and  our  recent  results  exploring  their  impacts  on  host  physiology  and  behavior,  including  susceptibility  to  bacterial  pathogens.    

Julia  Oh,  Ph.D.  Assistant  Professor,  The  Jackson  Laboratory  for  Genomic  Medicine  

The  human  skin  harbors  an  abundant  microbial  ecosystem  with  bidirectional  metabolic  exchanges  supporting  symbiotic  and  commensal  functions.  Sequence-­‐  based  analysis  of  microbial  community  structure  and  organization  of  the  human  microbiome  has  yielded  valuable  insight  into  the  microbial  diversity  and  function  of  its  different  body  niches.  Metagenomic  analyses  of  the  diverse  skin  sites  in  healthy  humans  demonstrate  that  contrasting  forces  of  the  skin’s  biogeography  and  individual  characteristics  shape  the  skin  microbiome  and  the  dynamics  of  its  bacteria,  fungi,  and  viruses.  However,  shifts  in  the  ecological  properties  of  the  skin  microbiome  are  significantly  associated  with  skin  disease,  disease  severity,  and  other  physiologic  host  factors  such  as  age  or  primary  immunodeficiency.  Understanding  the  function,  structure,  and  dynamics  of  the  microbiome  is  important  to  design  therapeutics  that  precisely  target  the  pathogen  of  interest,  yet  spare  the  surrounding  beneficial  microbiota.  

 

ABSTRACTS  

Justin  Cotney,  Ph.D.  Assistant  Professor,  Department  of  Genetics  and  Genome  Sciences  University  of  Connecticut  School  of  Medicine  

Defects  in  embryonic  patterning  resulting  in  craniofacial  abnormalities  are  common  birth  defects  affecting  more  than  1  in  750  live  births.  The  genetic  causes  of  these  defects  have  been  difficult  to  determine,  but  all  current  evidence  suggests  defective  gene  regulation  during  embryonic  development  underlies  these  birth  defects.  Most  of  the  individuals  affected  by  congenital  craniofacial  abnormalities  do  not  have  defects  in  other  tissues  or  organ  systems,  thus  are  relatively  tissue  specific  and  considered  non-­‐syndromic.    The  regulatory  programs  that  build  and  shape  the  craniofacial  complex  require  precisely  controlled  spatiotemporal  gene  expression.  Much  of  the  information  that  controls  these  gene  expression  programs  is  thought  to  be  encoded  in  the  large  expanses  of  the  genome  between  protein-­‐coding  genes  and  within  intronic  sequences.  Efforts  by  large  projects  such  as  ENCODE  and  the  Roadmap  Epigenome  Project  have  established  associations  of  many  biochemical  features  (modified  histones,  accessibility  to  DNAse  I  cleavage,  Pol  II  occupancy,  and  transcription)  with  functional  portions  of  the  genome  (genes,  promoters,  enhancers,  insulators,  etc.)  and  state  of  activity  (euchromatic,  heterochromatic,  activated,  transcribed,  or  repressed).    These  efforts  have  revealed  that  enhancers  are  typically  tissue  or  timepoint  specific  and  regulate  one  or  a  small  number  of  genes  over  very  large  genomic  distances.    The  tissue  specific  nature  of  enhancers  coupled  with  the  enrichment  of  a  variety  of  disease  phenotype  associations  from  genome-­‐wide  association  studies  (GWAS)  in  these  regulatory  sequences  suggest  that  defects  in  enhancers  are  at  fault  in  many  common  disorders.    The  non-­‐syndromic  nature  of  most  craniofacial  defects  indicate  they  are  potentially  enriched  for  defects  in  enhancer  activity  and  likely  to  be  “enhanceropathies”.    To  date  early  stages  of  human  craniofacial  development  have  not  been  interrogated  with  modern  functional  genomics  techniques  preventing  large  scale  integrative  analysis  of  genetic  associations  and  tissue-­‐specific  chromatin  states.    We  are  currently  generating  comprehensive  chromatin  state  maps  for  critical  stages  in  human  craniofacial  development  and  targeting  many  of  the  identified  enhancers  for  unbiased  long  range  interaction  mapping.    These  chromatin  profiles  and  enhancer-­‐promoter  contact  maps  will  allow  us  to  identify  causative  genetic  changes  in  human  patients  with  craniofacial  abnormalities  and  develop  mouse  models  through  targeted  genome  editing.  

Yuping  Zhang,  Ph.D.  Assistant  Professor,  Department  of  Statistics  University  of  Connecticut    

Recent  advances  in  high-­‐throughput  biotechnologies  have  generated  unprecedented  types  and  amounts  of  data  for  biomedical  research.  It  is  likely  that  integrating  results  from  diverse  experiments  may  lead  to  a  more  unified  and  global  view  of  complex  diseases.  In  this  talk,  I  will  address  statistical  approaches  developed  in  my  laboratory  in  data  integration  and  present  some  of  our  research  efforts  on  turning  diverse  biomedical  data  into  knowledge.  

Albert  Cheng,  Ph.D.  Assistant  Professor,  The  Jackson  Laboratory  for  Genomic  Medicine  

The  RNA-­‐guided  DNA  endonuclease  system  CRISPR-­‐Cas9  has  been  exploited  for  genome  editing  in  various  species.  The  nuclease-­‐deficient  mutant  dCas9  protein  can,  when  coupled  with  sgRNAs,  bind  specific  genomic  loci  without  inducing  DNA  cleavage,  thus  serving  as  a  programmable  DNA  binding  protein.  To  extend  the  utility  of  the  dCas9  system,  we  have  taken  advantage  of  the  ability  of  Pumilio  PUF  domains  to  bind  specific  8-­‐mer  RNA  sequences.  By  combining  these  two  systems,  we  established  the  Casilio  system,  which  allows  for  specific  and  independent  delivery  of  effector  proteins  to  specific  genomic  loci.  We  demonstrated  that  the  Casilio  system  enables  independent  up  and  down-­‐regulation  of  multiple  genes,  as  well  as  live-­‐cell  imaging  of  multiple  genomic  loci  simultaneously.  Importantly,  multiple  copy  of  PUF  binding  sites  can  be  incorporated  on  sgRNA  backbone,  therefore  allowing  for  local  multimerization  of  effectors.  In  addition,  the  PUF  domain  can  be  engineered  to  recognize  any  8-­‐mer  RNA  sequence,  therefore  enabling  the  generation  and  simultaneous  operation  of  many  Casilio  modules.  

 

ABSTRACTS

Sheida  Nabavi,  Ph.D.  Assistant  Professor,  Department  of  Computer  Science  and  Engineering  University  of  Connecticut  

With  advances  in  technologies,  multiple  types  of  high-­‐throughput  genomics  data  for  several  samples  are  available.  These  data  have  tremendous  potential  to  identify  new  and  clinically  valuable  biomarkers  to  guide  the  diagnosis,  assessment  of  prognosis,  and  treatment  of  complex  diseases,  such  as  cancer.  Integrating,  analyzing,  and  interpreting  big  and  noisy  genomics  data  to  obtain  biologically  meaningful  results,  however,  remains  highly  challenging.  The  main  goal  of  this  work  is  to  integrate  genomics  data  to  identify  candidate  biomarkers  of  drug  resistance  in  triple  negative  breast  cancer  (TNBC)  and  ovarian  cancer.  We  started  with  analyzing  genomics  and  transcriptomics  data  of  resistant  tumors  to  the  combination  of  PARP  and  PI3K  inhibitor  from  a  TNBC  mouse  model,  and  also  ovarian  cancer  responding  and  non-­‐responding  tumors  from  TCGA.  We  focus  on  somatic  mutations,  somatic  copy  number  variations,  fusion  genes  and  differentially  expressed  genes  for  the  integrative  analysis.  We  are  also  generating  new  sequencing  data  from  35  TNBC  and  ovarian  cancer  tumors  treated  with  the  combination  of  PARP  and  PIK3  inhibitor.  Mining  all  these  data  and  using  advanced  computational  methods  we  will  identify  a  short  list  of  potential  biomarkers  of  resistance  to  facilitate  the  biomarker  discovery  process.    

Stefan  Pinter,  Ph.D.  Assistant  Professor,  Department  of  Genetics  and  Genome  Sciences  

The  mammalian  X  chromosome  holds  a  special  place  in  the  hearts  of  geneticists  and  epigeneticists  alike.  X-­‐linked  monogenic  diseases  were  among  the  first  to  be  mapped,  and  X-­‐chromosome  inactivation  (XCI)  in  female  mammals  has  served  as  a  classic  model  of  epigenetics  for  more  than  5  decades.  Our  previous  work  revealed  how  the  long  non-­‐coding  RNA  Xist  spreads  in  cis  across  the  mouse  X  to  silence  genes.  Some  genes,  however,  mange  to  escape  XCI  and  continue  expression  from  the  otherwise  inactive  X  chromosome.  We  would  like  to  understand  the  mechanism(s)  behind  this  phenomenon.  In  addition,  some  X-­‐linked  variable  number  tandem  repeats  (VNTRs)  masquerade  as  escapees,  but  have  likely  functions  in  chromosome  topology.  We  will  develop  methodology  to  study  structure  and  function  of  X-­‐linked  and  autosomal  VNTRs  to  learn  how  they  may  inform  genome  architecture  and  regulation.  

Chia-­‐Lin  Wei,  Ph.D.  Genome  Technology,  The  Jackson  Laboratory  for  Genomic  Medicine  

The  dynamic  and  rapid  transition  of  genome  technologies  has  been  the  key  driving  force  for  the  advancement  of  genome  biology  and  its  biomedical  applications.  Genome  technologies  enable  us  to  detect  and  characterize  genetic  inheritance,  disease  susceptibility,  and  responses  to  environmental  influences.  These  cutting-­‐edge  genomic,  transcriptomic  and  epigenomic  technologies,  when  applied  effectively  to  examine  variations  in  genetic  makeup,  RNA  expression  and  epigenetic  modifications  at  population  scale  and  in  high  resolution,  provide  the  basis  for  deciphering  genome  structural  and  functional  interactions.  In  this  talk,  I  will  briefly  introduce  the  rapid  evolving  genome  technology  and  the  exciting  opportunity  they  offer  to  understand  genome  biology  and  pave  the  knowledge  base  for  precision  medicine.  

 

ABSTRACTS

Kendra  Maas,  Ph.D.  Facility  Scientist,  Microbial  Analysis,  Resources,  and  Services  Facility  UConn  Biotechnology  Bioservices  Center  

UConn  MARS  is  a  core  facility;  it  was  started  in  2014  to  provide  bacterial  microbiome  sequencing  as  a  service  to  the  UConn  community.  The  current  explosion  in  microbiome  research  is  fueled  by  the  mounting  evidence  that  nearly  all  systems  are  impacted  by  the  previously  unknown  microbes  that  inhabit  them.    The  technology  that  underpins  current  microbiome  sequencing  can  be  applied  to  nearly  any  other  target  gene,  i.e.  we  can  also  sequence  fungal  ITS  or  help  design  custom  targets.  Beyond  providing  the  wet  lab  sequencing,  I  can  help  design  experiments  and  assays,  do  the  bioinformatic  analysis  of  the  raw  sequences,  and  offer  guidance  (or  even  perform)  statistical  analysis  and  figure  plotting.  

In  addition  to  providing  next-­‐gen  DNA  sequencing  and  analysis,  our  equipment  (liquid  handling  robots,  high  throughput  screening  devices,  MiSeq,  etc.)  is  also  available  to  use  on  an  hourly  basis.  

Dennis  Wright,  Ph.D.   Sandra  Weller,  Ph.D.  Professor,  University  of  Connecticut   University  of  Connecticut  School  of  Medicine  

PITCH  is  a  new  program  collaborative  program  supported  by  the  Connecticut  Bioscience  Innovation  Fund,  the  University  of  Connecticut  and  Yale  University  to  provide  a  unique  opportunity  to  academic  investigators  to  accelerate  translational  drug  development  research  and  jumpstart  new  commercial  ventures  in  the  state.    The  presentation  wiWell  describe  the  structure  of  the  program,  the  application  process  and  overview  of  progress  in  the  program.