Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.
Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation.
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.|Department of Medical Oncology, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
Paloma
P
Cejas
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Lewyn
L
Li
Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Nicholas K
NK
O'Neill
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Melissa
M
Duarte
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Prakash
P
Rao
Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Michaela
M
Bowden
Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Chensheng W
CW
Zhou
Department of Medical Oncology, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.|Department of Pathology, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
Marta
M
Mendiola
Department of Pathology, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
Emilio
E
Burgos
Department of Medical Oncology, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
Jaime
J
Feliu
Precision Oncology Laboratory, Infanta Sofia University Hospital, Madrid, Spain.
Juan
J
Moreno-Rubio
Department of Surgery, Jimenez Diaz Foundation, Madrid, Spain.
Héctor
H
Guadalajara
Clinical Research Unit, Jimenez Diaz Foundation, Madrid, Spain.
Víctor
V
Moreno
Department of Surgery, Jimenez Diaz Foundation, Madrid, Spain.
Damián
D
García-Olmo
Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Joaquim
J
Bellmunt
Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Stephanie
S
Mullane
Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Michelle
M
Hirsch
Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Christopher J
CJ
Sweeney
Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Andrea
A
Richardson
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.
X Shirley
XS
Liu
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Myles
M
Brown
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Ramesh A
0000-0002-2828-1727
RA
Shivdasani
Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.|Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Henry W
HW
Long
D000818:Animals; D002277:Carcinoma / Q000235:genetics; D002295:Carcinoma, Transitional Cell / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D015179:Colorectal Neoplasms / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic; D005557:Formaldehyde; D020869:Gene Expression Profiling; D064593:Heterografts; D059014:High-Throughput Nucleotide Sequencing; D042421:Histone Code / Q000235:genetics*; D006801:Humans; D061986:MCF-7 Cells; D051379:Mice; D009369:Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D012333:RNA, Messenger / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D016707:Tissue Fixation; D059467:Transcriptome; D001749:Urinary Bladder Neoplasms / Q000235:genetics
D012333:RNA, Messenger; D005557:Formaldehyde