Literature DB >> 34103329

Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia.

Lindsey E Montefiori1, Sonja Bendig2, Zhaohui Gu3,4, Xiaolong Chen5, Petri Pölönen1, Xiaotu Ma5, Alex Murison6, Andy Zeng6, Laura Garcia-Prat6, Kirsten Dickerson1, Ilaria Iacobucci1, Sherif Abdelhamed1, Ryan Hiltenbrand1, Paul E Mead1, Cyrus M Mehr1, Beisi Xu7, Zhongshan Cheng7, Ti-Cheng Chang7, Tamara Westover1, Jing Ma1, Anna Stengel2, Shunsuke Kimura1, Chunxu Qu1, Marcus B Valentine8, Marissa Rashkovan9, Selina Luger10, Mark R Litzow11, Jacob M Rowe12, Monique L den Boer13, Victoria Wang14, Jun Yin15, Steven M Kornblau16, Stephen P Hunger17, Mignon L Loh18, Ching-Hon Pui19, Wenjian Yang20, Kristine R Crews20, Kathryn G Roberts1, Jun J Yang20, Mary V Relling20, William E Evans20, Wendy Stock21, Elisabeth M Paietta22, Adolfo A Ferrando9,23,24,25, Jinghui Zhang5, Wolfgang Kern2, Torsten Haferlach2, Gang Wu1,7, John E Dick6, Jeffery M Klco26, Claudia Haferlach27, Charles G Mullighan26.   

Abstract

Lineage-ambiguous leukemias are high-risk malignancies of poorly understood genetic basis. Here, we describe a distinct subgroup of acute leukemia with expression of myeloid, T lymphoid, and stem cell markers driven by aberrant allele-specific deregulation of BCL11B, a master transcription factor responsible for thymic T-lineage commitment and specification. Mechanistically, this deregulation was driven by chromosomal rearrangements that juxtapose BCL11B to superenhancers active in hematopoietic progenitors, or focal amplifications that generate a superenhancer from a noncoding element distal to BCL11B. Chromatin conformation analyses demonstrated long-range interactions of rearranged enhancers with the expressed BCL11B allele and association of BCL11B with activated hematopoietic progenitor cell cis-regulatory elements, suggesting BCL11B is aberrantly co-opted into a gene regulatory network that drives transformation by maintaining a progenitor state. These data support a role for ectopic BCL11B expression in primitive hematopoietic cells mediated by enhancer hijacking as an oncogenic driver of human lineage-ambiguous leukemia. SIGNIFICANCE: Lineage-ambiguous leukemias pose significant diagnostic and therapeutic challenges due to a poorly understood molecular and cellular basis. We identify oncogenic deregulation of BCL11B driven by diverse structural alterations, including de novo superenhancer generation, as the driving feature of a subset of lineage-ambiguous leukemias that transcend current diagnostic boundaries.This article is highlighted in the In This Issue feature, p. 2659. ©2021 American Association for Cancer Research.

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Year:  2021        PMID: 34103329      PMCID: PMC8563395          DOI: 10.1158/2159-8290.CD-21-0145

Source DB:  PubMed          Journal:  Cancer Discov        ISSN: 2159-8274            Impact factor:   39.397


  114 in total

1.  CONSERTING: integrating copy-number analysis with structural-variation detection.

Authors:  Xiang Chen; Pankaj Gupta; Jianmin Wang; Joy Nakitandwe; Kathryn Roberts; James D Dalton; Matthew Parker; Samir Patel; Linda Holmfeldt; Debbie Payne; John Easton; Jing Ma; Michael Rusch; Gang Wu; Aman Patel; Suzanne J Baker; Michael A Dyer; Sheila Shurtleff; Stephen Espy; Stanley Pounds; James R Downing; David W Ellison; Charles G Mullighan; Jinghui Zhang
Journal:  Nat Methods       Date:  2015-05-04       Impact factor: 28.547

2.  Cell of origin strongly influences genetic selection in a mouse model of T-ALL.

Authors:  Katherine E Berquam-Vrieze; Kishore Nannapaneni; Benjamin T Brett; Linda Holmfeldt; Jing Ma; Oksana Zagorodna; Nancy A Jenkins; Neal G Copeland; David K Meyerholz; C Michael Knudson; Charles G Mullighan; Todd E Scheetz; Adam J Dupuy
Journal:  Blood       Date:  2011-08-09       Impact factor: 22.113

3.  SomaticSniper: identification of somatic point mutations in whole genome sequencing data.

Authors:  David E Larson; Christopher C Harris; Ken Chen; Daniel C Koboldt; Travis E Abbott; David J Dooling; Timothy J Ley; Elaine R Mardis; Richard K Wilson; Li Ding
Journal:  Bioinformatics       Date:  2011-12-06       Impact factor: 6.937

4.  A far downstream enhancer for murine Bcl11b controls its T-cell specific expression.

Authors:  Long Li; Jingli A Zhang; Marei Dose; Hao Yuan Kueh; Ruzbeh Mosadeghi; Fotini Gounari; Ellen V Rothenberg
Journal:  Blood       Date:  2013-06-05       Impact factor: 22.113

5.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Authors:  Kai Ye; Marcel H Schulz; Quan Long; Rolf Apweiler; Zemin Ning
Journal:  Bioinformatics       Date:  2009-06-26       Impact factor: 6.937

Review 6.  Mixed-Phenotype Acute Leukemia: Diagnostic Criteria and Pitfalls.

Authors:  Nathan J Charles; Daniel F Boyer
Journal:  Arch Pathol Lab Med       Date:  2017-11       Impact factor: 5.534

7.  Cooperative genetic defects in TLX3 rearranged pediatric T-ALL.

Authors:  P Van Vlierberghe; I Homminga; L Zuurbier; J Gladdines-Buijs; E R van Wering; M Horstmann; H B Beverloo; R Pieters; J P P Meijerink
Journal:  Leukemia       Date:  2008-01-10       Impact factor: 11.528

Review 8.  The Genetics and Mechanisms of T-Cell Acute Lymphoblastic Leukemia.

Authors:  Francesca Gianni; Laura Belver; Adolfo Ferrando
Journal:  Cold Spring Harb Perspect Med       Date:  2020-03-02       Impact factor: 6.915

9.  Determining cell type abundance and expression from bulk tissues with digital cytometry.

Authors:  Aaron M Newman; Chloé B Steen; Chih Long Liu; Andrew J Gentles; Aadel A Chaudhuri; Florian Scherer; Michael S Khodadoust; Mohammad S Esfahani; Bogdan A Luca; David Steiner; Maximilian Diehn; Ash A Alizadeh
Journal:  Nat Biotechnol       Date:  2019-05-06       Impact factor: 54.908

10.  DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Authors:  Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M Stütz; Vladimir Benes; Jan O Korbel
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

View more
  10 in total

Review 1.  Redefining the biological basis of lineage-ambiguous leukemia through genomics: BCL11B deregulation in acute leukemias of ambiguous lineage.

Authors:  Lindsey E Montefiori; Charles G Mullighan
Journal:  Best Pract Res Clin Haematol       Date:  2021-10-23       Impact factor: 3.020

2.  The genomic landscape of pediatric acute lymphoblastic leukemia.

Authors:  Samuel W Brady; Kathryn G Roberts; Zhaohui Gu; Lei Shi; Stanley Pounds; Deqing Pei; Cheng Cheng; Yunfeng Dai; Meenakshi Devidas; Chunxu Qu; Ashley N Hill; Debbie Payne-Turner; Xiaotu Ma; Ilaria Iacobucci; Pradyuamna Baviskar; Lei Wei; Sasi Arunachalam; Kohei Hagiwara; Yanling Liu; Diane A Flasch; Yu Liu; Matthew Parker; Xiaolong Chen; Abdelrahman H Elsayed; Omkar Pathak; Yongjin Li; Yiping Fan; J Robert Michael; Michael Rusch; Mark R Wilkinson; Scott Foy; Dale J Hedges; Scott Newman; Xin Zhou; Jian Wang; Colleen Reilly; Edgar Sioson; Stephen V Rice; Victor Pastor Loyola; Gang Wu; Evadnie Rampersaud; Shalini C Reshmi; Julie Gastier-Foster; Jaime M Guidry Auvil; Patee Gesuwan; Malcolm A Smith; Naomi Winick; Andrew J Carroll; Nyla A Heerema; Richard C Harvey; Cheryl L Willman; Eric Larsen; Elizabeth A Raetz; Michael J Borowitz; Brent L Wood; William L Carroll; Patrick A Zweidler-McKay; Karen R Rabin; Leonard A Mattano; Kelly W Maloney; Stuart S Winter; Michael J Burke; Wanda Salzer; Kimberly P Dunsmore; Anne L Angiolillo; Kristine R Crews; James R Downing; Sima Jeha; Ching-Hon Pui; William E Evans; Jun J Yang; Mary V Relling; Daniela S Gerhard; Mignon L Loh; Stephen P Hunger; Jinghui Zhang; Charles G Mullighan
Journal:  Nat Genet       Date:  2022-09-01       Impact factor: 41.307

3.  Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.

Authors:  Shunsuke Kimura; Lindsey Montefiori; Ilaria Iacobucci; Yaqi Zhao; Qingsong Gao; Elisabeth M Paietta; Claudia Haferlach; A Douglas Laird; Paul E Mead; Zhaohui Gu; Wendy Stock; Mark Litzow; Jacob M Rowe; Selina M Luger; Stephen P Hunger; Georgina L Ryland; Breon Schmidt; Paul G Ekert; Alicia Oshlack; Sean M Grimmond; Jacqueline Rehn; James Breen; David Yeung; Deborah L White; Ibrahim Aldoss; Elias J Jabbour; Ching-Hon Pui; Manja Meggendorfer; Wencke Walter; Wolfgang Kern; Torsten Haferlach; Samuel Brady; Jinghui Zhang; Kathryn G Roberts; Piers Blombery; Charles G Mullighan
Journal:  Blood       Date:  2022-06-16       Impact factor: 25.476

4.  miR-4461 inhibits the progression of Gallbladder carcinoma via regulating EGFR/AKT signaling.

Authors:  Xingzhou Yan; Pinghua Yang; Hu Liu; Yongyang Zhao; Zhixiong Wu; Baohua Zhang
Journal:  Cell Cycle       Date:  2022-02-23       Impact factor: 5.173

5.  ZNF384 Fusion Oncoproteins Drive Lineage Aberrancy in Acute Leukemia.

Authors:  Kirsten M Dickerson; Chunxu Qu; Qingsong Gao; Ilaria Iacobucci; Zhaohui Gu; Hiroki Yoshihara; Emily A Backhaus; Yunchao Chang; Laura J Janke; Beisi Xu; Gang Wu; Evangelia K Papachristou; Clive S D'Santos; Kathryn G Roberts; Charles G Mullighan
Journal:  Blood Cancer Discov       Date:  2022-05-05

Review 6.  Latest Contributions of Genomics to T-Cell Acute Lymphoblastic Leukemia (T-ALL).

Authors:  Eulàlia Genescà; Celia González-Gil
Journal:  Cancers (Basel)       Date:  2022-05-17       Impact factor: 6.575

Review 7.  T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness.

Authors:  Valentina Bardelli; Silvia Arniani; Valentina Pierini; Danika Di Giacomo; Tiziana Pierini; Paolo Gorello; Cristina Mecucci; Roberta La Starza
Journal:  Genes (Basel)       Date:  2021-07-23       Impact factor: 4.096

8.  Integrative Genomic Analysis of Pediatric Myeloid-Related Acute Leukemias Identifies Novel Subtypes and Prognostic Indicators.

Authors:  Maarten Fornerod; Jing Ma; Sanne Noort; C Michel Zwaan; Tanja A Gruber; Yu Liu; Michael P Walsh; Lei Shi; Stephanie Nance; Yanling Liu; Yuanyuan Wang; Guangchun Song; Tamara Lamprecht; John Easton; Heather L Mulder; Donald Yergeau; Jacquelyn Myers; Jennifer L Kamens; Esther A Obeng; Martina Pigazzi; Marie Jarosova; Charikleia Kelaidi; Sophia Polychronopoulou; Jatinder K Lamba; Sharyn D Baker; Jeffrey E Rubnitz; Dirk Reinhardt; Marry M van den Heuvel-Eibrink; Franco Locatelli; Henrik Hasle; Jeffery M Klco; James R Downing; Jinghui Zhang; Stanley Pounds
Journal:  Blood Cancer Discov       Date:  2021-09-09

Review 9.  Early T-Cell Precursor ALL and Beyond: Immature and Ambiguous Lineage T-ALL Subsets.

Authors:  Eulàlia Genescà; Roberta la Starza
Journal:  Cancers (Basel)       Date:  2022-04-08       Impact factor: 6.639

Review 10.  Chromatin structure in cancer.

Authors:  Meng Wang; Benjamin D Sunkel; William C Ray; Benjamin Z Stanton
Journal:  BMC Mol Cell Biol       Date:  2022-07-28
  10 in total

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