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Kulkarni A, Mohan V, Tang TT, Post L, Chan YC, Manning M, Thio N, Parker BL, Dawson MA, Rosenbluh J, Vissers JH, Harvey KF. Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription. EMBO Rep 2024:10.1038/s44319-024-00217-3. [PMID: 39103676 DOI: 10.1038/s44319-024-00217-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024] Open
Abstract
The Hippo tumor suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs have been reported, with some entering clinical trials for different cancers with Hippo pathway deregulation, most notably, mesothelioma. Using genome-wide CRISPR/Cas9 screens we reveal that mutations in genes from the Hippo, MAPK, and JAK-STAT signaling pathways all modulate the response of mesothelioma cell lines to TEAD palmitoylation inhibitors. By exploring gene expression programs of mutant cells, we find that MAPK pathway hyperactivation confers resistance to TEAD inhibition by reinstating expression of a subset of YAP/TAZ target genes. Consistent with this, combined inhibition of TEAD and the MAPK kinase MEK, synergistically blocks proliferation of multiple mesothelioma and lung cancer cell lines and more potently reduces the growth of patient-derived lung cancer xenografts in vivo. Collectively, we reveal mechanisms by which cells can overcome small-molecule inhibition of TEAD palmitoylation and potential strategies to enhance the anti-tumor activity of emerging Hippo pathway targeted therapies.
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Affiliation(s)
- Aishwarya Kulkarni
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Varshini Mohan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Tracy T Tang
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Leonard Post
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Murray Manning
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Joseph Ha Vissers
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
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2
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Luck C, Jacobs KA, Okimoto RA. The Capicua C1 Domain is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597815. [PMID: 38895482 PMCID: PMC11185703 DOI: 10.1101/2024.06.06.597815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rearrangements between genes can yield neomorphic fusions that drive oncogenesis. Fusion oncogenes are made up of fractional segments of the partner genes that comprise them, with each partner potentially contributing some of its own function to the nascent fusion oncoprotein. Clinically, fusion oncoproteins driving one diagnostic entity are typically clustered into a single molecular subset and are often treated a similar fashion. However, knowledge of where specific fusion breakpoints occur in partner genes, and the resulting retention of functional domains in the fusion, is an important determinant of fusion oncoprotein activity and may differ between patients. This study investigates this phenomena through the example of CIC::DUX4, a fusion between the transcriptional repressor capicua (CIC) and the double homeobox 4 gene (DUX4), which drives an aggressive subset of undifferentiated round cell sarcoma. Using a harmonized dataset of over 100 patient fusion breakpoints from the literature, we show that most bona fide CIC::DUX4 fusions retain the C1 domain, which is known to contribute to DNA binding by wild type CIC. Mechanistically, deletion or mutation of the C1 domain reduces, but does not eliminate, activation of CIC target genes by CIC::DUX4. We also find that expression of C1-deleted CIC::DUX4 is capable of exerting intermediate transformation-related phenotypes compared with those imparted by full-length CIC::DUX4, but was not sufficient for tumorigenesis in a subcutaneous mouse model. In summary, our results suggest a supercharging role for the C1 domain in the activity of CIC::DUX4.
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Affiliation(s)
- Cuyler Luck
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Kyle A. Jacobs
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Ross A. Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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3
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Hendrickson PG, Oristian KM, Browne MR, Luo L, Ma Y, Cardona DM, Nash JO, Ballester PL, Davidson S, Shlien A, Linardic CM, Kirsch DG. Spontaneous expression of the CIC::DUX4 fusion oncoprotein from a conditional allele potently drives sarcoma formation in genetically engineered mice. Oncogene 2024; 43:1223-1230. [PMID: 38413794 PMCID: PMC11027086 DOI: 10.1038/s41388-024-02984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
CIC::DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of patient tumor samples and cell lines. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous soft tissue tumors and disseminated disease in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic Cic function and the distance between adjacent loxP sites. Characterization of soft tissue and presumed metastatic tumors showed that they consistently expressed the CIC::DUX4 fusion protein and many downstream markers of the disease credentialing the models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-sequencing maps, validate CIC::DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R Browne
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Joshua O Nash
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Pedro L Ballester
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Scott Davidson
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Corinne M Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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4
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Hendrickson PG, Oristian KM, Browne MR, Luo L, Ma Y, Cardona DM, Linardic CM, Kirsch DG. Expression of the CIC-DUX4 fusion oncoprotein mimics human CIC-rearranged sarcoma in genetically engineered mouse models. RESEARCH SQUARE 2023:rs.3.rs-3487637. [PMID: 37961185 PMCID: PMC10635354 DOI: 10.21203/rs.3.rs-3487637/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CIC-DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of patient tumor samples and cell lines. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous tumors and widespread metastasis in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic CIC function and the distance between loxP sites. Characterization of primary and metastatic mouse tumors showed that they consistently expressed the CIC-DUX4 fusion protein as well as other downstream markers of the disease credentialing these models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-seq maps, validate CIC-DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G. Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R. Browne
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Dianna M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Corinne M. Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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5
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Hendrickson PG, Oristian KM, Browne MR, Lou L, Ma Y, Cardona DM, Linardic CM, Kirsch DG. Expression of the CIC-DUX4 fusion oncoprotein mimics human CIC-rearranged sarcoma in genetically engineered mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559519. [PMID: 37808628 PMCID: PMC10557731 DOI: 10.1101/2023.09.26.559519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
CIC-DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of tissues and patients. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous tumors and widespread metastasis in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic CIC function and loxP site proximity. Characterization of primary and metastatic mouse tumors showed that they consistently expressed the CIC-DUX4 fusion protein as well as other downstream markers of the disease credentialing these models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-seq maps, validate CIC-DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G. Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R. Browne
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Lou
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Dianna M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Corinne M. Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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6
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Sgammeglia N, Widmer YF, Kaldun JC, Fritsch C, Bruggmann R, Sprecher SG. Memory phase-specific genes in the Mushroom Bodies identified using CrebB-target DamID. PLoS Genet 2023; 19:e1010802. [PMID: 37307281 DOI: 10.1371/journal.pgen.1010802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/29/2023] [Indexed: 06/14/2023] Open
Abstract
The formation of long-term memories requires changes in the transcriptional program and de novo protein synthesis. One of the critical regulators for long-term memory (LTM) formation and maintenance is the transcription factor CREB. Genetic studies have dissected the requirement of CREB activity within memory circuits, however less is known about the genetic mechanisms acting downstream of CREB and how they may contribute defining LTM phases. To better understand the downstream mechanisms, we here used a targeted DamID approach (TaDa). We generated a CREB-Dam fusion protein using the fruit fly Drosophila melanogaster as model. Expressing CREB-Dam in the mushroom bodies (MBs), a brain center implicated in olfactory memory formation, we identified genes that are differentially expressed between paired and unpaired appetitive training paradigm. Of those genes we selected candidates for an RNAi screen in which we identified genes causing increased or decreased LTM.
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Affiliation(s)
- Noemi Sgammeglia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Yves F Widmer
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jenifer C Kaldun
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Cornelia Fritsch
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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7
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The role and application of transcriptional repressors in cancer treatment. Arch Pharm Res 2023; 46:1-17. [PMID: 36645575 DOI: 10.1007/s12272-023-01427-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Gene expression is modulated through the integration of many regulatory elements and their associated transcription factors (TFs). TFs bind to specific DNA sequences and either activate or repress transcriptional activity. Through decades of research, it has been established that aberrant expression or functional abnormalities of TFs can lead to uncontrolled cell division and the development of cancer. Initial studies on transcriptional regulation in cancer have focused on TFs as transcriptional activators. However, recent studies have demonstrated several different mechanisms of transcriptional repression in cancer, which could be potential therapeutic targets for the development of specific anti-cancer agents. In the first section of this review, "Emerging roles of transcriptional repressors in cancer development," we summarize the current understanding of transcriptional repressors and their involvement in the molecular processes of cancer progression. In the subsequent section, "Therapeutic applications," we provide an updated overview of the available therapeutic targets for drug discovery and discuss the new frontier of such applications.
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8
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Gupta N, Song H, Wu W, Ponce RK, Lin YK, Kim JW, Small EJ, Feng FY, Huang FW, Okimoto RA. The CIC-ERF co-deletion underlies fusion-independent activation of ETS family member, ETV1, to drive prostate cancer progression. eLife 2022; 11:e77072. [PMID: 36383412 PMCID: PMC9668335 DOI: 10.7554/elife.77072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
Human prostate cancer can result from chromosomal rearrangements that lead to aberrant ETS gene expression. The mechanisms that lead to fusion-independent ETS factor upregulation and prostate oncogenesis remain relatively unknown. Here, we show that two neighboring transcription factors, Capicua (CIC) and ETS2 repressor factor (ERF), which are co-deleted in human prostate tumors can drive prostate oncogenesis. Concurrent CIC and ERF loss commonly occur through focal genomic deletions at chromosome 19q13.2. Mechanistically, CIC and ERF co-bind the proximal regulatory element and mutually repress the ETS transcription factor, ETV1. Targeting ETV1 in CIC and ERF-deficient prostate cancer limits tumor growth. Thus, we have uncovered a fusion-independent mode of ETS transcriptional activation defined by concurrent loss of CIC and ERF.
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Affiliation(s)
- Nehal Gupta
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Hanbing Song
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Wei Wu
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Rovingaile K Ponce
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Yone K Lin
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Ji Won Kim
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Eric J Small
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Felix Y Feng
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
- Department of Radiation Oncology, University of CaliforniaSan FranciscoUnited States
| | - Franklin W Huang
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
| | - Ross A Okimoto
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
- Helen Diller Family Comprehensive Cancer Center, University of CaliforniaSan FranciscoUnited States
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9
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Capicua suppresses YAP1 to limit tumorigenesis and maintain drug sensitivity in human cancer. Cell Rep 2022; 41:111443. [DOI: 10.1016/j.celrep.2022.111443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
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10
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Sharma S, Hourigan B, Patel Z, Rosenfeld JA, Chan KM, Wangler MF, Yi JS, Lehman A, Horvath G, Cloos PA, Tan Q. Novel CIC variants identified in individuals with neurodevelopmental phenotypes. Hum Mutat 2022; 43:889-899. [PMID: 35165976 DOI: 10.1002/humu.24346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/10/2022]
Abstract
Heterozygous pathogenic variants in CIC, which encodes a transcriptional repressor, have been identified in individuals with neurodevelopmental phenotypes. To date, 11 CIC variants have been associated with the CIC-related neurodevelopmental syndrome. Here, we describe three novel and one previously reported CIC variants in four individuals with neurodevelopmental delay. Notably, we report for the first time a de novo frameshift variant specific to the long isoform of CIC (CIC-L, NM_001304815.1:c.1100dup, p.Pro368AlafsTer16) in an individual with speech delay, intellectual disability, and autism spectrum disorder. Our investigation into the function of CIC-L reveals that partial loss of CIC-L leads to transcriptional derepression of CIC target genes. We also describe a missense variant (NM_015125.3:c.683G>A, p.Arg228Gln) in an individual with a history of speech delay and relapsed pre-B acute lymphoblastic leukemia. Functional studies of this variant suggest a partial loss of CIC transcriptional repressor activity. Our study expands the list of CIC pathogenic variants and contributes to the accumulating evidence that CIC haploinsufficiency or partial loss of function is a pathogenic mechanism causing neurodevelopmental phenotypes.
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Affiliation(s)
- Saloni Sharma
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Brenna Hourigan
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Zain Patel
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Katie M Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Joanna S Yi
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, Texas, USA
| | | | - Gabriella Horvath
- Division of Biochemical Genetics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul A Cloos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Qiumin Tan
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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11
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Yang S, Liu L, Yan Y, Jiang L, Han S, Shen D, Zhang B. CIC-NUTM1 Sarcomas Affecting the Spine: A Subset of CIC-Rearranged Sarcomas Commonly Present in the Axial Skeleton. Arch Pathol Lab Med 2021; 146:735-741. [PMID: 34525172 DOI: 10.5858/arpa.2021-0153-oa] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Tumors harboring CIC-NUTM1 fusion are a newly recognized rare sarcoma, but the documented cases are still limited. It is unclear whether it is the same as classic CIC-DUX4 sarcoma in terms of its clinical, pathologic, and behavioral aspects. OBJECTIVE.— To further explore the clinicopathologic characteristics of CIC-NUTM1 sarcoma. DESIGN.— The cases were diagnosed based on immunophenotype, next-generation sequencing, and fluorescence in situ hybridization tests and compared with the reported CIC-NUTM1 sarcomas in the literature. RESULTS.— Three cases of CIC-NUTM1 sarcomas involving the spine in adults were described. They were 2 men and 1 woman, aged 38 to 61 years. Two tumors were located in thoracic vertebrae and 1 in a cervical vertebra. All were locally advanced lesions destroying the bone and soft tissues without spinal cord involvement or metastasis. The tumors were composed of monomorphic small to medium-sized cells with round to epithelioid appearance. The architecture was lobulated and solid with diffuse or multifocal myxoid stroma. Next-generation sequencing revealed an in-frame fusion between CIC (exon 16 or 17) and NUTM1 (exon 5 or 6) in 3 cases. Fluorescence in situ hybridization confirmed CIC and NUTM1 breaks, and immunohistochemistry showed NUT staining in the nucleus. The patients died of disease 8 to 15 months (mean, 10.7 months) after presentation. Of the CIC-NUTM1 sarcomas reported in the literature along with our cases (n = 11), 8 cases developed in axial bone (5 spine, 3 skull base). CONCLUSIONS.— CIC-NUTM1 sarcomas showed distinct anatomic tropism for the axial skeleton and unfavorable behavior compared with classic CIC sarcoma.
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Affiliation(s)
- Shaomin Yang
- From the Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China (Yang, Zhang)
| | - LiLi Liu
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen)
| | - Yu Yan
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen)
| | - Liang Jiang
- and the Departments of Orthopedics (Jiang) and Radiology (Han), Peking University Third Hospital, Beijing, China
| | - Songbo Han
- and the Departments of Orthopedics (Jiang) and Radiology (Han), Peking University Third Hospital, Beijing, China
| | - Danhua Shen
- the Department of Pathology, Peking University People's Hospital, Beijing, China (Liu, Yan, Shen).,Zhang and Shen are co-lead authors of this paper
| | - Bo Zhang
- From the Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China (Yang, Zhang).,Zhang and Shen are co-lead authors of this paper
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Patel AL, Zhang L, Keenan SE, Rushlow CA, Fradin C, Shvartsman SY. Capicua is a fast-acting transcriptional brake. Curr Biol 2021; 31:3639-3647.e5. [PMID: 34166605 DOI: 10.1016/j.cub.2021.05.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/18/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Even though transcriptional repressors are studied with ever-increasing molecular resolution, the temporal aspects of gene repression remain poorly understood. Here, we address the dynamics of transcriptional repression by Capicua (Cic), which is essential for normal development and is commonly mutated in human cancers and neurodegenerative diseases.1,2 We report the speed limit for Cic-dependent gene repression based on live imaging and optogenetic perturbations in the early Drosophila embryo, where Cic was originally discovered.3 Our measurements of Cic concentration and intranuclear mobility, along with real-time monitoring of the activity of Cic target genes, reveal remarkably fast transcriptional repression within minutes of removing an optogenetic de-repressive signal. In parallel, quantitative analyses of transcriptional bursting of Cic target genes support a repression mechanism providing a fast-acting brake on burst generation. This work sets quantitative constraints on potential mechanisms for gene regulation by Cic.
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Affiliation(s)
- Aleena L Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Lili Zhang
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | | | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.
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Ong SLM, Szuhai K, Bovée JVMG. Gene fusions in vascular tumors and their underlying molecular mechanisms. Expert Rev Mol Diagn 2021; 21:897-909. [PMID: 34225547 DOI: 10.1080/14737159.2021.1950533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The group of vascular tumors contains many different entities, and is considered difficult by pathologists, as they often have overlapping histological characteristics. Chromosomal translocations have been identified in ~20% of mesenchymal tumors and are considered the drivers of tumor formation. Many translocations have been discovered over the past decade through next-generation sequencing. This technological advancement has also revealed several recurrent gene fusions in vascular tumors. AREAS COVERED This review will discuss the various vascular tumors for which recurrent gene fusions have been identified. The gene fusions and the presumed molecular mechanisms underlying tumorigenesis are shown, and potential implications for targeted therapies discussed. The identification of these gene fusions in vascular tumors has improved diagnostic accuracy, especially since several of these fusions can be easily detected using surrogate immunohistochemical markers. EXPERT OPINION The identification of gene fusions in a subset of vascular tumors over the past decade has improved diagnostic accuracy, and has provided the pathologists with novel diagnostic tools to accurately diagnose these often difficult tumors. Moreover, the increased understanding of the underlying molecular mechanisms can guide the development of targeted therapeutic strategies.
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Affiliation(s)
- Sheena L M Ong
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Li K, Shao S, Ji T, Liu M, Wang L, Pang Y, Chen M, Xu S, Zhang K, Wang Q, Zhuang Z, Wei L, Zhang Y, Chen Y, Wang Y, Zhang J, Chen K, Lian H, Zhong C. Capicua Regulates Dendritic Morphogenesis Through Ets in Hippocampal Neurons in vitro. Front Neuroanat 2021; 15:669310. [PMID: 34385910 PMCID: PMC8353115 DOI: 10.3389/fnana.2021.669310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Capicua (Cic), a transcriptional repressor frequently mutated in brain cancer oligodendroglioma, is highly expressed in adult neurons. However, its function in the dendritic growth of neurons in the hippocampus remains poorly understood. Here, we confirmed that Cic was expressed in hippocampal neurons during the main period of dendritogenesis, suggesting that Cic has a function in dendrite growth. Loss-of-function and gain-of function assays indicated that Cic plays a central role in the inhibition of dendritic morphogenesis and dendritic spines in vitro. Further studies showed that overexpression of Cic reduced the expression of Ets in HT22 cells, while in vitro knockdown of Cic in hippocampal neurons significantly elevated the expression of Ets. These results suggest that Cic may negatively control dendrite growth through Ets, which was confirmed by ShRNA knockdown of either Etv4 or Etv5 abolishing the phenotype of Cic knockdown in cultured neurons. Taken together, our results suggest that Cic inhibits dendritic morphogenesis and the growth of dendritic spines through Ets.
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Affiliation(s)
- Keqin Li
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuai Shao
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tongjie Ji
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lufeng Wang
- Department of Neurology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Mu Chen
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siyi Xu
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kuiming Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Wang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhongwei Zhuang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Wei
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanfei Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanlin Chen
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Wang
- Department of Emergency, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kui Chen
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Lian
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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