- Email: [email protected]
From Basic Knowledge to Effective Therapies
Cancer Cell
Previews potential role for local epigenetic-mediated silencing of the BCL2L11 IGR and potentially other glucocorticoid-controlled regulatory sites in glucocorticoid resistance. Importantly DNA methylation can alter CTCF binding, potentially linking increased focal methylation at the IGR with impaired enhancer-promoter looping. In addition, changes in chromatin accessibility could also be linked with DNA methylation, and the role of pioneering factors at this site remains to be fully explored. PU.1 binds to the IGR, yet PU.1 is prominently expressed in myeloid cells where the BCL2L11 IGR adopts a closed inactive chromatin configuration. Finally, it will be important to analyze the role of epigenetic heterogeneity and Darwinian selection of epi-alleles as drivers of glucocorticoid resistance in relapsed ALL (Ferrando and Lo´pez-Otı´n, 2017) and the potential role of this proposed mechanism in the response and resistance to glucocorticoid therapy in other lymphoid tumors.
REFERENCES Ferrando, A.A., and Lo´pez-Otı´n, C. (2017). Clonal evolution in leukemia. Nat. Med. 23, 1135–1145. Hunger, S.P., and Mullighan, C.G. (2015). Acute lymphoblastic leukemia in children. N. Engl. J. Med. 373, 1541–1552. Inaba, H., and Pui, C.H. (2010). Glucocorticoid use in acute lymphoblastic leukaemia. Lancet Oncol. 11, 1096–1106. Jing, D., Huang, Y., Liu, X., Sia, K.C.S., Zhang, J.C., Tai, X., Wang, M., Toscan, C.E., McCalmont, H., Evans, K., et al. (2018). Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia. Cancer Cell 34, this issue, 906–921. Mullighan, C.G., Zhang, J., Kasper, L.H., Lerach, S., Payne-Turner, D., Phillips, L.A., Heatley, S.L., Holmfeldt, L., Collins-Underwood, J.R., Ma, J., et al. (2011). CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235–239. Oshima, K., Khiabanian, H., da Silva-Almeida, A.C., Tzoneva, G., Abate, F., Ambesi-Impiombato, A., Sanchez-Martin, M., Carpenter, Z., Penson, A., Perez-Garcia, A., et al. (2016). Mutational landscape, clonal evolution patterns, and role of
RAS mutations in relapsed acute lymphoblastic leukemia. Proc. Natl. Acad. Sci. USA 113, 11306–11311. Piovan, E., Yu, J., Tosello, V., Herranz, D., AmbesiImpiombato, A., Da Silva, A.C., Sanchez-Martin, M., Perez-Garcia, A., Rigo, I., Castillo, M., et al. (2013). Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell 24, 766–776. Real, P.J., Tosello, V., Palomero, T., Castillo, M., Hernando, E., de Stanchina, E., Sulis, M.L., Barnes, K., Sawai, C., Homminga, I., et al. (2009). Gamma-secretase inhibitors reverse glucocorticoid resistance in T cell acute lymphoblastic leukemia. Nat. Med. 15, 50–58. Wang, Z., Malone, M.H., He, H., McColl, K.S., and Distelhorst, C.W. (2003). Microarray analysis uncovers the induction of the proapoptotic BH3only protein Bim in multiple models of glucocorticoid-induced apoptosis. J. Biol. Chem. 278, 23861–23867. Wei, G., Twomey, D., Lamb, J., Schlis, K., Agarwal, J., Stam, R.W., Opferman, J.T., Sallan, S.E., den Boer, M.L., Pieters, R., et al. (2006). Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 10, 331–342.
From Basic Knowledge to Effective Therapies Daniel B. Lipka,1,2 Pavlo Lutsik,1 and Christoph Plass1,3,* 1Division
of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany of Hematology and Oncology, Medical Center, Otto-von-Guericke-University, Magdeburg, Germany 3The German Cancer Research Consortium *Correspondence: [email protected] https://doi.org/10.1016/j.ccell.2018.11.013 2Department
In this issue of Cancer Cell, Ott et al. use integrative analysis of histone ChIP-seq and ATAC-seq to describe enhancer-based regulatory circuits in chronic lymphocytic leukemia. This work identified and validated transcription factor PAX5 as main driver of an oncogenic circuitry, which can be disrupted by BET bromodomain inhibition. Chronic lymphocytic leukemia (CLL) is the most common type of adult leukemia and is characterized by slowly proliferating B lymphocytes, which at the molecular level show defects in apoptosis. The clinical course of CLL is variable with indolent cases on one end and highly aggressive cases on the other end of the spectrum. Markers for aggressive forms of CLL include unmutated immunoglobulin heavy-chain variable region loci (IGHV) and aberrant expression of 70-kD zeta-associated protein
(ZAP-70), whereas indolent CLL cases show mutated IGHV and absence of ZAP-70 expression (Crespo et al., 2003). CLL is an excellent model system for basic and translational cancer research due to easy accessibility of malignant cells, the possibility to purify the malignant clones to highest purity, the availability of large cohorts of wellcharacterized biobanked samples from national and international clinical trials, and the availability of mouse models, recapitulating both indolent and aggres-
sive forms of the malignancy. Consequently, CLL has always been at the forefront of cancer research where the latest technologies have been applied in order to characterize the molecular defects underlying CLL pathogenesis. Very often, the information gained in such basic cancer research efforts has been translated into the clinic, either in form of novel diagnostic or prognostic models, or it has been used for the development of novel therapeutic approaches. This path is highlighted in
Cancer Cell 34, December 10, 2018 ª 2018 Elsevier Inc. 871
Cancer Cell
Previews
Figure 1. Schematic of the Transcriptional and Epigenetic Alterations in CLL and Their Therapeutic Potential as Proposed by Ott et al. in This Issue of Cancer Cell Integrated epigenomic and functional studies identified super-enhancer-driven, self-enforcing transcriptional programs, called oncogenic circuitries. Under normal conditions, PAX5 interacts with B cellspecific enhancers and controls expression of B cell transcription programs. In the context of CLL, an aberrant establishment of super-enhancers was observed. These seem to depend on a self-enforcing mechanism involving several transcription factors. Knockout experiments suggested PAX5 as an essential driver in CLL. On top of that, inhibition of the H3K27ac reader BRD4 was shown to attenuate the superenhancer-driven signals and to disrupt the CLL-associated oncogenic circuitry.
work from Do¨hner et al. applying fluorescence in situ hybridization for the detection of large genomic alterations, including deletions on chromosomes 6q21, 11q22-23, 13q14, and 17p13 (Do¨hner et al., 2000). These studies culminated in the establishment of genetic markers predicting the risk for disease progression, which are routinely used in the clinical setting today. Similarly, CLL was one of the first disease entities in which miRNA profiling has been applied. This resulted in the discovery of miRNA signatures associated with prognosis and risk of disease progression (Calin et al., 2004). Based on next-generation sequencing, the Spanish International Cancer Genome Consortium sequenced exomes and genomes of hundreds of CLL samples and identified recurrent gene mutations in NOTCH1, SF3B1, TP53, BIRC3, and POT1 (Puente et al., 2015). Another layer of complexity in the molecular architecture of CLL was uncovered at the epigenetic level by investigation of the DNA methylation landscape, which disclosed pathogenic roles for transcription factor dysregulation with hyperactive EGR and NFAT and reduced EBF and AP-1 programming (Oakes et al., 2016). Most importantly, this work also demonstrated that CLL originates from different 872 Cancer Cell 34, December 10, 2018
stages of normal B cell differentiation. During this differentiation process, normal B cells undergo massive epigenome-wide programming, and remainders of this process can be detected in the CLL epigenomes. Interestingly, these differentiation-associated DNA methylation changes are also able to explain the differential expression patterns of ZAP-70 in indolent and aggressive CLL cases. With respect to CLL treatment, the addition of the anti-CD20 antibody rituximab to fludarabine-based chemotherapy was the first molecularly targeted treatment for CLL and resulted in improved response rates and better overall survival. Nevertheless, patients with high-risk disease, especially those with deletion of 17p13, remained a major clinical challenge. The covalent BTK inhibitor ibrutinib showed very promising biological and clinical activity in an early phase 1 clinical study with relapsed or refractory B cell neoplasms. A subsequent phase 1b/2 study of ibrutinib in relapsed or refractory CLL patients demonstrated high overall response rates that were independent of clinical and genetic risk factors and resulted in progression-free and overall survival rates of 75% and 83%, respectively at 26 months (Byrd et al.,
2013). Ibrutinib was approved for the treatment of CLL by the FDA and EMA in 2014. The most recent milestone for the treatment of CLL was based on the observation that BCL2 is frequently overexpressed in CLL (Hanada et al., 1993). Later, it was demonstrated that CLL cell survival depends on BCL2 expression. This observation led to the pre-clinical development of BCL2 inhibitors. In a phase 1 dose-escalation study that enrolled mainly heavily pre-treated CLL patients with poor prognostic clinical or genetic features, the BCL2 inhibitor, venetoclax, showed impressive response rates in relapsed or refractory CLL cases (Roberts et al., 2016) and was approved by the FDA and the EMA in 2016. Due to toxicities of current therapies and the development of resistance mechanisms which eventually lead to disease relapse, novel therapeutic strategies are needed. Based on the availability of multi-omics approaches, integrated analysis of large datasets combining epigenetic and genetic information is now possible. This was elegantly performed in the study by Ott and colleagues published in the current issue of Cancer Cell (Ott et al., 2018). This work constitutes the latest example of integrated profiling combined with translational efforts driving basic science to novel therapeutic avenues. The authors use CLL to showcase how enhancer and superenhancer profiling in patient-derived samples in combination with measurements of chromatin accessibility can be used to model transcriptional regulatory circuits. Bioinformatic analysis followed by a CRISPR/Cas9 screen defined functional transcription factor dependencies in which PAX5 was discovered as one of few transcription factors that act as central regulatory nodes that are essential for the survival of neoplastic B cells in CLL (Figure 1). The authors further provide pre-clinical evidence that BET bromodomain inhibition has potent antineoplastic activity possibly by disrupting the CLL core regulatory circuitry. This study has potential clinical implications in the near future as it provides initial evidence for a selective anti-neoplastic effect of BET bromodomain inhibition on CLL cells and provides a molecular rationale for the biological activity of
Cancer Cell
Previews these inhibitors in CLL. The promise would be that BET bromodomain inhibition has less toxicity than currently approved therapies, especially with respect to severe infections as a result of immunosuppression. As acknowledged by the authors, this is not the first study investigating enhancer landscapes or chromatin accessibility on primary CLL samples; however, the novelty in the present study lies in integrative strategies exploring novel therapeutic options utilizing chromatin accessibility data and functional screens for the discovery of novel target structures. In particular, the combination of H3K27ac and ATAC-seq data allows for much more precise identification of cis-regulatory elements and thereby greatly enhances the identification of core regulatory circuities. The power of an integrated approach is also highlighted in an independent study by Ozer et al. characterizing BRD4-mediated transcriptional regulatory networks in CLL and promoting a novel BET inhibitor in a proof-of-concept study for a novel epigenetic therapy in CLL (Ozer et al., 2018). Future work applying similar strategies to other human malignancies, in particular to solid tumors, is now the logical next step. It will be interesting to explore whether other tumor types are also driven by aberrant transcriptional circuitries, and how these processes can
be interrupted and exploited therapeutically. In order to perform these analyses in solid tumors, methods for efficient purification of live tumor cell populations and for genome-wide molecular profiling of small cell populations are needed. Hope comes from rapid advances in single-cell profiling of transcriptional, genomic, and epigenomic landscapes that promise novel routes to address these issues. ACKNOWLEDGMENTS This work was supported in part by the PRECISE consortium with funds from the German Ministry of Science and Technology (BMBF) and the Helmholtz Foundation.
REFERENCES Byrd, J.C., Furman, R.R., Coutre, S.E., Flinn, I.W., Burger, J.A., Blum, K.A., Grant, B., Sharman, J.P., Coleman, M., Wierda, W.G., et al. (2013). Targeting BTK with ibrutinib in relapsed chronic lymphocytic leukemia. N. Engl. J. Med. 369, 32–42. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., et al. (2004). MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. USA 101, 11755–11760. Crespo, M., Bosch, F., Villamor, N., Bellosillo, B., Colomer, D., Rozman, M., Marce´, S., Lo´pez-Guillermo, A., Campo, E., and Montserrat, E. (2003). ZAP-70 expression as a surrogate for immunoglobulin-variable-region mutations in chronic lymphocytic leukemia. N. Engl. J. Med. 348, 1764–1775.
Do¨hner, H., Stilgenbauer, S., Benner, A., Leupolt, E., Kro¨ber, A., Bullinger, L., Do¨hner, K., Bentz, M., and Lichter, P. (2000). Genomic aberrations and survival in chronic lymphocytic leukemia. N. Engl. J. Med. 343, 1910–1916. Hanada, M., Delia, D., Aiello, A., Stadtmauer, E., and Reed, J.C. (1993). bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia. Blood 82, 1820– 1828. Oakes, C.C., Seifert, M., Assenov, Y., Gu, L., Przekopowitz, M., Ruppert, A.S., Wang, Q., Imbusch, C.D., Serva, A., Koser, S.D., et al. (2016). DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat. Genet. 48, 253–264. Ott, C.J., Federation, A.J., Schwartz, L.S., Kasar, S., Klitgaard, J.L., Lenci, R., Li, Q., Lawlor, M., Fernandes, S.M., Souza, A., et al. (2018). Enhancer architecture and essential core regulatory circuitry of chronic lymphocytic leukemia. Cancer Cell 34, this issue, 982–995. Ozer, H.G., El-Gamal, D., Powell, B., Hing, Z.A., Blachly, J.S., Harrington, B., Mitchell, S., Grieselhuber, N.R., Williams, K., Lai, T.H., et al. (2018). BRD4 Profiling identifies critical chronic lymphocytic leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor. Cancer Discov. 8, 458–477. Puente, X.S., Bea`, S., Valde´s-Mas, R., Villamor, N., Gutie´rrez-Abril, J., Martı´n-Subero, J.I., Munar, M., Rubio-Pe´rez, C., Jares, P., Aymerich, M., et al. (2015). Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature 526, 519–524. Roberts, A.W., Davids, M.S., Pagel, J.M., Kahl, B.S., Puvvada, S.D., Gerecitano, J.F., Kipps, T.J., Anderson, M.A., Brown, J.R., Gressick, L., et al. (2016). Targeting BCL2 with venetoclax in relapsed chronic lymphocytic leukemia. N. Engl. J. Med. 374, 311–322.
Cancer Cell 34, December 10, 2018 873
Previews potential role for local epigenetic-mediated silencing of the BCL2L11 IGR and potentially other glucocorticoid-controlled regulatory sites in glucocorticoid resistance. Importantly DNA methylation can alter CTCF binding, potentially linking increased focal methylation at the IGR with impaired enhancer-promoter looping. In addition, changes in chromatin accessibility could also be linked with DNA methylation, and the role of pioneering factors at this site remains to be fully explored. PU.1 binds to the IGR, yet PU.1 is prominently expressed in myeloid cells where the BCL2L11 IGR adopts a closed inactive chromatin configuration. Finally, it will be important to analyze the role of epigenetic heterogeneity and Darwinian selection of epi-alleles as drivers of glucocorticoid resistance in relapsed ALL (Ferrando and Lo´pez-Otı´n, 2017) and the potential role of this proposed mechanism in the response and resistance to glucocorticoid therapy in other lymphoid tumors.
REFERENCES Ferrando, A.A., and Lo´pez-Otı´n, C. (2017). Clonal evolution in leukemia. Nat. Med. 23, 1135–1145. Hunger, S.P., and Mullighan, C.G. (2015). Acute lymphoblastic leukemia in children. N. Engl. J. Med. 373, 1541–1552. Inaba, H., and Pui, C.H. (2010). Glucocorticoid use in acute lymphoblastic leukaemia. Lancet Oncol. 11, 1096–1106. Jing, D., Huang, Y., Liu, X., Sia, K.C.S., Zhang, J.C., Tai, X., Wang, M., Toscan, C.E., McCalmont, H., Evans, K., et al. (2018). Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia. Cancer Cell 34, this issue, 906–921. Mullighan, C.G., Zhang, J., Kasper, L.H., Lerach, S., Payne-Turner, D., Phillips, L.A., Heatley, S.L., Holmfeldt, L., Collins-Underwood, J.R., Ma, J., et al. (2011). CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235–239. Oshima, K., Khiabanian, H., da Silva-Almeida, A.C., Tzoneva, G., Abate, F., Ambesi-Impiombato, A., Sanchez-Martin, M., Carpenter, Z., Penson, A., Perez-Garcia, A., et al. (2016). Mutational landscape, clonal evolution patterns, and role of
RAS mutations in relapsed acute lymphoblastic leukemia. Proc. Natl. Acad. Sci. USA 113, 11306–11311. Piovan, E., Yu, J., Tosello, V., Herranz, D., AmbesiImpiombato, A., Da Silva, A.C., Sanchez-Martin, M., Perez-Garcia, A., Rigo, I., Castillo, M., et al. (2013). Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer Cell 24, 766–776. Real, P.J., Tosello, V., Palomero, T., Castillo, M., Hernando, E., de Stanchina, E., Sulis, M.L., Barnes, K., Sawai, C., Homminga, I., et al. (2009). Gamma-secretase inhibitors reverse glucocorticoid resistance in T cell acute lymphoblastic leukemia. Nat. Med. 15, 50–58. Wang, Z., Malone, M.H., He, H., McColl, K.S., and Distelhorst, C.W. (2003). Microarray analysis uncovers the induction of the proapoptotic BH3only protein Bim in multiple models of glucocorticoid-induced apoptosis. J. Biol. Chem. 278, 23861–23867. Wei, G., Twomey, D., Lamb, J., Schlis, K., Agarwal, J., Stam, R.W., Opferman, J.T., Sallan, S.E., den Boer, M.L., Pieters, R., et al. (2006). Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell 10, 331–342.
From Basic Knowledge to Effective Therapies Daniel B. Lipka,1,2 Pavlo Lutsik,1 and Christoph Plass1,3,* 1Division
of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany of Hematology and Oncology, Medical Center, Otto-von-Guericke-University, Magdeburg, Germany 3The German Cancer Research Consortium *Correspondence: [email protected] https://doi.org/10.1016/j.ccell.2018.11.013 2Department
In this issue of Cancer Cell, Ott et al. use integrative analysis of histone ChIP-seq and ATAC-seq to describe enhancer-based regulatory circuits in chronic lymphocytic leukemia. This work identified and validated transcription factor PAX5 as main driver of an oncogenic circuitry, which can be disrupted by BET bromodomain inhibition. Chronic lymphocytic leukemia (CLL) is the most common type of adult leukemia and is characterized by slowly proliferating B lymphocytes, which at the molecular level show defects in apoptosis. The clinical course of CLL is variable with indolent cases on one end and highly aggressive cases on the other end of the spectrum. Markers for aggressive forms of CLL include unmutated immunoglobulin heavy-chain variable region loci (IGHV) and aberrant expression of 70-kD zeta-associated protein
(ZAP-70), whereas indolent CLL cases show mutated IGHV and absence of ZAP-70 expression (Crespo et al., 2003). CLL is an excellent model system for basic and translational cancer research due to easy accessibility of malignant cells, the possibility to purify the malignant clones to highest purity, the availability of large cohorts of wellcharacterized biobanked samples from national and international clinical trials, and the availability of mouse models, recapitulating both indolent and aggres-
sive forms of the malignancy. Consequently, CLL has always been at the forefront of cancer research where the latest technologies have been applied in order to characterize the molecular defects underlying CLL pathogenesis. Very often, the information gained in such basic cancer research efforts has been translated into the clinic, either in form of novel diagnostic or prognostic models, or it has been used for the development of novel therapeutic approaches. This path is highlighted in
Cancer Cell 34, December 10, 2018 ª 2018 Elsevier Inc. 871
Cancer Cell
Previews
Figure 1. Schematic of the Transcriptional and Epigenetic Alterations in CLL and Their Therapeutic Potential as Proposed by Ott et al. in This Issue of Cancer Cell Integrated epigenomic and functional studies identified super-enhancer-driven, self-enforcing transcriptional programs, called oncogenic circuitries. Under normal conditions, PAX5 interacts with B cellspecific enhancers and controls expression of B cell transcription programs. In the context of CLL, an aberrant establishment of super-enhancers was observed. These seem to depend on a self-enforcing mechanism involving several transcription factors. Knockout experiments suggested PAX5 as an essential driver in CLL. On top of that, inhibition of the H3K27ac reader BRD4 was shown to attenuate the superenhancer-driven signals and to disrupt the CLL-associated oncogenic circuitry.
work from Do¨hner et al. applying fluorescence in situ hybridization for the detection of large genomic alterations, including deletions on chromosomes 6q21, 11q22-23, 13q14, and 17p13 (Do¨hner et al., 2000). These studies culminated in the establishment of genetic markers predicting the risk for disease progression, which are routinely used in the clinical setting today. Similarly, CLL was one of the first disease entities in which miRNA profiling has been applied. This resulted in the discovery of miRNA signatures associated with prognosis and risk of disease progression (Calin et al., 2004). Based on next-generation sequencing, the Spanish International Cancer Genome Consortium sequenced exomes and genomes of hundreds of CLL samples and identified recurrent gene mutations in NOTCH1, SF3B1, TP53, BIRC3, and POT1 (Puente et al., 2015). Another layer of complexity in the molecular architecture of CLL was uncovered at the epigenetic level by investigation of the DNA methylation landscape, which disclosed pathogenic roles for transcription factor dysregulation with hyperactive EGR and NFAT and reduced EBF and AP-1 programming (Oakes et al., 2016). Most importantly, this work also demonstrated that CLL originates from different 872 Cancer Cell 34, December 10, 2018
stages of normal B cell differentiation. During this differentiation process, normal B cells undergo massive epigenome-wide programming, and remainders of this process can be detected in the CLL epigenomes. Interestingly, these differentiation-associated DNA methylation changes are also able to explain the differential expression patterns of ZAP-70 in indolent and aggressive CLL cases. With respect to CLL treatment, the addition of the anti-CD20 antibody rituximab to fludarabine-based chemotherapy was the first molecularly targeted treatment for CLL and resulted in improved response rates and better overall survival. Nevertheless, patients with high-risk disease, especially those with deletion of 17p13, remained a major clinical challenge. The covalent BTK inhibitor ibrutinib showed very promising biological and clinical activity in an early phase 1 clinical study with relapsed or refractory B cell neoplasms. A subsequent phase 1b/2 study of ibrutinib in relapsed or refractory CLL patients demonstrated high overall response rates that were independent of clinical and genetic risk factors and resulted in progression-free and overall survival rates of 75% and 83%, respectively at 26 months (Byrd et al.,
2013). Ibrutinib was approved for the treatment of CLL by the FDA and EMA in 2014. The most recent milestone for the treatment of CLL was based on the observation that BCL2 is frequently overexpressed in CLL (Hanada et al., 1993). Later, it was demonstrated that CLL cell survival depends on BCL2 expression. This observation led to the pre-clinical development of BCL2 inhibitors. In a phase 1 dose-escalation study that enrolled mainly heavily pre-treated CLL patients with poor prognostic clinical or genetic features, the BCL2 inhibitor, venetoclax, showed impressive response rates in relapsed or refractory CLL cases (Roberts et al., 2016) and was approved by the FDA and the EMA in 2016. Due to toxicities of current therapies and the development of resistance mechanisms which eventually lead to disease relapse, novel therapeutic strategies are needed. Based on the availability of multi-omics approaches, integrated analysis of large datasets combining epigenetic and genetic information is now possible. This was elegantly performed in the study by Ott and colleagues published in the current issue of Cancer Cell (Ott et al., 2018). This work constitutes the latest example of integrated profiling combined with translational efforts driving basic science to novel therapeutic avenues. The authors use CLL to showcase how enhancer and superenhancer profiling in patient-derived samples in combination with measurements of chromatin accessibility can be used to model transcriptional regulatory circuits. Bioinformatic analysis followed by a CRISPR/Cas9 screen defined functional transcription factor dependencies in which PAX5 was discovered as one of few transcription factors that act as central regulatory nodes that are essential for the survival of neoplastic B cells in CLL (Figure 1). The authors further provide pre-clinical evidence that BET bromodomain inhibition has potent antineoplastic activity possibly by disrupting the CLL core regulatory circuitry. This study has potential clinical implications in the near future as it provides initial evidence for a selective anti-neoplastic effect of BET bromodomain inhibition on CLL cells and provides a molecular rationale for the biological activity of
Cancer Cell
Previews these inhibitors in CLL. The promise would be that BET bromodomain inhibition has less toxicity than currently approved therapies, especially with respect to severe infections as a result of immunosuppression. As acknowledged by the authors, this is not the first study investigating enhancer landscapes or chromatin accessibility on primary CLL samples; however, the novelty in the present study lies in integrative strategies exploring novel therapeutic options utilizing chromatin accessibility data and functional screens for the discovery of novel target structures. In particular, the combination of H3K27ac and ATAC-seq data allows for much more precise identification of cis-regulatory elements and thereby greatly enhances the identification of core regulatory circuities. The power of an integrated approach is also highlighted in an independent study by Ozer et al. characterizing BRD4-mediated transcriptional regulatory networks in CLL and promoting a novel BET inhibitor in a proof-of-concept study for a novel epigenetic therapy in CLL (Ozer et al., 2018). Future work applying similar strategies to other human malignancies, in particular to solid tumors, is now the logical next step. It will be interesting to explore whether other tumor types are also driven by aberrant transcriptional circuitries, and how these processes can
be interrupted and exploited therapeutically. In order to perform these analyses in solid tumors, methods for efficient purification of live tumor cell populations and for genome-wide molecular profiling of small cell populations are needed. Hope comes from rapid advances in single-cell profiling of transcriptional, genomic, and epigenomic landscapes that promise novel routes to address these issues. ACKNOWLEDGMENTS This work was supported in part by the PRECISE consortium with funds from the German Ministry of Science and Technology (BMBF) and the Helmholtz Foundation.
REFERENCES Byrd, J.C., Furman, R.R., Coutre, S.E., Flinn, I.W., Burger, J.A., Blum, K.A., Grant, B., Sharman, J.P., Coleman, M., Wierda, W.G., et al. (2013). Targeting BTK with ibrutinib in relapsed chronic lymphocytic leukemia. N. Engl. J. Med. 369, 32–42. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., et al. (2004). MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. USA 101, 11755–11760. Crespo, M., Bosch, F., Villamor, N., Bellosillo, B., Colomer, D., Rozman, M., Marce´, S., Lo´pez-Guillermo, A., Campo, E., and Montserrat, E. (2003). ZAP-70 expression as a surrogate for immunoglobulin-variable-region mutations in chronic lymphocytic leukemia. N. Engl. J. Med. 348, 1764–1775.
Do¨hner, H., Stilgenbauer, S., Benner, A., Leupolt, E., Kro¨ber, A., Bullinger, L., Do¨hner, K., Bentz, M., and Lichter, P. (2000). Genomic aberrations and survival in chronic lymphocytic leukemia. N. Engl. J. Med. 343, 1910–1916. Hanada, M., Delia, D., Aiello, A., Stadtmauer, E., and Reed, J.C. (1993). bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia. Blood 82, 1820– 1828. Oakes, C.C., Seifert, M., Assenov, Y., Gu, L., Przekopowitz, M., Ruppert, A.S., Wang, Q., Imbusch, C.D., Serva, A., Koser, S.D., et al. (2016). DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat. Genet. 48, 253–264. Ott, C.J., Federation, A.J., Schwartz, L.S., Kasar, S., Klitgaard, J.L., Lenci, R., Li, Q., Lawlor, M., Fernandes, S.M., Souza, A., et al. (2018). Enhancer architecture and essential core regulatory circuitry of chronic lymphocytic leukemia. Cancer Cell 34, this issue, 982–995. Ozer, H.G., El-Gamal, D., Powell, B., Hing, Z.A., Blachly, J.S., Harrington, B., Mitchell, S., Grieselhuber, N.R., Williams, K., Lai, T.H., et al. (2018). BRD4 Profiling identifies critical chronic lymphocytic leukemia oncogenic circuits and reveals sensitivity to PLX51107, a novel structurally distinct BET inhibitor. Cancer Discov. 8, 458–477. Puente, X.S., Bea`, S., Valde´s-Mas, R., Villamor, N., Gutie´rrez-Abril, J., Martı´n-Subero, J.I., Munar, M., Rubio-Pe´rez, C., Jares, P., Aymerich, M., et al. (2015). Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature 526, 519–524. Roberts, A.W., Davids, M.S., Pagel, J.M., Kahl, B.S., Puvvada, S.D., Gerecitano, J.F., Kipps, T.J., Anderson, M.A., Brown, J.R., Gressick, L., et al. (2016). Targeting BCL2 with venetoclax in relapsed chronic lymphocytic leukemia. N. Engl. J. Med. 374, 311–322.
Cancer Cell 34, December 10, 2018 873