Targeting CCL2/CCR2 Signaling Overcomes MEK Inhibitor Resistance in Acute Myeloid Leukemia

PURPOSE

Emerging evidence underscores the critical role of extrinsic factors within the microenvironment in protecting leukemia cells from therapeutic interventions, driving disease progression, and promoting drug resistance in acute myeloid leukemia (AML). This finding emphasizes the need for the identification of targeted therapies that inhibit intrinsic and extrinsic signaling to overcome drug resistance in AML.

EXPERIMENTAL DESIGN

We performed a comprehensive analysis utilizing a cohort of ∼300 AML patient samples. This analysis encompassed the evaluation of secreted cytokines/growth factors, gene expression, and ex vivo drug sensitivity to small molecules. Our investigation pinpointed a notable association between elevated levels of CCL2 and diminished sensitivity to the MEK inhibitors (MEKi). We validated this association through loss-of-function and pharmacologic inhibition studies. Further, we deployed global phosphoproteomics and CRISPR/Cas9 screening to identify the mechanism of CCR2-mediated MEKi resistance in AML.

RESULTS

Our multifaceted analysis unveiled that CCL2 activates multiple prosurvival pathways, including MAPK and cell-cycle regulation in MEKi-resistant cells. Employing combination strategies to simultaneously target these pathways heightened growth inhibition in AML cells. Both genetic and pharmacologic inhibition of CCR2 sensitized AML cells to trametinib, suppressing proliferation while enhancing apoptosis. These findings underscore a new role for CCL2 in MEKi resistance, offering combination therapies as an avenue to circumvent this resistance.

CONCLUSIONS

Our study demonstrates a compelling rationale for translating CCL2/CCR2 axis inhibitors in combination with MEK pathway-targeting therapies, as a potent strategy for combating drug resistance in AML. This approach has the potential to enhance the efficacy of treatments to improve AML patient outcomes.

Clinical Correlates of Venetoclax-Based Combination Sensitivities to Augment Acute Myeloid Leukemia Therapy

The BCL2 inhibitor venetoclax combined with the hypomethylating agent azacytidine shows significant clinical benefit in a subset of patients with acute myeloid leukemia (AML); however, resistance limits response and durability. We prospectively profiled the ex vivo activity of 25 venetoclax-inclusive combinations on primary AML patient samples to identify those with improved potency and synergy compared with venetoclax + azacytidine (Ven + azacytidine). Combination sensitivities correlated with tumor cell state to discern three patterns: primitive selectivity resembling Ven + azacytidine, monocytic selectivity, and broad efficacy independent of cell state. Incorporation of immunophenotype, mutation, and cytogenetic features further stratified combination sensitivity for distinct patient subtypes. We dissect the biology underlying the broad, cell state-independent efficacy for the combination of venetoclax plus the JAK1/2 inhibitor ruxolitinib. Together, these findings support opportunities for expanding the impact of venetoclax-based drug combinations in AML by leveraging clinical and molecular biomarkers associated with ex vivo responses.

SIGNIFICANCE

By mapping drug sensitivity data to clinical features and tumor cell state, we identify novel venetoclax combinations targeting patient subtypes who lack sensitivity to Ven + azacytidine. This provides a framework for a taxonomy of AML informed by readily available sets of clinical and genetic features obtained as part of standard care. See related commentary by Becker, p. 437 . This article is featured in Selected Articles from This Issue, p. 419.

Abstract A06: Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL)

Introduction Oncogenic programs are facilitated by activators of transcriptional machinery, including certain CDKs. CDK9, a component of the positive transcription elongation factor b (pTEFb) complex, has arisen as an attractive target due to its regulation of MYC and MCL1 transcription (Hashiguchi et al, 2019). Nevertheless, we and others have observed resistance to CDK9i in vitro and in vivo. Here we studied the effects of CDK9 inhibition using the novel selective CDK9 inhibitor AZD4573, currently under evaluation in clinical trials. Methods A panel of NHL cell lines (OCI-LY3/19, SUDHL4/10/16, VAL, U2932) and primary NHL cells were employed. Response to CDK9i was characterized using LC-MS proteomic analysis, RNA-Seq, and CRISPR-Cas9 Screening. Results NHL cells treated with AZD4573 for 6h exhibited a dose dependent reduction in phospho-RNAPIISer2, as well as loss of MYC and Mcl-1. CDK9i potently inhibited proliferation and induced apoptosis in a panel of NHL cell lines (IC50 range 5-30 nM). Two DLBCL cell lines underwent LC-MS proteomic analysis following AZD4573 treatment (30 nM, 3h). Treated cells exhibited rapid loss of MYC, Mcl-1, PIM3 and JUNB protein levels. We observed broad transcriptional repression via RNA-seq, including downregulation of PIM3 and JUNB (30 nM, 3h). However, a subset of genes, including MYC, PIM1 and JUNB underwent early transcriptional recovery, confirmed by immunoblotting, thus identifying candidate genes which may account for resistance to CDK9i. PIM kinases cooperate with the PI3K/ATK signaling pathway, and have been proposed as therapeutic targets in cancer. We next used SGI1776 (PIM1 specific) and AZD1208 (pan-PIM) in combination with AZD4573, and found synergy between them in a panel of 4 cell lines and primary samples. OCI-LY3 xenograft mice treated with a combination of AZD4573 (15 mg/kg; IP; once weekly) and AZD1208 (30 mg/kg; oral gavage, twice weekly) demonstrated restricted tumor growth and increased survival compared to control. To further understand pathways mediating resistance to CDK9i, we carried out a genome-wide loss of function CRISPR-Cas9 library screen. Two Cas9-expressing NHL cell lines were transduced with a CRISPR library comprised of ~5 unique sgRNA per gene. Loss of AKT, RPTOR, or mTOR, among others, sensitized cells to AZD4573. Concurrent treatment with PI3K inhibitors synergistically suppressed proliferation of NHL cell lines and primary cells treated with AZD4573 in vitro. OCI-LY3 xenograft mice were treated with AZD4573 (15 mg/kg; IP; once weekly), Copanlisib (15 mg/kg; IP; twice weekly), or a combination of both. Combo treatment restricted tumor growth and prolonged survival to a greater extent than either drug alone. Conclusions CDK9i with AZD4573 downregulated numerous oncoproteins. However, a subset of genes including MYC and PIM3 recovered transcription. PI3K/AKT pathway was implicated in resistance to CDK9i in CRISPR library screens. Concurrent targeting of pro-survival pathways (e.g., PIM, PI3K) partially reversed resistance to CDK9i.

Citation Format: Elana Thieme, Duanchen Sun, Nur Bruss, Geeta Sharma, Tingting Liu, Daniel Coleman, Tamilla Nechiporuk, Daniel Bottomly, Shannon McWeeney, Patrick Pirrotte, Zheng Xia, Alexey Danilov. Strategies to circumvent resistance to cyclin-dependent kinase-9 inhibition (CDK9i) in non-Hodgkin lymphoma (NHL) [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A06.

Monocytic differentiation and AHR signaling as Primary Nodes of BET Inhibitor Response in Acute Myeloid Leukemia

To understand mechanisms of response to BET inhibitors (BETi), we mined the Beat AML functional genomic dataset and performed genome-wide CRISPR screens on BETi- sensitive and BETi- resistant AML cells. Both strategies revealed regulators of monocytic differentiation, SPI1, JUNB, FOS, and aryl-hydrocarbon receptor signaling (AHR/ARNT), as determinants of BETi response. AHR activation synergized with BETi while inhibition antagonized BETi-mediated cytotoxicity. Consistent with BETi sensitivity dependence on monocytic differentiation, ex vivo sensitivity to BETi in primary AML patient samples correlated with higher expression of monocytic markers CSF1R, LILRs, and VCAN. In addition, HL-60 cell line differentiation enhanced its sensitivity to BETi. Further, screens to rescue BETi sensitivity identified BCL2 and CDK6 as druggable vulnerabilities. Finally, monocytic AML patient samples refractory to venetoclax ex vivo were significantly more sensitive to combined BETi + venetoclax. Together, our work highlights mechanisms that could predict BETi response and identifies combination strategies to overcome resistance.

The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance

Our study details the stepwise evolution of gilteritinib resistance in FLT3-mutated acute myeloid leukemia (AML). Early resistance is mediated by the bone marrow microenvironment, which protects residual leukemia cells. Over time, leukemia cells evolve intrinsic mechanisms of resistance, or late resistance. We mechanistically define both early and late resistance by integrating whole-exome sequencing, CRISPR-Cas9, metabolomics, proteomics, and pharmacologic approaches. Early resistant cells undergo metabolic reprogramming, grow more slowly, and are dependent upon Aurora kinase B (AURKB). Late resistant cells are characterized by expansion of pre-existing NRAS mutant subclones and continued metabolic reprogramming. Our model closely mirrors the timing and mutations of AML patients treated with gilteritinib. Pharmacological inhibition of AURKB resensitizes both early resistant cell cultures and primary leukemia cells from gilteritinib-treated AML patients. These findings support a combinatorial strategy to target early resistant AML cells with AURKB inhibitors and gilteritinib before the expansion of pre-existing resistance mutations occurs.

Abstract LT022: The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance

In acute myeloid leukemia (AML), activating mutations in FLT3 are the most common genetic abnormality. Multiple FLT3 inhibitors have been developed, including the FDA-approved inhibitor gilteritinib. However, AML patients only respond to gilteritinib for approximately 6 months due to the emergence of drug resistance. While gilteritinib eliminates blasts in peripheral circulation, residual blasts in the bone marrow microenvironment are protected by cytokines and growth factors. Persistence of these residual cells represents early resistance to treatment. How these cells adapt to survive in the marrow microenvironment remains unclear, but over time resistant subclones resume growth and lead to relapsed disease. At relapse, many patients have intrinsic resistance mutations, what we term late resistance. In this study, we used a stepwise model that charts the temporal evolution of early to late gilteritinib resistance. To recapitulate early resistance, we cultured the FLT3-ITD+ AML cell lines, MOLM-14 and MV4;11, with exogenous microenvironmental ligands that allow cells to become resistant to gilteritinib in a ligand-dependent manner. After 7 weeks, all cultures with ligand resumed growth (early resistance), whereas cells without ligand never resumed growth. Following ligand withdrawal, the cells become transiently sensitive to gilteritinib but resumed growth after 2 months (late resistance). We comprehensively analyzed early and late resistance by integrating whole exome sequencing, CRISPR/Cas9 screening, proteomics, metabolomics, and small-molecule inhibitor screening. Early resistance is characterized by slowly dividing cells and metabolic reprogramming, particularly with respect to lipid metabolism. Early resistant cultures also became uniquely dependent on Aurora kinase B (AURKB) for survival. We then validated these findings in primary AML cells from patients (N=11) treated with gilteritinib and found that early resistant cells demonstrated reduced cell cycle and alterations in lipid metabolism. Gene expression analysis of sequential stromal cell samples from AML patients (N=13) pre- and post gilteritinib treatment showed an increase in lipid metabolism following gilteritinib treatment, indicating that the microenvironment is also dynamic and in crosstalk with neighboring AML cells. Primary early resistant AML cells also became dependent on AURKB signaling, and were exquisitely sensitive to the combination of AURKB inhibitors and gilteritinib. In contrast, late resistance is driven by an expansion of pre-existing NRAS mutant subclones, consistent with the resistance profile of AML patients on gilteritinib. Metabolic reprogramming continued to evolve in late resistance with further dependence upon lipid metabolism. Our study provides mechanistic understanding of how the marrow microenvironment contributes to extrinsic early resistance, which then leads to late intrinsic resistance. We also define a unique vulnerability to AURKB inhibitors in early resistance that may thwart the expansion of late resistant NRAS subclones.

Citation Format: Sunil K. Joshi, Tamilla Nechiporuk, Daniel Bottomly, Paul Piehowski, Julie A. Reisz, Janét Pittsenbarger, Andy Kaempf, Sara J.C. Gosline, Yi-Ting Wang, Tao Liu, Cristina E. Tognon, Angelo D’Alessandro, Jeffrey W. Tyner, Shannon K. McWeeney, Karin D. Rodland, Brian J. Druker, Elie Traer. The AML microenvironment catalyzes a step-wise evolution to gilteritinib resistance [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr LT022.

Genome-wide CRISPR screen identifies regulators of MAPK and MTOR pathways mediating sorafenib resistance in acute myeloid leukemia

Drug resistance impedes the long-term effect of targeted therapies in acute myeloid leukemia (AML), necessitating the identification of mechanisms underlying resistance. Approximately 25% of AML patients carry FLT3 mutations and develop post-treatment insensitivity to FLT3 inhibitors, including sorafenib. Using a genomewide CRISPR screen, we identified LZTR1, NF1, TSC1 and TSC2, negative regulators of the MAPK and MTOR pathways, as mediators of resistance to sorafenib. Analyses of ex vivo drug sensitivity assays in samples from patients with FLT3-ITD AML revealed that lower expression of LZTR1, NF1, and TSC2 correlated with sensitivity to sorafenib. Importantly, MAPK and/or MTOR complex 1 (MTORC1) activity was upregulated in AML cells made resistant to several FLT3 inhibitors, including crenolanib, quizartinib, and sorafenib. These cells were sensitive to MEK inhibitors, and the combination of FLT3 and MEK inhibitors showed enhanced efficacy, suggesting the effectiveness of such treatment in AML patients with FLT3 mutations and those with resistance to FLT3 inhibitors.

Abstract 325: A genome-wide CRISPR screen on AML cells reveals the TP53 apoptotic network is a primary mediator of resistance to BCL2 inhibition

Therapeutics targeted to specific proteins known to drive or modulate progression of acute myeloid leukemia (AML) have shown limited effectiveness as resistance frequently develops during their clinical use. Similar to many cancers, a stalled process of programmed cell death in apoptosis-primed cells is one of the prevalent mechanisms of drug resistance in AML. The intrinsic mitochondrial apoptotic pathway is controlled by a rheostat of anti-apoptotic and pro-apoptotic proteins and perturbing the balance toward pro-apoptotic responses remains a focus of many small molecular therapeutics. Venetoclax, an inhibitor of anti-apoptotic gene BCL2, approved for treatment of a certain subtypes of chronic lymphocytic leukemia (CLL), shows limited success as a monoagent in AML clinical trials due to an inherent resistance in approximately 37% of all patients (IC50 > 5μM). To identify mechanisms underlying intrinsic and acquired resistance to the BCL2 inhibitor, venetoclax, we used a genome-wide CRISPR/Cas9 screen to identify genes whose inactivation results in loss of venetoclax sensitivity in MOLM13 cells, derived from an AML patient that harbored mutation in FLT3-ITD, one of the major genetic landscapes of AML. Interrogation with two independently derived genome-wide libraries yielded identical top candidates TP53, BAX and PMAIP1. We also observed other gene targets that implicate the mitochondrial intrinsic, TP53-controlled pro-apoptotic pathway in the acquisition of venetoclax resistance. Correlatively, in a large AML cohort (Beat AML dataset), patients with loss of function mutations in TP53, or either low expression of TP53 or BAX exhibited statistically significant lower levels of responses to venetoclax ex vivo. Resultant venetoclax resistant cells with inactivation of TP53 or BAX had significantly reduced capacity for apoptosis when treated with venetoclax and exhibited elevated pro-survival signaling exemplified by increased levels of MAPK and AKT. In addition, loss of TP53 led to changes in the ratio of anti-apoptotic proteins BCL2, BCL-xL and MCL1 implicating TP53 as a major transcriptional regulator of the apoptotic rheostat in MOLM13 cells. Evaluation of the TP53 and BAX knockout cells for sensitivities to a panel of small molecule inhibitors revealed loss of sensitivities to a wide range of additional inhibitors including FLT3, AKT, multi-kinase inhibitors as well as a surprising gain of sensitivity to NTRK inhibitors relying on alternative pathways of cell death. Our results provide an independent confirmation of TP53 and its apoptotic network involvement to the venetoclax response in AML cells and suggest strategies to overcome resistance.

Citation Format: Tamilla Nechiporuk, Stephen E. Kurtz, Olga Nikolova, Amanda d'Almeida, Kevin Watanabe-Smith, Mara Rosenberg, Brian Druker, Jeffrey W. Tyner, Shannon K. McWeeney. A genome-wide CRISPR screen on AML cells reveals the TP53 apoptotic network is a primary mediator of resistance to BCL2 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 325.

Abstract 4763: Genome-wide CRISPR screening identifies TSC1 as a regulator of sorafenib resistance in acute myeloid leukemia

Hematologic malignancies represent the fifth most common type of cancer and fourth most common cause of cancer-related deaths. These malignancies are characterized by a clonal expansion of hematopoietic progenitor cells that proliferate in the bone marrow, peripheral blood, lymph nodes and other organs. Genetic analyses of these diseases have led to the identification of specific genetic lesions that drive leukemogenesis, which has subsequently led to the development of targeted drugs. Acute myeloid leukemia (AML) is a fast progressing blood malignancy with impaired differentiation and proliferation of myeloid precursors. It is one of the most common leukemias in adults. AML is known for its molecular and biological heterogeneity, and a variety of genetic lesions have been implicated in the disease. FMS-like tyrosine kinase 3 (FLT3) mutations including FLT3 internal tandem duplication (ITD) or point mutations in the tyrosine kinase domain (TKD) are found in around 30% of AML patients.

Sorafenib, a multi-kinase inhibitor that targets FLT3, RAF, VEGFR, FGFR, KIT and RET, is approved for use in hepatocarcinoma, renal cell carcinoma, and thyroid carcinoma treatments. Addition of sorafenib to standard treatment prolonged AML patient survival with or without FMS- like tyrosine kinase 3 (FLT3) mutations, although relapse caused by drug-resistance has limited its usefulness. Understanding the mechanism of resistance to targeted drugs, therefore, is necessary to improve treatment regimens for AML patients. We aim to elucidate resistance mechanisms to sorafenib in AML cells using genome-wide CRISPR screening. Two genome-scale human CRISPR knockout (KO) libraries were used to identify genes whose loss-of-function contribute to lower sensitivity to sorafenib in the MOLM13 AML cells. We verified 10 genes from the top hits showing consistency between the two CRISPR libraries, one of which was Tuberous Sclerosis 1 (TSC1). To validate these findings, TSC1 KO cells were generated using lentiCRISPRv2 system and single sgRNA sequence. Drug sensitivity assays confirmed increase in sorafenib resistance of TSC1 KO cells compared to parental cells or cells harboring non-targeting sgRNA. In addition to the sorafenib resistant phenotype, TSC1 KO cells were resistant to a panel of FLT3 inhibitors, quizartinib, crenolanib, gilteritinib, and UNC2025A. Moreover, RNA sequencing results from 271 AML patient peripheral blood or bone marrow samples revealed that lower RNA expression of Tuberous Sclerosis 1 (TSC1) correlated with lower sensitivity to sorafenib. TSC2 was also observed as a hit gene in both CRISPR libraries and lower TSC2 RNA levels also correlated with lower sensitivity to sorafenib, emphasizing TSC1/2 as an important pathway in sorafenib resistance.

Citation Format: Alisa Damnernsawad, Tamilla Nechiporuk, Steve E. Kurtz, Wesley R. Horton, Olga Nikolova, Shannon K. McWeeney, Jeffrey W. Tyner. Genome-wide CRISPR screening identifies TSC1 as a regulator of sorafenib resistance in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4763.

The TP53 Apoptotic Network Is a Primary Mediator of Resistance to BCL2 Inhibition in AML Cells

To study mechanisms underlying resistance to the BCL2 inhibitor venetoclax in acute myeloid leukemia (AML), we used a genome-wide CRISPR/Cas9 screen to identify gene knockouts resulting in drug resistance. We validated TP53, BAX, and PMAIP1 as genes whose inactivation results in venetoclax resistance in AML cell lines. Resistance to venetoclax resulted from an inability to execute apoptosis driven by BAX loss, decreased expression of BCL2, and/or reliance on alternative BCL2 family members such as BCL2L1. The resistance was accompanied by changes in mitochondrial homeostasis and cellular metabolism. Evaluation of TP53 knockout cells for sensitivities to a panel of small-molecule inhibitors revealed a gain of sensitivity to TRK inhibitors. We relate these observations to patient drug responses and gene expression in the Beat AML dataset. Our results implicate TP53, the apoptotic network, and mitochondrial functionality as drivers of venetoclax response in AML and suggest strategies to overcome resistance. SIGNIFICANCE: AML is challenging to treat due to its heterogeneity, and single-agent therapies have universally failed, prompting a need for innovative drug combinations. We used a genetic approach to identify genes whose inactivation contributes to drug resistance as a means of forming preferred drug combinations to improve AML treatment.See related commentary by Savona and Rathmell, p. 831.This article is highlighted in the In This Issue feature, p. 813.

Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms

FLT3 mutations are prevalent in AML patients and confer poor prognosis. Crenolanib, a potent type I pan-FLT3 inhibitor, is effective against both internal tandem duplications and resistance-conferring tyrosine kinase domain mutations. While crenolanib monotherapy has demonstrated clinical benefit in heavily pretreated relapsed/refractory AML patients, responses are transient and relapse eventually occurs. Here, to investigate the mechanisms of crenolanib resistance, we perform whole exome sequencing of AML patient samples before and after crenolanib treatment. Unlike other FLT3 inhibitors, crenolanib does not induce FLT3 secondary mutations, and mutations of the FLT3 gatekeeper residue are infrequent. Instead, mutations of NRAS and IDH2 arise, mostly as FLT3-independent subclones, while TET2 and IDH1 predominantly co-occur with FLT3-mutant clones and are enriched in crenolanib poor-responders. The remaining patients exhibit post-crenolanib expansion of mutations associated with epigenetic regulators, transcription factors, and cohesion factors, suggesting diverse genetic/epigenetic mechanisms of crenolanib resistance. Drug combinations in experimental models restore crenolanib sensitivity.

FLT3 is commonly mutated in acute myeloid leukaemia and treatment with FLT3 inhibitors often ends with relapse. Here, the authors perform exome sequencing of samples from patients treated with the FLT3 inhibitor, crenolanib, to show that resistance occurs due to diverse molecular mechanisms, not primarily due to secondary FLT3 mutations.

Non-CpG methylation by DNMT3B facilitates REST binding and gene silencing in developing mouse hearts

The dynamic interaction of DNA methylation and transcription factor binding in regulating spatiotemporal gene expression is essential for embryogenesis, but the underlying mechanisms remain understudied. In this study, using mouse models and integration of in vitro and in vivo genetic and epigenetic analyses, we show that the binding of REST (repressor element 1 (RE1) silencing transcription factor; also known as NRSF) to its cognate RE1 sequences is temporally regulated by non-CpG methylation. This process is dependent on DNA methyltransferase 3B (DNMT3B) and leads to suppression of adult cardiac genes in developing hearts. We demonstrate that DNMT3B preferentially mediates non-CpG methylation of REST-targeted genes in the developing heart. Downregulation of DNMT3B results in decreased non-CpG methylation of RE1 sequences, reduced REST occupancy, and consequently release of the transcription suppression during later cardiac development. Together, these findings reveal a critical gene silencing mechanism in developing mammalian hearts that is regulated by the dynamic interaction of DNMT3B-mediated non-CpG methylation and REST binding.

The REST remodeling complex protects genomic integrity during embryonic neurogenesis

The timely transition from neural progenitor to post-mitotic neuron requires down-regulation and loss of the neuronal transcriptional repressor, REST. Here, we have used mice containing a gene trap in the Rest gene, eliminating transcription from all coding exons, to remove REST prematurely from neural progenitors. We find that catastrophic DNA damage occurs during S-phase of the cell cycle, with long-term consequences including abnormal chromosome separation, apoptosis, and smaller brains. Persistent effects are evident by latent appearance of proneural glioblastoma in adult mice deleted additionally for the tumor suppressor p53 protein (p53). A previous line of mice deleted for REST in progenitors by conventional gene targeting does not exhibit these phenotypes, likely due to a remaining C-terminal peptide that still binds chromatin and recruits co-repressors. Our results suggest that REST-mediated chromatin remodeling is required in neural progenitors for proper S-phase dynamics, as part of its well-established role in repressing neuronal genes until terminal differentiation.

DOI:http://dx.doi.org/10.7554/eLife.09584.001

In the brain, cells called neurons connect to each other to form complex networks through which information is rapidly processed. These cells start to form in the developing brains of animal embryos when “neural” stem cells divide in a process called neurogenesis. For this process to proceed normally, particular genes in the stem cells have to be switched on or off at different times. This ensures that the protein products of the genes are only made when they are needed.

Proteins called transcription factors can bind to DNA to activate or inactivate particular genes; for example, a transcription factor called REST inactivates thousands of genes that are needed by neurons. During neurogenesis, the production of REST normally declines, and some studies have shown that if the production of this protein is artificially increased, the formation of neurons is delayed. However, other studies suggest that REST may not play a major role in neurogenesis.

Here, Nechiporuk et al. re-examine the role of REST in mice. The experiments used genetically modified mice in which the gene that encodes REST was prematurely switched off in neural stem cells. Compared with normal mice, these mutant mice had much smaller brains that contained fewer neurons because the stem cells stopped dividing earlier than normal. Unexpectedly, many genes that are normally switched off by REST, were not significantly changed, while genes that are not normally regulated by REST – such as the gene that encodes a protein called p53 – were active.

It is known from previous work that p53 is expressed when cells are exposed to harmful conditions that can damage DNA. This helps to prevent cells from becoming cancerous. Nechiporuk et al. found that cells that lacked REST had higher levels of DNA damage than normal cells due to errors during the process of copying DNA before a cell divides. Furthermore, when both REST and p53 were absent, the neural stem cells became cancerous and formed tumors in the mice.

Nechiporuk et al.’s findings suggest that REST protects the DNA of genes that are needed for neurons to form and work properly. The new challenge is to understand where in the genome the damage is occurring.

DOI:http://dx.doi.org/10.7554/eLife.09584.002

Dlg5 maintains apical aPKC and regulates progenitor differentiation during lung morphogenesis

Cell polarity plays an important role in tissue morphogenesis; however, the mechanisms of polarity and their role in mammalian development are still poorly understood. We show here that membrane-associated guanylate kinase protein Dlg5 is required for proper branching morphogenesis and progenitor differentiation in mammalian lung. We found that during lung development Dlg5 functions as an apical-basal polarity protein, which is necessary for the apical maintenance of atypical protein kinase C (aPKC). These results identify Dlg5 as a regulator of apical polarity complexes and uncover the critical function of Dlg5 in branching morphogenesis and differentiation of lung progenitor cells.

Failure of epithelial tube maintenance causes hydrocephalus and renal cysts in Dlg5-/- mice

Epithelial tubes represent fundamental building blocks of metazoan organisms; however, the mechanisms responsible for their formation and maintenance are not well understood. Here, we show that the evolutionarily conserved coiled-coil MAGUK protein Dlg5 is required for epithelial tube maintenance in mammalian brain and kidneys. We demonstrate that Dlg5(-/-) mice develop fully penetrant hydrocephalus and kidney cysts caused by a deficiency in membrane delivery of cadherin-catenin adhesion complexes and loss of cell polarity. Dlg5 travels with cadherin-containing vesicles and binds to syntaxin 4, a t-SNARE protein that regulates fusion of transport vesicles with the lateral membrane domain. We propose that Dlg5 functions in plasma membrane delivery of cadherins by linking cadherin-containing transport vesicles with the t-SNARE targeting complex. These findings show that Dlg5 is causally involved in hydrocephalus and renal cysts and reveal that targeted membrane delivery of cadherin-catenin adhesion complexes is critical for cell polarity and epithelial tube maintenance.

Planar Cell Polarity Planes the Inconveniences of Cell Division into a Smooth Morphogenetic Process

Cell divisions are necessary, but also very disruptive for morphogenesis. Dividing cells lose many intercellular contacts and polarized features. This breaks the magnificent topology of the developing embryo and, if left unrepaired, can lead to severe tissue disorganization. A recent study demonstrated that cells use the planar cell polarity pathway to reestablish polarity and reintegrate daughter cells into developing tissue.

ETL, a novel seven-transmembrane receptor that is developmentally regulated in the heart. ETL is a member of the secretin family and belongs to the epidermal growth factor-seven-transmembrane subfamily

Using differential display of rat fetal and postnatal cardiomyocytes, we have identified a novel seven-transmembrane receptor, ETL. The cDNA-predicted amino acid sequence of ETL indicated that it encodes a 738-aa protein composed of a large extracellular domain with epidermal growth factor (EGF)-like repeats, a seven-transmembrane domain, and a short cytoplasmic tail. ETL belongs to the secretin family of G-protein-coupled peptide hormone receptors and the EGF-TM7 subfamily of receptors. The latter are characterized by a variable number of extracellular EGF and cell surface domains and conserved seven transmembrane-spanning regions. ETL mRNA expression is up-regulated in the adult rat and human heart. In situ hybridization analyses revealed expression in rat cardiomyocytes and abundant expression in vascular and bronchiolar smooth muscle cells. In COS-7 cells transfected with Myc-tagged rat ETL, rat ETL exists as a stable dimer and undergoes endoproteolytic cleavage of the extracellular domain. The proteolytic activity can be abolished by a specific mutation, T455A, in this domain. In transfected mammalian cells, ETL is associated with cell membranes and is also observed in cytoplasmic vesicles. ETL is the first seven-transmembrane receptor containing EGF-like repeats that is developmentally regulated in the heart.

The mouse SCA2 gene: cDNA sequence, alternative splicing and protein expression

Spinocerebellar ataxia type 2 (SCA2) is caused by expansion of a CAG trinucleotide repeat located in the coding region of the human SCA2 gene. Sequence analysis revealed that SCA2 is a novel gene of unknown function. In order to provide insights into the molecular mechanisms of pathogenesis of SCA2 and to identify conserved domains, we isolated and characterized the mouse homolog of the SCA2 gene. Sequence and amino acid analysis revealed 89% identity at the nucleotide and 91% identity at the amino acid level. However, there was no extended polyglutamine tract in the mouse SCA2 cDNA, suggesting that the normal function of SCA2 is not dependent on this domain. Northern blot analysis of different mouse tissues indicated that the mouse SCA2 gene was expressed in most tissues, but at varying levels. Alternative splicing seen in human SCA2 was conserved in the mouse. By northern blot analysis, SCA2 was expressed during embryogenesis as early as day 8 of gestation (E8). Immunohistochemical staining using affinity-purified antibodies demonstrated that ataxin 2 was expressed in the cytoplasm of Purkinje cells as well as in other neurons of the CNS.

Genomic structure of the human gene for spinocerebellar ataxia type 2 (SCA2) on chromosome 12q24.1

Spinocerebellar ataxia type 2 (SCA2) is a member of a group of neurodegenerative diseases that are caused by instability of a DNA CAG repeat. We report the genomic structure of the SCA2 gene. Its 25 exons, encompassing approximately 130 kb of genomic DNA, were mapped onto the physical map of the region. Exonic sizes varied from 37 to 890 bp, and intronic sizes ranged from 323 bp to more than 15 kb. The CAG repeat was contained in the 5' coding region of the gene in exon 1. Determination of the splice junction sequences indicated the presence of only one deviation from the GT-AG rule at the donor splice site of intron 9, which contained a GC instead of a GT dinucleotide. Exon 10, immediately downstream from this rare splice donor site, was alternatively spliced. Alternative splicing does not affect the reading frame and is predicted to encode an isoform containing 70 amino acids less.

A high-resolution PAC and BAC map of the SCA2 region

The spinocerebellar ataxia type 2 (SCA2) gene has been localized to chromosome 12q24.1. To characterize this region and to aid in the identification of the SCA2 gene, we have constructed a 3.9-Mb physical map, which covers markers D12S1328 and D12S1329 known to flank the gene. The map comprises a contig of 84 overlapping yeast artificial chromosomes (YACs), P1 artificial chromosomes (PACs), and bacterial artificial chromosomes (BACs) onto which we placed 82 PCR markers. We localized eight genes and expressed sequence tags on this map, many of which had not been precisely mapped before. In contrast to YACs, which showed a high degree of chimerism and deletions in this region, PACs and BACs were stable. Only 1 in 65 PACs contained a small deletion, and 2 in 18 BACs were chimeric. The high-resolution physical map, which was used in the identification of the SCA2 gene, will be useful for the positional cloning of other disease genes mapped to this region.

Moderate expansion of a normally biallelic trinucleotide repeat in spinocerebellar ataxia type 2

The gene for spinocerebellar ataxia type 2 (SCA2) has been mapped to 12q24.1. A 1.1-megabase contig in the candidate region was assembled in P1 artificial chromosome and bacterial artificial chromosome clones. Using this contig, we identified a CAG trinucleotide repeat with CAA interruptions that was expanded in patients with SCA2. In contrast to other unstable trinucleotide repeats, this CAG repeat was not highly polymorphic in normal individuals. In SCA2 patients, the repeat was perfect and expanded to 36-52 repeats. The most common disease allele contained (CAG)37, one of the shortest expansions seen in a CAG expansion syndrome. The repeat occurs in the 5'-coding region of SCA2 which is a member of a novel gene family.

Expression of neurofibromatosis 2 transcript and gene product during mouse fetal development

Neurofibromatosis 2 (NF2) is an autosomal dominant inherited disorder that predisposes to benign tumors of the nervous system as well as a variety of ocular abnormalities. In contrast to NF1, NF2 is associated with only minor developmental abnormalities. The human NF2 gene encodes a tumor suppressor protein, termed schwannomin or merlin, which is a member of a superfamily of proteins thought to link cytoskeletal elements to cell membrane components. To determine the pattern of NF2 gene expression in mouse embryos, we sequenced the mouse NF2 gene and used in situ hybridization and antischwannomin antibodies to determine the developmental expression of the NF2 gene. Schwannomin was detected in most differentiated tissues but was undetectable in undifferentiated tissues. In particular, schwannomin was not detectable in mitotic neuroepithelial cells, the perichondrium, the liver, the neocortex, and the ventricular zone of the developing cerebral cortex. In the heart, expression was observed in all developmental stages beginning on embryonic day 8. In the eye, which shows developmental abnormalities in NF2 patients, expression was detected in the cells of the lens and in the pigment epithelium but weakly detected in retinal neurons. The most striking example of tightly regulated NF2 expression was observed in cells migrating from the ventricular zone to the cortical plate on embryonic days 15 and 16. Only cells in the intermediate zone expressed schwannomin, indicating that schwannomin may play an important role in cellular migration.

Genetic mapping of the spinocerebellar ataxia type 2 gene on human chromosome 12

The dominant spinocerebellar ataxias are a genetically heterogeneous group of diseases leading to premature death of neurons in the cerebellum and other parts of the nervous system. The mutation causing SCA1 is on human chromosome (CHR) 6p and SCA3 is on CHR 14q. To refine the location of the SCA2 gene on CHR 12q, we performed genetic linkage analysis between the SCA2 locus and nine Ioci (D12S58, D12S78, D12S317, D12S330, D12S353, D12S84, D12S105, D12S79, and PLA2) in three SCA2 families. The highest pairwise lod scores were obtained between SCA2 and D12S84/D12S105 and D12S79. We determined the best order and genetic distances among these loci in ten multigenerational families by multipoint linkage analysis and established the following order: D12S101-D12S58/IGF1- D12S78-D12S317-D12S330/D12S353-D12S84/D 12S105-D12S79-PLA2. Using this genetic map, multipoint linkage analysis placed SCA2 between D12S84/D12S105 and D12S79.

Identification of three new microsatellite markers in the spinocerebellar ataxia type 2 (SCA2) region and 1.2 Mb physical map

Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disease recently mapped to chromosome 12q close to the locus D12S84 by genetic linkage analysis. To generate additional genetic markers in the SCA2 region, we constructed a physical map of the region using yeast artificial chomosome (YAC), P1 artificial chromosome (PAC) and cosmid clones. The physical map was found to agree well with the genetic map. Three novel microsatellite markers were isolated and physically mapped. A novel approach to isolate CAG repeats directly from YAC DNAs is described.

Alternative transcripts in the mouse neurofibromatosis type 2 (NF2) gene are conserved and code for schwannomins with distinct C-terminal domains

Mutations in the neurofibromatosis type 2 (NF2) gene predispose individuals to the development of nervous system tumors and ocular abnormalities. The NF2 gene product, schwannomin, is a member of a superfamily of proteins thought to link cytoskeletal elements to cell membrane components. These proteins share significant homologies in the N-terminal and alpha-helical domains, but diverge in the C-terminus. During our efforts to characterize mouse NF2 transcripts, we identified four different transcripts by cDNA analysis and reverse-transcribed PCR that contained different sequences in the 3' end of the coding sequences. In human cell lines three isoforms encoding two distinct schwannomins were detected. The mouse and human transcripts containing 61 and 60 bp inserts, respectively, have not been previously described. The isoforms encode schwannomins with significantly altered C-termini and were expressed at different relative levels in adult mouse tissues and during mouse embryogenesis. These results suggest that schwannomin isoforms have distinct functional roles and predict the existence of human mutations involving the C-terminus of schwannomin.

Differential expression and tissue distribution of type I and type II neurofibromins during mouse fetal development

Mutations in the NF1 gene may cause developmental abnormalities and the formation of a variety of tumors of neural crest origin in humans. The NF1 gene codes for a large protein, neurofibromin (nf), which is structurally and functionally related to yeast and human ras-GTPase-activating proteins (ras-GAPs). Recently, two transcripts coding for type I and type II nf with different ras-GAP activity have been identified. Since ras proteins do not appear to be significantly regulated during mouse development, we examined if differential expression of neurofibromins may provide evidence for a role of nfs in regulating ras-mediated cell proliferation and differentiation. Nfs were expressed as early as E8. At E11 a marked increase of NF1 transcripts occurred and was associated with expression of nfs in all tissues. Type I and type II nfs each showed a different time course of expression and tissue localization, with type II nf present mainly from E8 through E10, although in the heart type II nf was present at E12. In some tissues such as heart and dorsal root ganglia rapid increases and decreases of nfs were detected related to differentiation of these tissues. These results are consistent with a role of nfs in regulating ras-mediated cell proliferation and differentiation during development and support distinct functional roles for type I and type II nfs.