Therapeutic targeting Tudor domains in leukemia via CRISPR-Scan Assisted Drug Discovery

Epigenetic dysregulation has been reported in multiple cancers including leukemias. Nonetheless, the roles of the epigenetic reader Tudor domains in leukemia progression and therapy remain unexplored. Here, we conducted a Tudor domain-focused CRISPR screen and identified SGF29, a component of SAGA/ATAC acetyltransferase complexes, as a crucial factor for H3K9 acetylation, ribosomal gene expression, and leukemogenesis. To facilitate drug development, we integrated the CRISPR tiling scan with compound docking and molecular dynamics simulation, presenting a generally applicable strategy called CRISPR-Scan Assisted Drug Discovery (CRISPR-SADD). Using this approach, we identified a lead inhibitor that selectively targets SGF29's Tudor domain and demonstrates efficacy against leukemia. Furthermore, we propose that the structural genetics approach used in our study can be widely applied to diverse fields for de novo drug discovery.

Epigenetic Control of Translation Checkpoint and Tumor Progression via RUVBL1-EEF1A1 Axis

Epigenetic dysregulation is reported in multiple cancers including Ewing sarcoma (EwS). However, the epigenetic networks underlying the maintenance of oncogenic signaling and therapeutic response remain unclear. Using a series of epigenetics- and complex-focused CRISPR screens, RUVBL1, the ATPase component of NuA4 histone acetyltransferase complex, is identified to be essential for EwS tumor progression. Suppression of RUVBL1 leads to attenuated tumor growth, loss of histone H4 acetylation, and ablated MYC signaling. Mechanistically, RUVBL1 controls MYC chromatin binding and modulates the MYC-driven EEF1A1 expression and thus protein synthesis. High-density CRISPR gene body scan pinpoints the critical MYC interacting residue in RUVBL1. Finally, this study reveals the synergism between RUVBL1 suppression and pharmacological inhibition of MYC in EwS xenografts and patient-derived samples. These results indicate that the dynamic interplay between chromatin remodelers, oncogenic transcription factors, and protein translation machinery can provide novel opportunities for combination cancer therapy.

ACTR5 controls CDKN2A and tumor progression in an INO80-independent manner

Epigenetic dysregulation of cell cycle is a hallmark of tumorigenesis in multiple cancers, including hepatocellular carcinoma (HCC). Nonetheless, the epigenetic mechanisms underlying the aberrant cell cycle signaling and therapeutic response remain unclear. Here, we used an epigenetics-focused CRISPR interference screen and identified ACTR5 (actin-related protein 5), a component of the INO80 chromatin remodeling complex, to be essential for HCC tumor progression. Suppression of ACTR5 activated CDKN2A expression, ablated CDK/E2F-driven cell cycle signaling, and attenuated HCC tumor growth. Furthermore, high-density CRISPR gene tiling scans revealed a distinct HCC-specific usage of ACTR5 and its interacting partner IES6 compared to the other INO80 complex members, suggesting an INO80-independent mechanism of ACTR5/IES6 in supporting the HCC proliferation. Last, our study revealed the synergism between ACTR5/IES6-targeting and pharmacological inhibition of CDK in treating HCC. These results indicate that the dynamic interplay between epigenetic regulators, tumor suppressors, and cell cycle machinery could provide novel opportunities for combinational HCC therapy.

Abstract 2967: ACTR5 maintains hepatocellular carcinoma via H3K9 epigenetic silencing of CDKN2A

Hepatocellular carcinoma (HCC) is one of the most common cancers (>800,000 new cases each year worldwide) and a leading cause of cancer mortality (~700,000 deaths per year globally), with an average 5-year survival rate of 20~30%. The prevalence of HCC and the unmet clinical needs emphasize the urge for novel regimens for these malignancies. In this study, we performed an epigenetics-focused CRISPR interference (CRISPRi) library screen in the HepG2-dCas9-Krab cells (a total of 3,669 sgRNAs targeting 728 chromatin regulator genes at their transcription start sites) and identified ACTR5 as a novel essential gene in HCC. CRISPR depletion of ACTR5 led to arrested cell cycle and attenuated HCC tumor progression in vivo. Transcriptomic analysis revealed a significantly increased CDKN2A expression in the sgACTR5 transduced HCC cells, which led to the activation of Rb and repression of CDK6 and E2F signaling. Meanwhile, histone modification profiling identified loss of H3K9me2 and Hek9me3 at the CDKN2A promoters upon ACTR5 depletion, indicating the involvement of the epigenetic silencing of tumor suppressors (including CDKN2A) underlying the ACTR5-driven HCC progression. Mechanistically, we found that CRISPR targeting the ACTR5’s interacting protein IES6 (also known as INO80C) recapitulated the sgACTR5 phenotypes, highlighting the collaborative roles between these two partners. We then conducted a high-density CRISPR gene tiling scan using a sgRNA library that targets every NGG protospacer adjacent motif (PAM) within the ACTR5 (284 sgRNAs) and IES6 (90 sgRNAs) coding exons. This saturating mutagenesis screen revealed the requirement of 2 regions (G502-S519 and I552-C569) within ACTR5’s 2nd Actin-fold domain for IES6 interaction. Reciprocally, our unbiased screen identified a previously uncharacterized domain (T163-V187) in IES6’s C-terminal region to mediate the ACTR5-IES6 complex formation. To investigate the clinical impact of ACTR5, we examined the response of HCC cells to various inhibitors upon ACTR5 depletion. While sgACTR5 did not affect the cellular response to sorafenib (an FDA-approved RAF and VEGF inhibitor for HCC patients), we found that suppression of ACTR5 sensitized the HCC cells to ribociclib (a CDK6 inhibitor) and UNC0642 (an H3K9 methyltransferase G9a and GLP inhibitor). Based on these observations, we rationalized a combination treatment of ribociclib/UNC0642 that synergistically suppresses the proliferation of the HCC cells. In summary, our study revealed a pivotal role of ACTR5 (and its complex member IES6) in supporting the CDK6-driven cell cycle progression via an H3K9me2 H3K9me3-mediated silencing of CDKN2A. These notions can be exploited to develop novel combinational therapies against the difficult to cure liver cancers.

Citation Format: Xiaobao Xu, Lu Yang, Anthony Chan, Sheela Pangeni Pokharel, Mingli Li, Qiao Liu, Nicole Mattson, Chun-wei Chen. ACTR5 maintains hepatocellular carcinoma via H3K9 epigenetic silencing of CDKN2A [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2967.

Abstract 2920: Targeting integrin alpha V beta 5 heterodimer stability using a novel small molecular inhibitor for tumor suppression

The cell surface proteome provides a pivotal interphase that connects the intracellular signaling with external environments, which may harbor molecular targets for therapeutic development. To identify essential cell surface proteins in cancers, we established a CRISPR library that contains 2,910 sgRNAs targeting 582 genes encoding cell surface receptors (to cytokines, extracellular matrices [ECM], etc.), molecular channels, and signaling components. We then screened this library in 3 solid cancer (MDA-MB-231, SW620, PANC1) and 3 liquid cancer (MV4-11, HUT78, CCRF-CEM) cell models expressing the Cas9 endonuclease, and observed an essential role of ITGAV (Integrin Alpha V) specifically in the solid cancer. As integrins require the dimerization between an alpha and beta subunit to function as cell surface ECM receptors, we further developed a focused CRISPR library with 650 sgRNAs targeting all 26 integrin alpha and beta subunits. This validation screen revealed a strong correlation between ITGAV and ITGB5 (Integrin Beta 5) in solid tumors. CRISPR targeting either ITGAV or ITGB5 led to attenuated cell proliferation with increased cell cycle stalling and apoptosis. Knockout of ITGAV-ITGB5 also suppressed the capacity of tumor cells to migrate and invade through the ECM, highlighting the therapeutic benefit via blocking the ITGAV-ITGB5 heterodimer. To identify novel compounds that can disrupt ITGAV-ITGB5 dimerization, we first modeled a 3D crystal structure of ITGAV (PDB ID: 3IJE) using AutoSite (Scripps) to reveal the protein surface pockets amenable to the small molecular binding. This analysis revealed an AVB pocket at the N-terminal extracellular domain of ITGAV, which is in close contact with the beta subunit. CRISPR targeting this AVB pocket abolished the ITGAV-ITGB5 heterodimers (detected by an AV-B5-complex antibody) and induced rapid cell death, rationalizing this pocket for further therapeutic development. Based on these observations, we computationally docked >100,000 compounds from the NCI DTP Open Chemicals Repository using AutoDock Vina (Scripps), subsequently obtaining the top 500 binder compounds for in-lab validation, and identified a lead AVB pocket inhibitor “Cpd_2” (C32H40N4). Treatment of Cpd_2 killed tumor cells and diminished the AV-B5-complex antibody stain. Furthermore, we confirmed the capacity of Cpd_2 to dissociate ITGAV and ITGB5 on the cell surface by a NanoBRET energy transfer system. Of note, while the traditional ITGAV inhibitor cilengitide (an RGD peptide mimic) blocked the ECM interaction and detached the cells from TC dishes, they failed to dissociate the ITGAV-ITGB5 heterodimer nor induce rapid cell death. In summary, our study highlights a novel strategy of targeting the ITGAV-ITGB5 heterodimer stability by the small molecular inhibitor Cpd_2 for future anti-tumor treatment.

Citation Format: Nicole Mattson, Kazuya Miyashita, Anthony Chan, Lu Yang, Sheela Pangeni Pokharel, Wei Lu, Mingli Li, Qiao Liu, Xiaobao Xu, Mingye Feng, Chun-Wei Chen. Targeting integrin alpha V beta 5 heterodimer stability using a novel small molecular inhibitor for tumor suppression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2920.

An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia

Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rγnull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2 A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.

MicroRNA-148a-3p is a candidate mediator of increased bone marrow adiposity and bone loss following spinal cord injury

Spinal cord injury is often followed by osteoporosis characterized by rapid and severe bone loss. This leads to an increased risk of osteoporotic fracture in people with spinal cord injury, resulting in increased healthcare costs, morbidity, and mortality. Though it is common, the mechanisms underlying this osteoporosis are not completely understood and treatment options are limited. No biomarkers have been identified for predicting fracture risk. In this study, we sought to investigate microRNA mediated mechanisms relating to osteoporosis following spinal cord injury. We studied subjects with acute SCI (n=12), chronic SCI (n=18), and controls with no SCI (n=23). Plasma samples from all subjects underwent transcriptomic analysis to quantify microRNA expression, after which miR-148a-3p was selected for further study. We performed CT scans of the knee on all subjects with SCI and analyzed these scans to quantify bone marrow adipose tissue volume. MiR-148a-3p was upregulated in subjects with acute SCI vs chronic SCI, as well as in acute SCI vs no SCI. Subjects with chronic SCI had greater levels of marrow adiposity in the distal femoral diaphysis compared to subjects with acute SCI. MiR-148a-3p levels were negatively associated with distal femoral diaphysis marrow adiposity. A multivariable model showed that miR-148a-3p and BMI explained 24% of variation in marrow adiposity. A literature search revealed that miR-148a-3p has multiple bone and fat metabolism related targets. Our findings suggest that miR-148a-3p is a mediator of osteoporosis following spinal cord injury and a potential future therapeutic target.

Factors affecting microbial formation of nitrate-nitrogen in soil and their effects on fertilizer nitrogen use efficiency

Mineralization of soil organic matter is governed by predictable factors with nitrate-N as the end product. Crop production interrupts the natural balance, accelerates mineralization of N, and elevates levels of nitrate-N in soil. Six factors determine nitrate-N levels in soils: soil clay content, bulk density, organic matter content, pH, temperature, and rainfall. Maximal rates of N mineralization require an optimal level of air-filled pore space. Optimal air-filled pore space depends on soil clay content, soil organic matter content, soil bulk density, and rainfall. Pore space is partitioned into water- and air-filled space. A maximal rate of nitrate formation occurs at a pH of 6.7 and rather modest mineralization rates occur at pH 5.0 and 8.0. Predictions of the soil nitrate-N concentrations with a relative precision of 1 to 4 microg N g(-1) of soil were obtained with a computerized N fertilizer decision aid. Grain yields obtained using the N fertilizer decision aid were not measurably different from those using adjacent farmer practices, but N fertilizer use was reduced by >10%. Predicting mineralization in this manner allows optimal N applications to be determined for site-specific soil and weather conditions.