Scientific Advances: Modeling erythroleukemia through CRISPR multiplex gene editing in mouse hematopoietic stem cells

March 24, 2021.

A collaborative effort between the labs of Charles Mullighan, St Jude Children’s Research Hospital, and Benjamin Ebert, Dana-Farber Cancer Institute, to identify the driving factors in acute erythroid leukemia was recently published in the journal Blood. Acute erythroid leukemia (AEL) is a rare cancer that is characterized by proliferation of leukemic erythroblasts in the bone marrow.  Although recurrent gene mutations have been identified in AEL, the effect of these genetic alterations on cancer initiation and progression was unclear. In the current study, the authors selected 10 genes (Trp53, Tet2, Dnmt3a, Asxl1, Ezh2, Stag2, Bcor, Ppm1d, Rb1, and Nfix) to target in mouse hematopoietic stem and progenitor cells (HSPCs) using 6 differential gRNA pools. The transduced HSPCs were transplanted into mice and subsequent leukemic transformation was observed. Analysis of the cells revealed that combinatorial disruption of Bcor, Trp53, Dnmt3a, Rb1, and Nfix resulted in AEL, and the leukemic cells also acquired secondary mutations in transcription factors and signaling genes. The newly established erythroleukemia mouse model was used to find therapeutic strategies against AEL. Talazoparib (PARP-inhibitor) and Decitabine (demethylating drug) showed efficacy against leukemic cells with Trp53 and Bcor mutations. In addition, CDK7/9 inhibitors were shown to mediate an anti-tumor response in AEL cells with mutations in Trp53, Bcor, and Dnmt3a.

For more information, see:
Iacobucci, I., et al. (2021) Modeling and targeting of erythroleukemia by hematopoietic genome editing. Blood 137: 1628–1640.

Zhang, J.P., Tao Cheng, T. (2021) Modeling acute erythroid leukemia via CRISPR. Blood 137: 1565–1567.

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Scientific Advances: A childhood cancer dependency map

Check out our latest CRISPR news updates here:

Kimberly Stegmaier from the Dana Farber Cancer Research Institute led a tour-de-force endeavor to characterize unique genetic vulnerabilities in childhood cancer cell lines. In total, 82 genome-wide CRISPR screens were performed using the Avana lentiviral gRNA library, targeting over 18,000 human genes. The authors focused on pediatric cell lines from solid tumors, such as Ewing sarcoma, medulloblastoma, neuroblastoma and osteosarcoma, because therapeutic progress against these childhood cancers has been relatively limited. Data from the CRISPR screens were combined with whole exome and RNA seq analysis to generate the most comprehensive pediatric tumor dependency map to date.

Contrary to expectations, the authors found that the number of genetic vulnerabilities in pediatric tumor cell lines was similar to adult cancers, despite a much lower mutation load observed in childhood malignancies. Identified vulnerabilities include the methyltransferase EZH2 (neuroblastoma), MDM2 / MDM4 (Ewing sarcoma, rhabdoid tumors), receptor tyrosine kinases ALK / BRAF (rhabdoid tumors), and SMARCB1-associated proteasome dependency. Importantly, a considerable number of identified genetic vulnerabilities were unique to pediatric cancers, in correlation with unique genetic drivers in childhood cancer. The pediatric cancer dependency map will greatly facilitate the development of personalized treatments based on genetic signatures in childhood tumors.

For more information, see:
Dharia, N.V., Kugener, G., Guenther, L.M. et al. (2021) A first-generation pediatric cancer dependency map. Nat. Genet.

Keywords: CRISPR screen, pediatric cancer, genetic vulnerability

Also, see our ‘At a glance’ section for more information on recent genome-wide CRISPR screens in cancer cells.

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Review: A perspective on human germline gene editing

March 18, 2021.

Because it is associated with human reproduction, human heritable gene editing can evoke spiritual, religious, or deeply personal issues for many. A review in Cell provides an overview of the current status of human gene editing along with a nice summary of the ethical considerations. The authors review the principals of beneficence (therapeutic benefit), non-maleficence (safety risks), autonomy (reproductive rights of parents vs. lack of offspring’s ability to consent) and justice (unequal access to technology).

For more information, see:
Turocy, J. et al. (2021) Heritable human genome editing: Research progress, ethical considerations, and hurdles to clinical practice. Cell 184: 1561-1574.

Keywords: CRISPR, Germline, Ethics  

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At a glance

March 10

Proof of principle for bone marrow gene editing in vivo in a pre-clinical mouse model
At the recent Keystone symposia on Precision Genome Editing, Sean Burns presented an update on CRISPR gene editing of bone marrow cells in vivo.

Keywords: CRISPR,  bone marrow, in vivo gene editing

March 8

Book Reviews. Like to read about CRISPR?
Two books revolving around CRISPR were recently published:

  • CRISPR People: The Science and Ethics of Editing Humans Henry T. Greely, MIT Press (2021)
  • The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race. Walter Isaacson, Simon & Schuster (2021)

For more information, see: Scully, J.L. (2021) A biographer and a bioethicist take on the CRISPR revolution. Nature

Keywords: CRISPR,  books

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Scientific Advances: CRISPR-mediated gene repression relieves chronic pain

March 10, 2021.

Chronic pain is a debilitating condition that is currently treated with addictive opioids. Moreno et al. published a study in Science Translational Medicine describing the application of CRISPR dead-Cas9 and zinc fingers proteins to relieve pain. Packaged within adeno-associated viral (AAV) particles, the gene editing tools were injected into the spinal intrathecal space of mice in order to locally suppress the expression of the NaV1.7 gene. A single AAV injection with dCas9 fused to the Krüppel-associated box (KRAB) gene repressor was documented to provide specific and long-lasting pain relief (up to 44 weeks), without inducing loss of other sensations or apparent side effects. The authors are confident that the observed pain relief by NaV1.7 repression presents an exciting novel therapeutic opportunity for the management of chronic pain in patients.

For more information, see:
Moreno, A.M., et al. (2021) Long-lasting analgesia via targeted in situ repression of NaV1.7 in mice. Science Translational Medicine 13: eaay9056. DOI: 10.1126/scitranslmed.aay9056
Servick, K. (2021) Gene-silencing injection reverses pain in mice. Science DOI:10.1126/science.abi4517
Remmel, A. (2021) CRISPR-based gene therapy dampens pain in mice. Nature

Keywords: CRISPR, dCas9, KRAB gene repression, chronic pain

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Scientific Advances: CRISPR reduces low-density lipoprotein (LDL) cholesterol in pre-clinical study

March 9, 2021.

While developing a new lipid nanoparticle (LNP)-based in vivo delivery platform for CRISPR/Cas9 gene editing in the liver, Qiu et al. focused on the disruption of the Angiopoietin-like 3 (Angptl3) gene. This gene is a potential target for therapeutic interventions against human lipoprotein metabolism disorders. Using a pre-clinical mouse model, the authors were able to demonstrate specific and efficient Angptl3 disruption using their LNP delivery system, resulting in a profound reduction of low-density lipoprotein cholesterol, and triglyceride serum levels.

For more information, see: Qiu, M., et al. (2021) Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing of Angptl3. PNAS 118, e2020401118. DOI: 10.1073/pnas.2020401118

Keywords: CRISPR, Therapy, Cholesterol  

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At a glance

Feb. 24. Imperial College London organizes the annual Schrödinger lecture. This year, the lecture was given by Dr. Jennifer A. Doudna. You can find the Schrödinger lecture 2021 on YouTube:

For more information see: Keywords: CRISPR,  Schrödinger lecture, Imperial College London, Dr. Jennifer A. Doudna

Feb. 18. Cre-controlled tissue-specific CRISPR expression in model organisms

For more information see: Hans, S., et al. (2021) Cre-controlled CRISPR mutagenesis provides fast and easy conditional gene inactivation in zebrafish. Nat. Commun. 12: 1125.

Keywords: CRISPR,  Cre, model organisms, tissue-specific expression

Feb. 11. Inhibition of DNA-PKcs increases CRISPR deletion size and enhances sensitivity of pooled CRISPR screens.

For more information see: Bosch-Guiteras, N., et al. (2021) Enhancing CRISPR deletion via pharmacological delay of DNA-PKcs. Genome Research. doi: 10.1101/gr.265736.120

Keywords: CRISPR,  deletion, pooled screen, DNA-PKcs inhibition

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Scientific Advances: CRISPR screen identifies 105 gene combinations resulting in loss of cellular fitness

February 26, 2021.

From the labs of Stephen Jackson and David Adams, a study was published in Nature Communications in which the systematic disruption of 1191 gene pairs was analyzed. The authors focused on gene pairs, including paralogs, that evolved to provide genetic redundancy in order to safeguard essential cellular processes. However, genetic redundancy is also critical for the survival of malignant cells in light of their mutation loads and abnormal karyotypes. Overall, 105 unique gene combinations were identified that reduced cellular fitness after co-disruption, with 27 combinations inducing synthetic sickness across multiple tumor cell lines. Among these consistent hits were two paralogs of unknown function: FAM50A/FAM50B. This offers potentially a new therapeutic approach against cancer based on synthetic lethality as FAM50B silencing has been documented in various malignancies.  

For more information, see: Thompson, N.A., et al. (2021) Combinatorial CRISPR screen identifies fitness effects of gene paralogues. Nat. Commun. 12, 1302.

Keywords: CRISPR screen, Synthetic lethality, FAM50

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Scientific Advances: In vivo CRISPR screens identify novel regulatory switches for effector T cells

Back-to-back manuscripts from the labs of Junwei Shi and Hongbo Chi in Cell present data from in vivo pooled CRISPR screens dissecting the molecular pathways involved in the differentiation of naïve CD8+ T cells into effector and memory cells. In both studies, genetic switches (Fli1 & Pofut1) were identified that enhanced the activity of T effector cells against infectious pathogens or tumors.

For more information, see:
Chen, Z., et al. (2021) In vivo CD8+ T cell CRISPR-screening reveals control by Fli1 in infection and cancer. Cell.
Huang, H., et al. (2021) In vivo CRISPR-screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions. Cell.

Keywords: CRISPR, in vivo screens, CD8+, T cells, immunotherapy

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Reminder: CRISPR Genome Editing Course

March 16 – April 1, 2021.

Registration deadline for the CRISPR Genome Editing course: February  15, 2021.

Under the umbrella of Oncology Graduate School Amsterdam (OOA), a CRISPR course will be given to PhD students at Cancer Center Amsterdam (CCA) and the Netherlands Cancer Institute (NCI).

The course is free of charge and is limited to 28 participants. Lectures will be available to a wider audience either at the Piet Borst Auditorium (NCI) or through Zoom starting March 16, 2021.

For more information and the preliminary program, see:

Keywords: CRISPR, Course, PhD student, Oncology Graduate School Amsterdam

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