Month: February 2021

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: https://www.youtube.com/watch?app=desktop&v=-ls9Fsy7Va0

For more information see: https://www.imperial.ac.uk/events/129421/the-schrodinger-lecture-2021-crispr/ 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. https://doi.org/10.1038/s41467-021-21427-6

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

Questions? Email: crispr@amsterdamumc.nl

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. https://doi.org/10.1038/s41467-021-21478-9

Keywords: CRISPR screen, Synthetic lethality, FAM50

Questions? Email: crispr@amsterdamumc.nl

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. https://doi.org/10.1016/j.cell.2021.02.019.
Huang, H., et al. (2021) In vivo CRISPR-screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions. Cell. https://doi.org/10.1016/j.cell.2021.02.021.

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

Questions? Email: crispr@amsterdamumc.nl

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: https://www.ooa-graduateschool.org/cms/wp-content/uploads/Announcement-CRISPR-course_final-1.pdf

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

Questions? Email: crispr@amsterdamumc.nl

In the latest issue of the journal Cell, back-to-back manuscripts are published detailing the application of CRISPR base editors to interrogate the functional significance of nucleotide variants in genes that operate in the DNA damage response (DDR). In the lab of John Doench, initial screens involved nucleotide variants in the cancer predisposition genes BRCA1/2 and anti-apoptotic genes MCL1 and BCL2L1. Furthermore, massive pooled screens were performed targeting over 3500 genes with the potential to test the functional significance of over 52k nucleotide variants reported in the ClinVar database. The group of Alberto Ciccia also used cytosine base editors with over 2k sgRNAs in order to create nucleotide variants in 86 genes involved in DNA replication, damage signaling, homology directed and interstrand crosslink repair. The generated data provide new insights into functional protein domains and identified nucleotide variants associated with gain or loss of function in numerous DDR genes.

For more information, see:
Hanna, R.E., et al. (2021) Massively parallel assessment of human variants with base editor screens. Cell 184: 1064-1080.e20. https://doi.org/10.1016/j.cell.2021.01.012.
Cuella-Martin, R., et al. (2021) Functional interrogation of DNA damage response variants with base editing screens. Cell 184: 1081-1097.e19. https://doi.org/10.1016/j.cell.2021.01.041.
Koch, L. (2021) Finding function with base editing screens. Nature Reviews Genetics https://doi.org/10.1038/s41576-021-00340-0.

Keywords: CRISPR, base editors, gRNA tiling, screens, variants of uncertain significance (VUS), DDR

Questions? Email: crispr@amsterdamumc.nl

The design of prime editing guide (peg) RNAs including the position of the template for reverse transcriptase activity can be complex. In Nature Communications, Hsu and colleagues present a software tool for the design of pegRNAs.

For more information, see: Hsu, J.Y., et al. (2021) PrimeDesign software for rapid and simplified design of prime editing guide RNAs. Nat. Commun. 12: 1034. https://doi.org/10.1038/s41467-021-21337-7. https://drugthatgene.pinellolab.partners.org/

Keywords: CRISPR, Prime Editing, Design Tool, pegRNAs  

Questions? Email: crispr@amsterdamumc.nl

Investigating differences between the brains of extant and extinct species of Homo is important for understanding what makes humans unique. A team of researchers, led by Alysson Muotri, used CRISPR to introduce the Neanderthal form of a gene called NOVA1 into human pluripotent stem cells and cultured brain-like organoids alongside normal human organoids for comparison. Organoids with the Neanderthal version of NOVA1 were smaller with rough, complex surfaces, different levels of synapse proteins, and had a less orderly neuron firing pattern. Muotri’s team plans to use this system to explore other reverted genes to gain insight into the evolutionary pathways that produced modern humans.

For more information, see:
Trujillio, C.L., et al. (2021) Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment. Science 371, eaax2537. DOI: 10.1126/science.aax2537
Penissi, E. (2021) Neanderthal-inspired ‘minibrains’ hint at what makes modern humans special. Science 371, abh0331. DOI:10.1126/science.abh0331

Keywords: CRISPR, IPSCs, Organoids, Neuroscience

Questions? Email: crispr@amsterdamumc.nl

To model malignant transformation in the lab, CRISPR/Cas9 was used to introduced three cancer driver mutations in induced pluripotent stem cells (iPSCs). The modified iPSCs were then subjected to hematopoietic differentiation. Remarkably, the cells mimicked the three distinct stages of malignant transformation as a consequence of the introduced mutation(s): 1) clonal hematopoiesis (ASXL1), 2) myelodysplastic syndrome (ASXL1 + SRFS2), and 3) leukemia (ASXL1 + SRFS2 + NRAS). The modeling of leukemic transformation enabled the analysis of transcriptome and chromatin landscape changes, resulting in the identification of potential novel drug targets in dysregulated cell autonomous inflammatory signaling.

For more information, see:
Wang, T., et al. (2021) Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of myeloid leukemia and identifies early disease targets. Cell Stem Cell. https://doi.org/10.1016/j.stem.2021.01.011.

Keywords: CRISPR, Acute Myeloid Leukemia, IPSC, Malignant Transformation, Modeling

Questions? Email: crispr@amsterdamumc.nl

In the lab of Isaac Hilton, a programmable chromatin kinase called dCas9-dMSK1 was developed to enable histone phosphorylation and mediate targeted changes in chromatin and gene expression. The programmable kinase is a fusion protein combining a nuclease-dead Cas9 with a truncated version of the human histone kinase MSK1 that displays hyperactivity. The authors demonstrate that particularly hyperphosphorylation of histone H3 serine 28 in promoter regions directly correlates with elevated expression level. Interestingly, the programmable chromatin kinase was also applied in a genome wide CRISPR activation screen to identify genes that mediate resistance to the BRAF V600E inhibitor in melanoma cells following increased expression.

For more information, see:
Li, J., et al. (2021) Programmable human histone phosphorylation and gene activation using a CRISPR/Cas9-based chromatin kinase. Nat. Commun. 12, 896. https://doi.org/10.1038/s41467-021-21188-2

Keywords: CRISPR, histone, phosphorylation, chromatin, gene expression

Questions? Email: crispr@amsterdamumc.nl