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[Weekly News] Deadly Link Between Industrial Pollutants and Fatty Liver: CRISPR Screening Reveals the Answer

The CRISPR/Cas system, a revolutionary tool in modern biological science, impacts fields ranging from medicine and agriculture to environmental conservation. Every week, new research developments and application cases related to CRISPR continue to emerge, bringing profound changes to our lives.

Below is a brief overview of the latest CRISPR-related research and industry news from the past week:

I. Research Update

i. CRISPR Screening

1. Article Title: A novel molecular pathway of lipid accumulation in human hepatocytes caused by PFOA and PFOS

Journal: Environment international（IF:10.3）

Link: https://doi.org/10.1016/j.envint.2024.108962

Exposure to PFOA and PFOS, two persistent environmental pollutants widely used in industrial and consumer products, has been linked to non-alcoholic fatty liver disease (NAFLD), but the molecular mechanisms are unclear. This study identified a novel pathway through which PFOA and PFOS at human-relevant doses (<10 μM) lead to hepatocyte lipid accumulation. Using CRISPR-Cas9 genome screening and transcriptional assays in HepG2 cells, the study found that the gene nudt7 is significantly downregulated by PFOA and PFOS exposure. This downregulation reduces Ace-CoA hydrolase activity, leading to increased lipid accumulation in liver cells. This mechanism may explain the association between PFAS exposure and NAFLD in humans.

2. Article Title: STING is crucial for the survival of RUNX1::RUNX1T1 leukemia cells

Journal: Leukemia（IF: 12.8）

Link: https://doi.org/10.1038/s41375-024-02383-8

Acute myeloid leukemia (AML) patients with the RUNX1::RUNX1T1 (AE) fusion gene generally have a favorable prognosis, but about 50% of them relapse within 2.5 years and develop resistance to further chemotherapy. Through a genome-wide CRISPR screen, researchers identified fatty acid desaturase 2 (FADS2) as a key downstream factor of Stimulator of Interferon Genes (STING) inhibition that mediates cell death in AE leukemia cells. The study reveals that both genetic and pharmacological inhibition of STING significantly suppresses the growth of AE leukemia cells. In a mouse model, STING deletion reduced leukemia development and extended lifespan. These findings highlight the critical role of STING in the survival of AE-positive AML cells and suggest STING as a potential therapeutic target, with FADS2 playing a crucial role in the mechanism identified through CRISPR screening.

3. Article Title: Genome-Wide CRISPR Screen Identifies KEAP1 Perturbation as a Vulnerability of ARID1A-Deficient Cells

Journal: Cancer（IF: 6.575）

Link: https://doi.org/10.3390/cancers16172949

ARID1A, a key subunit of the BAF chromatin remodeling complex, is frequently mutated in cancers, especially in clear cell ovarian carcinoma (CCOC). Despite its significance, targeted therapies for ARID1A-deficient cancers are limited. This study identifies KEAP1 as a critical vulnerability in ARID1A-deficient CCOC using genome-wide CRISPR screening. Disrupting KEAP1 selectively inhibits the growth of ARID1A-KO cell lines and primary endometrial epithelial cells by exacerbating genome instability rather than affecting NRF2 signaling. These findings suggest KEAP1 as a potential therapeutic target in ARID1A-deficient cancers.

4. Article Title: An unbiased lncRNAs dropout CRISPR-Cas9 screen reveals RP11-350G8.5 as a novel therapeutic target for Multiple Myeloma

Journal: blood（IF: 21）

Link: https://doi.org/10.1182/blood.2023021991

This study explored the role of long non-coding RNAs (lncRNAs) in Multiple Myeloma (MM) using a CRISPR-Cas9 loss-of-function screen targeting 671 lncRNAs. Researchers identified RP11-350G8.5 as a crucial oncogenic lncRNA that supports tumor growth and is associated with poor prognosis in MM patients. Inhibition of RP11-350G8.5 showed anti-tumor effects both in vitro and in vivo, making it a promising therapeutic target, particularly for patients with Bortezomib-resistant MM.

5. Article Title: Functional overlap of inborn errors of immunity and metabolism genes defines T cell metabolic vulnerabilities

Journal: Science immunology（IF: 17.6）

Link: https://doi.org/10.1126/sciimmunol.adh0368

Inborn errors of metabolism (IEMs) and inborn errors of immunity (IEIs) are complex Mendelian diseases. CRISPR screening revealed significant overlap in immune and metabolic functions between IEM and IEI genes. Key findings include the role of Gfpt1 in T cell function and Bcl11b in preventing CD4 T cell metabolic stress. These results highlight the close link between metabolism and immunity, expanding our understanding of these diseases and offering insights for new therapeutic strategies.

6. Article Title: Chromatin-Focused CRISPR Screens Identify Resistance Mechanisms to Menin Inhibitors in KMT2A-Rearranged Leukaemia

Journal: Blood（IF: 21）

Link: https://doi.org/10.1182/blood.2023023644

Menin inhibitors show promise for treating acute myeloid leukemia (AML) with KMT2A rearrangements (KMT2A-r), but resistance remains a challenge. This study identifies a resistance mechanism independent of traditional Menin-MLL targets. It reveals that non-canonical Menin targets, co-occupied by Menin and repressive H2AK119ub marks, are downregulated after Menin inhibition. Loss of PRC1.1 subunits, like PCGF1 or BCOR, leads to resistance by reactivating these targets, including MYC. Inhibiting MYC or using venetoclax can overcome resistance in PRC1.1-deficient leukemia cells. These findings suggest new strategies for treating AML with compromised PRC1.1 function.

7. Article Title: CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant

Journal: bioRxiv : the preprint server for biology

Link: https://doi.org/10.1101/2024.04.26.591412

Functional enhancer annotation is crucial for understanding tissue-specific transcription and prioritizing disease-related non-coding variants. This study used a CRISPR interference screen in human pluripotent stem cells (hPSCs) to identify a long-range enhancer ∼664 kb from the ONECUT1 promoter, which is vital for pancreatic differentiation. Deleting this enhancer led to a significant loss of ONECUT1 expression and impaired pancreatic development. The enhancer contains a type 2 diabetes-associated variant (rs528350911) that disrupts GATA binding, supporting its role in metabolic disease. This work highlights the importance of enhancer discovery in understanding both monogenic and complex diseases.

ii. CRISPR Detection

1. Article Title: High-Throughput and Integrated CRISPR/Cas12a-Based Molecular Diagnosis Using a Deep Learning Enabled Microfluidic System

Journal: ACS nano （IF: 15.8）

Link: https://doi.org/10.1021/acsnano.4c05734

CRISPR/Cas-based molecular diagnostics hold great promise for rapid and sensitive pathogen detection, especially for SARS-CoV-2. However, challenges such as limited throughput and complex reagent preparation hinder widespread use. This study introduces the mutaSCAN system, which uses CRISPR/Cas12a and nonextraction RT-LAMP in a microfluidic multiplate setup for high-throughput detection of SARS-CoV-2 variants. The system, aided by deep-learning and self-developed reagents, detects the virus in under 30 minutes with a sensitivity of 250 copies/mL and a throughput of up to 96 samples per round. Clinical tests showed 98% accuracy for routine detection and 100% accuracy for mutation testing, with no false positives in negative samples.

2. Article Title: From Lab to Home: Ultrasensitive Rapid Detection of SARS-CoV-2 with a Cascade CRISPR/Cas13a-Cas12a System Based Lateral Flow Assay

Journal: Analytical chemistry (IF: 6.7)

Link: https://doi.org/10.1021/acs.analchem.4c02726

CRISPR/Cas-based diagnostics typically require nucleic acid amplification for sensitivity, which is time-consuming and prone to contamination, making them unsuitable for at-home testing. This study introduces CLEAR, an advanced CRISPR/Cas13a-Cas12a-based lateral flow assay for direct, ultrasensitive detection of SARS-CoV-2 RNA without amplification. CLEAR achieves 1 aM sensitivity and shows 100% accuracy in clinical tests. It is a low-cost, user-friendly solution ideal for at-home use, overcoming the limitations of traditional PCR systems and offering a promising tool for public health, especially in resource-limited settings.

3. Article Title: An accurate and convenient method for Mycoplasma pneumoniae via one-step LAMP-CRISPR/Cas12b detection platform

Journal: Frontiers in cellular and infection microbiology（IF: 4.6）

Link: https://doi.org/10.3389/fcimb.2024.1409078

Mycoplasma pneumoniae (MP) is a major cause of respiratory infections in children and adolescents, requiring early and accurate detection to prevent outbreaks. This study highlights a novel CRISPR-based detection method for direct detection of MP. The method combines loop-mediated isothermal amplification (LAMP) with CRISPR/Cas12b in a one-pot reaction. This CRISPR detection system, completed in 1 hour at 57°C, achieved a limit of detection (LOD) of 33.7 copies per reaction and demonstrated 100% specificity. When tested on 272 clinical samples, this LAMP-CRISPR/Cas12b method showed 88.11% sensitivity, 100% specificity, and 93.75% overall consistency. These results underscore the potential of LAMP-CRISPR/Cas12b as a simple and reliable tool for MP diagnosis, particularly in resource-limited settings.

II. Industry

1. Tome Biosciences, despite raising $213 million in 2023, is cutting operations due to shifting investor sentiment in the gene editing space. The company is maintaining core expertise and exploring strategic options, including potential sales, but has not disclosed details on employee impact or pipeline changes.

https://www.fiercebiotech.com/biotech/young-gene-editing-biotech-explores-strategic-options-investors-pullback

2. Aadi Bioscience's Fyarro is expected to fail its phase 2 solid tumor trial, leading the company to halt the study and lay off 80% of its R&D staff. This setback significantly impacts the company's hopes for Fyarro, the only drug in its pipeline, after previously expressing optimism about the trial's potential impact on patients.

https://www.fiercepharma.com/pharma/aadi-lays-80-rd-workforce-fyarro-heads-phase-2-fail?_gl=1*7ebzim*_gcl_au*MTczNjg4OTk4My4xNzI0NzQ1OTgx*_ga*NDQ4MTQyMjM5LjE3MjQ3NDU4OTI.*_ga_KG49 J84SR4*MTcyNDgxNzUxNi4yLjEuMTcyNDgxNzYzNy4wLjAuMA..

3. Aldevron's latest whitepaper, Next-Generation CRISPR Approaches, highlights how recent FDA and EMA approvals for CRISPR therapies are driving innovation in the cell and gene therapy space, while detailing various manufacturing strategies and specific requirements to support the full development of CRISPR therapies.

https://www.aldevron.com/download-whitepaper-crispr-approach?utm_medium=social&utm_source=cmn&utm_campaign=rnp_gene-editing_24-green&utm_term=crispr

4. McKesson plans to expand its oncology platform by investing nearly $2.5 billion to acquire a 70% stake in Community Oncology Revitalization Enterprise Ventures (Core Ventures), a business and administrative services arm launched by Florida Cancer Specialists & Research Institute (FCS). This deal will integrate Core Ventures into McKesson's oncology network, aiming to enhance patient care and reduce overall costs while allowing FCS to remain independent.

https://www.fiercehealthcare.com/providers/mckesson-spending-25b-majority-stake-florida-community-oncology

EDITGENE focuses on CRISPR technology, offering a range of high-quality gene editing services and in vitro diagnostic products.

These include but are not limited to: CRISPR Library Screening, Cell Line Engineering, Monoclonal Cell Line Screening, CRISPR Detection.

We are committed to providing the most efficient technical services for CRISPR-related, gene function research, in vitro diagnostics, and therapeutic research.

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