Small Pathology, Big News
Exploring the significant stories of the tiny world that is molecular pathology
George Francis Lee | | News
Using human reference genomes always comes with challenges. For one, biases can be introduced, ultimately affecting how researchers interpret the sequences of other human genomes. In a bid to curtail these disadvantages, a paper has proposed the use of a graph-based system called a pangenome to visualize genetic diversity more accurately. The author’s example saw better genomic alteration identification than standard thanks to its use of 94 highly accurate and nearly complete genome assemblies from 47 individuals representing diverse ancestries (1).
To examine the potential of epigenetic biomarkers for diabetes and related conditions, researchers have analyzed type 2 diabetes and possible links to kidney dysfunction. They found that DNA methylation levels were linked to renal function in type 2 diabetes, and previously unknown CpG sites showed associations with baseline estimated glomerular filtration rate. The genes that were near to the CpG sites and included in prediction models were related to pathways associated with kidney disease pathogenesis. Methylation biomarkers could help assess risk in type 2 diabetes and provide insights into the pathogenesis of kidney diseases (2).
Markers… In Space!
Leveraging recent progress in spatial transcriptomics (ST), researchers have developed an algorithm – SpaceMarkers – that is capable of inferring molecular changes that result from interactions between cells. The algorithm gleans its bioinformation from latent space analysis of ST data and can analyze tumor-immune interactions through a combination of spatial transcriptomics and single-cell RNA sequencing data (3).
An Inflammatory Comment
The liver tumor mutation LKB1 is strongly associated with deregulated inflation, but the underlying reasons why have not been understood. A recent study, however, has established that inflammatory potential downstream of LKB1 loss is driven epigenetically through deregulated signaling by CREB-regulated transcription coactivator 2 (CRTC2). Researchers identified that LKB1 mutations make cells more sensitive to inflammatory stimuli, leading to increased production of cytokines and chemokines – highlighting a previously unknown anti-inflammatory process that links metabolic and epigenetic states and potential cell inflammation.
In the Driver’s Seat
Using neuron-specific gene regulatory networks, a study into Alzheimer’s disease has highlighted 1,563 neuronal key drivers of the condition. One significant interesting target, JMJD6, displayed significant influence towards Aβ and tau levels (5).
A Prime Example
In place of standard mouse models, a team has developed an in vivo system by using a prime editor in the mouse germline. This facilitated more rapid and precise engineer mutations in cell lines and organoids derived from primary tissues – notably those commonly observed in pancreatic cancer (6).
The Search For SPOCK2
Investigation of the SPOCK2 protein in the extracellular matrix and its relationship to pancreatic ductal adenocarcinoma (PDAC) has found that i) it is downregulated in PDAC cell lines, and ii) its expression is increased by demethylation. Moreover, stymied SPOCK2 resulted in cell growth, while high numbers were associated with better patient outcomes (7).
Know the Score
Researchers exploring the crosstalk between four major RNA adenosine modifications in gastric cancer have developed a scoring model named “WRM_Score” that is linked to patient prognosis and immune checkpoint inhibitors efficacy – providing a reliable predictor for gastric cancer outcomes (8).
- WW Liao et al., Nature, 617, 312 (2023). PMID: 37165242.
- KY Li et al., Nat Commun, 14, 2543 (2023). PMID: 37188670.
- A Deshpande et al., Cell Syst, 14, 285 (2023). PMID: 37080163.
- SE Compton et al., Mol Cell, (2023). PMID: 37172591.
- JP Merchant et al., Commun Biol, 6, 503 (2023). PMID: 37188718.
- ZA Ely et al., Nat Biotechnol, (2023). PMID: 37169967.
- U Aghamaliyev et al., J Cancer Res Clin Oncol [Online ahead of print] (2023). PMID: 37188984.
- X Li et al., Funct Integr Genomics (2023). PMID: 37188931.