Mutational profiles in rat gliomas are comparable to a subset of human gliomas

A new analysis of the genetic makeup of rat brain and heart tumors highlights morphological and molecular similarities to those found in humans, according to researchers from the Division of Translational Toxicology. This is the first study demonstrating genetic alterations in rat tumors resulting from life-time exposure to radiofrequency radiation (RFR).

Recent research indicates that exposing rats to RFR over the course of their lifetime can lead to increased incidence of gliomas and cardiac schwannomas. Gliomas are one of the most commonly diagnosed types of brain cancer, whereas cardiac schwannomas are rare tumors that grow around the nerve cells. The relevance of these findings for human health is poorly understood, in part because much remains unknown about the molecular and genetic makeup of these rare cancers in rats.

To address this knowledge gap, the authors designed a rat-specific, targeted next-generation sequencing (NGS) panel based on genes commonly altered in human gliomas. Mutations were examined in 14 gliomas and nine schwannomas that developed due to life-time RFR exposure or spontaneously (only gliomas) due to aging. The identified mutations in rat tumors were compared to the Catalogue of Somatic Mutations in Cancer (COSMIC) to see whether they were genetically similar to human cancers.

The results indicate that rat gliomas are structurally similar to low-grade human gliomas, and that approximately 25% of the genetic mutations in the rat tumors are also altered in human cancer. Interestingly, none of the rat gliomas displayed mutations in the Idh1 or Idh2 genes that are common in human adult grade II/III gliomas and secondary glioblastoma multiforme but instead appear to be wild-type Idh1/Idh2 that are frequent in human primary glioblastoma. These results suggest that there may be unique species-specific differences in mutational profiles and the corresponding morphological features between human and rat gliomas. Additional studies on a greater number of rat tumors using NGS approaches will provide a more comprehensive translational insight into these tumors. According to the authors, these data demonstrate that targeted NGS panels are an important tool to examine the translational relevance of genetic alterations in rodent tumors to human disease. (BR)

Citation: Brooks AM, Vornoli A, Kovi RC, Ton TVT, Xu M, Mashal A, Tibaldi E, Gnudi F, Li JL, Sills RC, Bucher JR, Mandrioli D, Belpoggi F, Pandiri AR. 2024. Genetic profiling of rat gliomas and cardiac schwannomas from life-time radiofrequency radiation exposure study using a targeted next-generation sequencing gene panel. PLoS One 19(1):e0296699.

New method for measuring microbiomes

A general framework called ANCOM-BC2 enables multigroup analysis of compositions of microbiomes, which are collections of microbes, according to NIEHS researchers and their collaborators.

The differential abundance analysis of microbial taxa between two study groups is well-discussed in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison.

To address this need, the researchers proposed a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. The researchers illustrated their methodology through two real datasets. The first example explored the effects of aridity on the soil microbiome, and the second example investigated the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.

ANCOM-BC2 allows researchers to infer patterns in microbial abundance over ordered categories of exposure variables. For example, it allows a researcher to test whether a particular microbe increased (or decreased) in abundance over ordered disease categories (e.g., very healthy to least healthy). According to the authors, this is a unique feature of ANCOM-BC2, because such a methodology for pattern analysis has not been previously discussed in the literature.

The accompanying freely downloadable software package can be accessed through the previously developed software suite by the authors, which includes ANCOM, ANCOM-BC, and SECOM. (JW)

Citation: Lin H, Peddada SD. 2024. Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures. Nat Methods 21(1):83–91.

Innate immunity relies on cholesterol synthesis

Sterol biosynthesis regulates the innate immune response, according to NIEHS researchers and their collaborators. To demonstrate this, they studied Smith-Lemli-Opitz syndrome (SLOS), a rare heritable deficiency of cholesterol due to defective cholesterol biosynthesis.

SLOS is an autosomal recessive, multiple malformation, neurodevelopmental disorder caused by pathological variants of 7-dehydrocholesterol reductase (DHCR7), a cholesterol biosynthesis enzyme. Increased susceptibility to infection has been described but is poorly understood.

Because Toll-like Receptors (TLRs) of the innate immune system are activated in cholesterol-enriched regions of the plasma membrane, the researchers tested whether TLR signaling is defective in SLOS. TLR activation had been proposed to depend on membrane cholesterol, but previous studies had generally manipulated membrane cholesterol using nonselective and nonphysiological chemicals.

To test TLR signaling, the researchers studied dermal fibroblasts and peripheral blood immune cells from individuals with SLOS, complementing this with studies of Dhcr7-deficient mice and cell lines. TLR pro-inflammatory responses were found to be attenuated.

According to the authors, the implications of their findings include the following. First, SLOS provides genetic evidence for the requirement for sterol biosynthesis in innate immunity. Second, the findings suggest that compromised TLR signaling may underlie susceptibility to infection in SLOS. Third, because several widely used medications (e.g., trazodone, aripiprazole) inhibit DHCR7, the researchers propose that patients on these medications may have suppressed TLR responses. The authors suggest that DHCR7 inhibitors should be examined for repurposing as modulators of innate immune overactivation. (JW)

Citation: Gabor K, Mesev EV, Madenspacher J, Meacham JM, Rai P, Moon S, Wassif CA, Shaikh SR, Tucker CJ, Karmaus PW, Bianconi S, Porter FD, Fessler MB. 2024. Sterol biosynthesis regulates TLR signaling and the innate immune response in Smith-Lemli-Opitz syndrome model. J Clin Invest e167633.

How transcription factors achieve exquisite specificity

A protein called CHD4 monitors chromatin interactions and modulates gene regulation by transcription factors, according to NIEHS researchers and their collaborators.

Transcription factors face multiple challenges in establishing new gene regulatory networks during development, in response to physiological or environmental signals, and during in vitro cellular reprogramming. These proteins must find appropriate recognition motifs within the genome, and they also must contend with physical barriers, including chromatin, which is a mixture of DNA and proteins that form chromosomes found in cells. In eukaryotes with large genomes, including humans, transcription factors with short recognition motifs must find the correct loci, and only the correct loci, among the potentially millions of matches to their binding motif.

To explore this topic, the researchers measured the effects of CHD4 depletion in breast cancer cells. As a chromatin remodeling factor, CHD4 is known to regulate gene expression and DNA damage responses and is involved in multiple developmental processes, including neural development and cardiac development.

The results showed that in unchallenged, steady-state breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During transcription factor-driven cellular reprogramming, CHD4 activity is necessary to prevent inappropriate chromatin opening, which results in activation of genes unrelated to reprogramming. The researchers propose that CHD4 acts as a chromatin proofreading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors. (JW)

Citation: Saotome M, Poduval DB, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade PA, Takaku M. 2024. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Res; doi: 10.1093/nar/gkae025 [Online 28 Jan. 2024].

Plasma proteomic signatures of adult asthma

A large-scale proteomics study identified more than 100 plasma proteins associated with asthma in adults, according to NIEHS researchers and their collaborators.

Asthma is a chronic respiratory disease affecting more than 300 million individuals worldwide. The disease is complex and not completely understood. Plasma proteomics is an evolving technique that can both generate biomarkers and provide insights into disease mechanisms.

Toward this goal, the researchers analyzed protein abundance in plasma in nearly 13,000 adults with and without asthma by combining data from two large studies. According to the authors, this is the largest proteomic study of adult asthma to date.

The results revealed 115 of 4,860 proteins were significantly associated with asthma. Multiple signaling pathways related to airway inflammation and pulmonary injury were enriched among these proteins. A proteomic score generated using machine learning provided predictive value for asthma. The researchers demonstrated that the plasma proteome can be used in aggregate to provide prognostic information on asthma status.

In addition to validating previous associations, the researchers identified many novel proteins that could inform development of diagnostic biomarkers and therapeutic targets in asthma management. (JW)

Citation: Smilnak GJ, Lee Y, Chattopadhyay A, Wyss AB, White JD, Sikdar S, Jin J, Grant AJ, Motsinger-Reif AA, Li JL, Lee M, Yu B, London SJ. 2024. Plasma protein signatures of adult asthma. Allergy; doi: 10.1111/all.16000 [Online ahead of print 23 Jan. 2024].