The December 2022 EMM Editor’s Choice Article is “A cross-sectional clinical study in women to investigate possible genotoxicity and hematological abnormalities related to the use of black cohosh botanical dietary supplements” (https://onlinelibrary.wiley.com/doi/10.1002/em.22516) by Smith-Roe SL, Garantziotis S, Church RL, Bemis JC, Torous DK, Shepard KG, Hobbs CA, Waidyanatha S, Mutlu E, Shockley KR, Kissling GE, McBride SJ, Xie G, Cristy T, Pierfelice J, Witt KL. 

The July 2022 EMM Editor’s Choice article is “A comprehensive literature review and meta-analysis of the prevalence of pan-cancer BRCA mutations, homologous recombination repair gene mutations, and homologous recombination deficiencies,” (https://onlinelibrary.wiley.com/doi/10.1002/em.22505) by Changxia Shao,  Jun Wan,  Fred C. Lam,  Huilin Tang,  Andrew R. Marley,  Yiqing Song,  Chelsey Miller,  Madeline Brown,  Jiali Han, and Gboyega Adeboyeje.

It is well known that cellular DNA damage detection and repair is critical in the maintenance of genomic stability during cellular division. One particularly vital pathway in DNA damage repair is the homologous recombination repair (HRR) pathway. BRCA1 and BRCA2 proteins are recruited to the damaged replication fork sites leading to a cascade of events resulting in the recruitment of further checkpoint signaling proteins and repair kinases. Mutations in the BRCA proteins are known to play a role in the development of cancers such as breast and ovarian. Fortunately, data from recent clinical trials have reported that BRCA1/2 are sensitive to enzyme poly-ADP ribose polymerase 1 (PARP1), leading to the FDA approval of six PARP inhibitors for the treatment of BRCA1/2 mutant cancers. Such a discovery has led to the development of biomarkers that can predict homologous recombination deficiency (HRD) in BRCA wild-type tumors in hopes of expanding clinical use of PARP inhibitors (PARPi). Therefore, the authors have performed a comprehensive review providing information on the prevalence of germline and somatic BRCA mutations, HRR mutations and HRD positivity in patients.

The authors identified studies of interest by first filtering for articles on patients possessing solid tumors containing germline BRCA1/2 mutations (gBRCA1/2m), somatic BRCA1/2 mutations (sBRCA1/2m), HRR gene mutations, or HRD positivity reported in the past 10 years. Search engines utilized were OVID, MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and Cochrane Reviews. Once studies were collected, meta-analyses were conducted to evaluate the prevalence and confidence intervals of BRCA1/2 mutations and HRD positivity.

The authors search yielded 265 publications on BRCA1/2 mutation prevalence, 189 on HRR gene mutation prevalence, and 7 on HRD positivity prevalence. The prevalences of gBRCA1m and BRCA2m were 7.8% and 5.7% for breast cancer, 13.5% and 6.6% for ovarian cancer, 0.5% and 3.5% for prostate cancer, and1.1% and 4.1% for pancreatic cancer, respectively. The prevalences of sBRCA1m and BRCA2m were 3.4% and 2.7% for breast cancer, 4.7% and 2.9% for ovarian cancer, 5.7% and 3.2% for prostate cancer, and 1.2% and 2.9% for pancreatic cancer, respectively. The authors were able to identify 180 studies that evaluated mutations in one or more HRR genes other than BRCA1/2, and reported the prevalence of these mutations as such: ATM at 5.2%, CHEK2 at 1.6% and PALB2 showing the highest prevalence at 0.9%. The seven studies that evaluated HRD positivity in breast, ovarian, and prostate cancer patients documented the prevalence to be 56% overall (95% CI=48%–64%).

This comprehensive literature review and meta-analysis documents the prevalence of BRCA1/2and HRR pathway gene mutations and HRD positivity in multiple cancer types. As there is a need for improvement in precision medicine the authors believe their contribution can be useful, specifically in targeted therapy and chemotherapy selection. With evidence that PARPi provides positive outcomes, in conjunction with platinum agents, standardized biomarker assays could provide to be beneficial in discovering novel combination therapies to improve outcomes for cancer patients.

Of time, space, and linear models

The April 2022 EMM Editor’s Choice article is “In vitro relationships of galactic cosmic radiation and epigenetic clocks in human bronchial epithelial cells,” (https://doi.org/10.1002/em.22483) by Jamaji C. Nwanaji-Enwerem, Philippe Boileau, Andres Cardenas.

Science fiction writers such as Isaac Azimov may have led us to forget how inhospitable space really is. Outside of the protective cocoon of the Earth’s magnetosphere, protons and ions fly through space near the speed of light, tearing through shielding and shredding DNA in its track.

In their recent paper, Nwanaji-Enwerem and colleagues attempted to quantify the genomic wear-and-tear effect of being exposed to space radiation (Nwanaji-Enwerem et al. 2022). The question the authors asked is: “How much faster do cells age when exposed to space radiation?” An elegant and straightforward question, that leads to a not-so-straightforward answer.

The authors used a publicly available dataset from human cells exposed to space-relevant types of radiation. Specifically, they looked at the most plastic, modifiable part of the genome: the epigenome. Except for rare mutations occurring in a stochastic manner, the DNA sequence is stable through time. The methylation marks providing context to the sequence, however, are highly responsive to their environment. The authors used three different algorithms using hundreds of epigenetic DNA methylation alterations previously validated to reflect cellular aging, what are called “epigenetic clocks.”

So: more radiation, more aging? For one of these three clocks, the answer was a statistically robust “yes.” That clock, the epiTOC2 model, effectively tracks aging through estimates of cell divisions. However, that is also where the clear answers stop. The epiTOC2 model could only demonstrated significant increases in aging for 56Fe particles, the most potent type of radiation. In the case of X-rays and 28Si radiation, no such association was demonstrated. A second and third clock which track aging in cell divisions and days, respectively, did not respond to radiation. Is epiTOC2 a better clock? If so, why would it fail to track the damage due to the two other types of radiation?

In this work, the authors made a very reasonable assumption: more radiation, more aging. They used a linear no-threshold (LNT) model to evaluate the relationship. However, this is not a completely resolved question in radiation biology (Weber and Zanzonico 2017). In fact, many indications point to a non-linear relationship between radiation and biological effects, particularly at low doses. There are at least three other competing models: one where low doses of radiation have larger effects than in the LNT model (hypersensitivity), one where low doses have smaller effects than in the LNT model (threshold), and finally, one where low doses have a beneficial biological effect (hormetic). The lowest dose analyzed in this study is 0.1Gy, which is the poster child for low radiation doses, straight in the middle of that uncertainty zone.

Our scientific tools are infinitely better at describing linear relationships. Personally, Nwanaji-Enwerem and colleagues effectively convinced me that there is a relationship between radiation exposure and aging. But as much as I wish that radiation followed a linear no-threshold model, this study also hints that our best tools are probably a square peg in a round hole when it comes to looking at the relationship between dose and effect.

 

Reference:

Nwanaji-Enwerem, Jamaji C., Philippe Boileau, Jonathan M. Galazka, and Andres Cardenas. 2022. “In Vitro Relationships of Galactic Cosmic Radiation and Epigenetic Clocks in Human Bronchial Epithelial Cells.” Environmental and Molecular Mutagenesis 63 (4): 184–89. https://doi.org/10.1002/em.22483.

Weber, Wolfgang, and Pat Zanzonico. 2017. “The Controversial Linear No-Threshold Model.” Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine 58 (1): 7–8. https://doi.org/10.2967/jnumed.116.182667.

The January 2022 EMM Editor's Choice article is “Human genetic risk of treatment with antiviral nucleoside analog drugs that induce lethal mutagenesis: the special case of molnupiravir" (https://onlinelibrary.wiley.com/doi/ftr/10.1002/em.22471) by Michael D. Waters, Stafford Warren, Claude Hughes, Philip Lewis, Fengyu Zhang.

In this review, the authors propose that the genotoxicity of molnupiravir (MOV), an antiviral with emergency use authorization for COVID-19 treatment, should be further investigated using human-centric methods before final FDA approval. This is based on MOV being considered for a more widespread use for other known and future RNA viral infections as well as base substitution mutagenicity of its active metabolite, β-d-N4-hydroxycytidine (NHC), which is not detected in the usual in vivo assays that mostly reveal clastogenic effects. This is because both MOV and NHC are apparently unique gene mutagens like 5-(2-chloroethyl)-2'-deoxyuridine (CEDU), an antiviral drug which was developed for treatment of herpes simplex infections. [See below --Table 3 from the article]. They support this argument by describing known mechanisms of action observed for other congener nucleoside analogs (NAs) and for NHC reported in the literature.

MOV induces genome catastrophe by lethal mutagenesis in viral genomes and is 100 times more potent than its congener drugs, ribavirin (RBV) and favipiravir (FAV or FPV). Because it’s designed effect is RNA mutagenesis, more work is required to answer whether it is mutagenic to human DNA. To date, there is no satisfactory answer to this because in vivo genotoxicity assays (which are more sensitive to clastogenic compounds) range from negative to equivocal, while a number of in vitro studies signal that MOV and its metabolite, NHC, can cause host DNA mutation.

The authors cover some history of the research on MOV and NHC, as well as congener drugs RBV and FPV. NHC has exhibited DNA mutagenic activity in eukaryotic systems, as have the congeners. While RBV and FPV are mutagenic, they have targeted use in chronic viral diseases such as HIV-AIDS and hepatitis C, where the benefit of this compound outweighs the risk when used under physician care. However, the risk to benefit analysis is altered when considering such drugs for non-chronic viral infections and outpatient use before symptoms develop in a large patient population. The authors describe a study called “MOVe-AHEAD” studying the efficacy of MOV in at-risk nonhospitalized (outpatient) adults and discovered that ≥90% of the people treated had no benefit yet were exposed to the risk of the drug. Quality preclinical safety evaluations, tolerability, and pharmacokinetics should be conducted and perhaps augmented with human error-corrected next generation sequencing (ec-NGS) and the human PIG-A assay before full approval due to the greater patient population targeted and the equivocal genotoxicity results in the body of MOV and NHC research results. The authors conclude that incorporation of ec-NGS studies and PIG-A could provide an unequivocal answer to whether MOV is mutagenic to humans when used as prescribed, thereby aiding the evaluation of this drug for regulatory decisions.