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Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life’s oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O₂, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution.

Most natural populations are affected by seasonal changes in temperature, rainfall, or resource availability. Seasonally fluctuating selection could potentially make a large contribution to maintaining genetic polymorphism in populations. However, previous theory suggests that the conditions for multilocus polymorphism are restrictive. Here, we explore a more general class of models with multilocus seasonally fluctuating selection in diploids. In these models, the multilocus genotype is mapped to fitness in two steps. The first mapping is additive across loci and accounts for the relative contributions of heterozygous and homozygous loci—that is, dominance. The second step uses a nonlinear fitness function to account for the strength of selection and epistasis. Using mathematical analysis and individual-based simulations, we show that stable polymorphism at many loci is possible if currently favored alleles are sufficiently dominant. This general mechanism, which we call “segregation lift,” requires seasonal changes in dominance, a phenomenon that may arise naturally in situations with antagonistic pleiotropy and seasonal changes in the relative importance of traits for fitness. Segregation lift works best under diminishing-returns epistasis, is not affected by problems of genetic load, and is robust to differences in parameters across loci and seasons. Under segregation lift, loci can exhibit conspicuous seasonal allele-frequency fluctuations, but often fluctuations may be small and hard to detect. An important direction for future work is to formally test for segregation lift in empirical data and to quantify its contribution to maintaining genetic variation in natural populations.

Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRAS G12D -driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS–KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer. Using somatic genome editing and Tuba-seq, Tang et al. uncover a previously uncharacterized role for HRAS and NRAS in impairing KRAS–KRAS interaction to suppress lung tumour growth.

Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signaling is incomplete. To uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumor barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumor growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogs interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signaling. Furthermore, HRAS and NRAS mutations identified in KRAS-driven human tumors partially abolished this effect. By comparing the tumor-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogs are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role of the phenomenon we term RAS paralog imbalance in oncogenic KRAS-driven lung cancer.

The hundreds of mitochondrial pseudogenes in the human nuclear genome sequence (numts) constitute an excellent system for studying and dating DNA duplications and insertions. These pseudogenes are associated with many complete mitochondrial genome sequences and through those with a good fossil record. By comparing individual numts with primate and other mammalian mitochondrial genome sequences, we estimate that these numts arose continuously over the last 58 million years. Our pairwise comparisons between numts suggest that most human numts arose from different mitochondrial insertion events and not by DNA duplication within the nuclear genome. The nuclear genome appears to accumulate mtDNA insertions at a rate high enough to predict within-population polymorphism for the presence/absence of many recent mtDNA insertions. Pairwise analysis of numts and their flanking DNA produces an estimate for the DNA duplication rate in humans of 2.2 x 10(-9) per numt per year. Thus, a nucleotide site is about as likely to be involved in a duplication event as it is to change by point substitution. This estimate of the rate of DNA duplication of noncoding DNA is based on sequences that are not in duplication hotspots, and is close to the rate reported for functional genes in other species.

Early childhood infections have been implicated in the development of immune-mediated diseases, such as allergies, asthma, and type 1 diabetes. We set out to investigate the immunomodulatory effects of early viral infections experienced before the age of one year on the peripheral regulatory T cell population (Treg) and circulating cytokines in a birth-cohort study of Estonian and Finnish infants. We show here a temporal association of virus infection with the expression of FOXP3 in regulatory T cells. Infants with rhinovirus infection during the preceding 30 days had a higher FOXP3 expression in Treg cells and decreased levels of several cytokines related to Th1 and Th2 responses in comparison to the children without infections. In contrast, FOXP3 expression was significantly decreased in highly activated (CD4+CD127−/loCD25+FOXP3high) regulatory T cells (TregFOXP3high) in the infants who had enterovirus infection during the preceding 30 or 60 days. After enterovirus infections, the cytokine profile showed an upregulation of Th1- and Th17-related cytokines and a decreased activation of CCL22, which is a chemokine derived from dendritic cells and associated with Th2 deviation. Our results reveal that immunoregulatory mechanisms are up-regulated after rhinovirus infections, while enterovirus infections are associated with activation of proinflammatory pathways and decreased immune regulation.

Background: It is current practice to perform concomitant coronary artery bypass grafting (CABG) in patients with infective endocarditis (IE) who have relevant coronary artery disease (CAD). However, CABG may add complexity to the operation. We aimed to investigate the impact of concomitant CABG on perioperative outcomes in patients undergoing surgery for IE. Methods: We retrospectively used data of surgically treated IE patients between 1994 and 2018 in six German cardiac surgery centers. We performed inverse probability weighting (IPW), multivariable adjustment, chi-square analysis, and Kaplan–Meier survival estimates. Results: CAD was reported in 1242/4917 (25%) patients. Among them, 527 received concomitant CABG. After adjustment for basal characteristics between CABG and no-CABG patients using IPW, concomitant CABG was associated with higher postoperative stroke (26% vs. 21%, p = 0.003) and a trend towards higher postoperative hemodialysis (29% vs. 25%, p = 0.052). Thirty-day mortality was similar in both groups (24% vs. 23%, p = 0.370). Multivariate Cox regression analysis after IPW showed that CABG was not associated with better long-term survival (HR: 1.00, 95% CI: 0.82–1.23, p = 0.998). Conclusion: In endocarditis patients with CAD, adding CABG to valve surgery may be associated with a higher likelihood of postoperative stroke without adding long-term survival benefits. Therefore, in the absence of critical CAD, concomitant CABG may be omitted without impacting outcome. The results are limited due to a lack of data on the severity of CAD, and therefore there is a need for a randomized trial.

PurposeInappropriate implantable cardioverter-defibrillator (ICD) shocks are associated with greater healthcare resource utilization, poorer quality-of-life, and higher mortality. We aimed to investigate the performance of enhanced supraventricular tachycardia (SVT) discrimination algorithms (morphology discrimination, rate stability, and sudden or chamber onset) for reducing inappropriate ICD therapies in patients with ICD/cardiac resynchronization therapy devices.MethodsThis prospective, non-randomized, multicenter study (ReduceIT) study took place at 56 sites across Germany and Estonia. Adults at risk of sudden cardiac death undergoing St. Jude Medical™ ICD or CRT-D implantation were included. The primary endpoint was freedom from inappropriate ICD shock at 12 months and was analyzed in the intention to treat (ITT) and per-protocol population.ResultsOverall, 733 patients (65.9 ± 11.4 years) were included, of which 40.9% and 59.1% received a single- and dual-chamber detection device, respectively. During follow-up (median 11.9 [0–21.6] months), 96.3% of patients experienced no inappropriate therapy (ITT). The sensitivity, specificity, and accuracy for VT/VF were 91.9%, 95.5%, and 94.7%, respectively. In the per-protocol population (n = 620), the proportion of patients free from inappropriate shock at 12 months was 98.4% (n = 610; 95% CI 97.1–99.2%) and exceeded the expected value of 93% (p < 0.0001) which was derived from the rates in the SPICE, ATPonFastVT, and DECREASE studies. A total of 44 patients (6.0%) died during follow-up, 19 deaths were cardiac-related which is consistent with a meta-analysis of EMPIRIC, MADIT-RIT, ADVANCE III, and PROVIDE. Serious device and procedure-related adverse effects occurred in 9.8% of patients.ConclusionsIn ICD/CRT-D devices with advanced SVT discriminators, device programming according to clinical setting and detection chamber significantly reduces the rate of inappropriate ICD shocks without compromising patient safety. The algorithms and settings described herein have particular clinical importance and their employment may be of benefit to ICD recipients.