Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains

Salmonella enterica Typhimurium is a serious pathogen that is involved in human nontyphoidal infections. Tackling Typhimurium infections is difficult due to the species' dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN). While traditional biomolecular methods provide characterizations of specific regulators, it is laborious to construct the global TRN structure from this bottom-up approach. Here, we used a machine learning technique to understand the transcriptional signatures of S. enterica Typhimurium from the top down, as a whole and in individual strains. Furthermore, we conducted cross-strain comparison of 6 strains in serovar Typhimurium to investigate similarities and differences in their TRNs with pan-genomic analysis. By decomposing all the publicly available RNA-Seq data of Typhimurium with independent component analysis (ICA), we obtained over 400 independently modulated sets of genes, called iModulons. Through analysis of these iModulons, we 1) discover three transport iModulons linked to antibiotic resistance, 2) describe concerted responses to cationic antimicrobial peptides (CAMPs), 3) uncover evidence towards new regulons, and 4) identify two iModulons linked to bile responses in strain ST4/74. We extend this analysis across the pan-genome to show that strain-specific iModulons 5) reveal different genetic signatures in pathogenicity islands that explain phenotypes and 6) capture the activity of different phages in the studied strains. Using all high-quality publicly-available RNA-Seq data to date, we present a comprehensive, data-driven Typhimurium TRN. It is conceivable that with more high-quality datasets from more strains, the approach used in this study will continue to guide our investigation in understanding the pan-transcriptome of Typhimurium. Interactive dashboards for all gene modules in this project are available at https://imodulondb.org/ to enable browsing for interested researchers.

The interaction of climate history and evolution impacts alpine biodiversity assembly differently in freshwater and on land

Quaternary climate fluctuations can affect biodiversity assembly through speciation in two non-mutually-exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation during ice-free periods. Here we detected biogeographic and genetic signatures associated with both mechanisms in the generation of the European Alps biodiversity. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age, and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome may be attributable to a faster range expansion of these taxa after glacial retreats, though fewer stable environments may also have contributed to differences between terrestrial areas and lakes. The high proportion of young, endemic species make the Alps vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct histories.

Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.

Host-associated phages disperse across the extraterrestrial analogue Antarctica

Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples especially from polar regions yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating or prophages) across the Antarctic continent can be tracked via their genetic signatures and benefits our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria including Ralstonia spp. Betaproteobacteria of this genus have been found in Antarctic snow as well as on space-related equipment. We reconstructed the complete genome of a temperate phage with near-complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which appeared in seawater from the Western Antarctic Peninsula with up to 5538 km to the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp. disperse over long distances despite harsh conditions of the Antarctic continent. Due to the additional identification of 14 phages associated with two R. pickettii draft genomes isolated from space equipment, we conclude implications for the spread of biological contaminants in extraterrestrial settings.

Dedifferentiated Melanoma: A Diagnostic Histological Pitfall! Review of the Literature with Case Presentation

Dedifferentiated melanoma is a particular form of malignant melanoma with a progressive worsening of the patient’s clinical outcome. It is well known that melanoma can assume different histo-morphological patterns, to which specific genetic signatures correspond, sometimes but not always. In this review we address the diagnostic difficulties in correctly recognizing this entity, discuss the major differential diagnoses of interest to the dermatopathologist, and conduct a review of the literature with particular attention and emphasis on the latest molecular discoveries regarding the dedifferentiation/undifferentiation mechanism and more advanced therapeutic approaches.

Malignant Melanoma of the Genitourinary System

Introduction/Objective Malignant melanoma (MM) of mucosal membranes (excluding anus and head and neck) is a rare but aggressive disease with poor outcome. There is little information available on the development mechanism, risk factors, and management of this tumor, mainly due to the low number of cases. Methods/Case Report We performed a comprehensive literature review on mucosal MM (between 1970-2020). We identified 52 papers reporting 242 patients with primary genitourinary melanomas (limited to urothelium, vagina and cervix). A comprehensive review of the demographics, stage, treatment and survival was performed. Results (if a Case Study enter NA) The demographics are provided in Table 1. In 204 cases, lesions were located in the urothelium (urethra: 202, bladder: 2) followed by 34 in the vagina and 4 in uterine cervix. None of the cases had any other known primary source of MM. Molecular studies in a subset of cases revealed alterations in c-KIT, NRAS, BRAF (non-V600E and V600E), TP53 and NF1 (Table 2). Tumor stage was provided in a few (n=10) cases (stage 1=1, stage 2=1, stage 3=3 & stage 4=5). 3 patients had distant metastasis (brain, retroperitoneal and inguinal lymph nodes). Treatment data was available in 178 cases. 177 patients were managed by surgery. In addition to surgery, 10 received chemotherapy, 7 received immunotherapy and chemotherapy, 2 received chemoradiation, 1 received immunotherapy and 1 received radiotherapy. In 43 patients, the treatment regimen was not provided. The outcome was available in 178 cases (range of follow up between 3-97 months), showing 15 deaths of disease. Median survival based on available information in 28 patients was 82% (5-year survival). Table 1 legend: Demographics of genitourinary malignant melanoma cases. Table 2 legend: Frequency of molecular alterations in genitourinary malignant melanoma. Conclusion Similarities in genetic signatures of mucosal and skin MM suggest similar mechanism of development; however, unlike skin melanoma, there is less BRAF mutation and more of PI3K/AKT/mTOR pathway alterations in mucosal MM. Prolonged administration of chemotherapy (i.e., methotrexate) and immune-modulating agents (i.e., natalizumab) may be a risk factor. In light of absence of a definite adjuvant therapy, tumor stage at the time of diagnosis and proper surgical removal have central role in the prognosis and survival of patients.

Experimental Evolution of West Nile Virus at Higher Temperatures Facilitates Broad Adaptation and Increased Genetic Diversity

West Nile virus (WNV, Flaviviridae, Flavivirus) is a mosquito-borne flavivirus introduced to North America in 1999. Since 1999, the Earth’s average temperature has increased by 0.6 °C. Mosquitoes are ectothermic organisms, reliant on environmental heat sources. Temperature impacts vector–virus interactions which directly influence arbovirus transmission. RNA viral replication is highly error-prone and increasing temperature could further increase replication rates, mutation frequencies, and evolutionary rates. The impact of temperature on arbovirus evolutionary trajectories and fitness landscapes has yet to be sufficiently studied. To investigate how temperature impacts the rate and extent of WNV evolution in mosquito cells, WNV was experimentally passaged 12 times in Culex tarsalis cells, at 25 °C and 30 °C. Full-genome deep sequencing was used to compare genetic signatures during passage, and replicative fitness was evaluated before and after passage at each temperature. Our results suggest adaptive potential at both temperatures, with unique temperature-dependent and lineage-specific genetic signatures. Further, higher temperature passage was associated with significantly increased replicative fitness at both temperatures and increases in nonsynonymous mutations. Together, these data indicate that if similar selective pressures exist in natural systems, increases in temperature could accelerate emergence of high-fitness strains with greater phenotypic plasticity.