Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.The Gram-negative bacterium Haemophilus influenzae colonizes the human nasopharynx and can cause a spectrum of diseases (1). Members of this species can be separated into those that are encapsulated and those that do not express a capsule, so-called nontypeable H. influenzae (NTHi) (2). Encapsulated strains belong to one of six distinct capsular serotypes (a, b, c, d, e, and f) of which type b strains are notoriously associated with invasive disease (3). NTHi are associated with common pediatric diseases, including otitis media (OM) (4, 5), and with exacerbations of chronic obstructive pulmonary disease (COPD) in adults (6).Although capsule-based vaccines against serotype b strains exist, NTHi vaccine candidates containing outer-membrane proteins have been unsuccessful due to their inability to induce functional antibodies to epitopes representative of the phenotypic variation within the population, resulting in poor coverage against heterologous strains (7–9). To devise containment strategies based on vaccination, it is therefore essential to characterize the population structure of the NTHi strains and their genomic variability. Classification schema based on ribotyping (10), multilocus enzyme electrophoresis (11, 12), and multilocus sequence typing (MLST) (13–15) have shown that isolates of encapsulated H. influenzae could be classified into a small number of monophyletic lineages, with reduced diversity (12, 16) and genetically distinct from NTHi strains, that constitute the vast majority of the circulating population (11). Despite these efforts, there is still a substantial lack of knowledge regarding the structure of the NTHi population, mainly attributable to the impact that homologous recombination has on the evolution of the genomes of this pathogen, which is higher in NTHi compared with capsulated strains (15). So far, data on isolates from carriers and those with disease have shown little correlation between MLST typing and the clinical source or the geographical origin of the strains studied (17).Whole-genome sequencing can be used to characterize the population structure of large collections of isolates of bacterial pathogens (18–20) and to study the microevolution of virulent lineages (21, 22). Here, we use whole-genome sequencing of NTHi isolates of diverse clinical and geographical origin to assess population structure. Analysis of single nucleotide polymorphisms (SNPs) revealed six statistically supported clusters of isolates that correlated with the composition of the accessory genome. Our data lay the foundation for a comprehensive definition of the population structure of NTHi that can underpin the development of strategies to fight NTHi-associated disease.     

Identifying asymptomatic spreaders of antimicrobial-resistant pathogens in hospital settings

Antimicrobial-resistant organisms (AMROs) can colonize people without symptoms for long periods of time, during which these agents can spread unnoticed to other patients in healthcare systems. The accurate identification of asymptomatic spreaders of AMRO in hospital settings is essential for supporting the design of interventions against healthcare-associated infections (HAIs). However, this task remains challenging because of limited observations of colonization and the complicated transmission dynamics occurring within hospitals and the broader community. Here, we study the transmission of methicillin-resistant Staphylococcus aureus (MRSA), a prevalent AMRO, in 66 Swedish hospitals and healthcare facilities with inpatients using a data-driven, agent-based model informed by deidentified real-world hospitalization records. Combining the transmission model, patient-to-patient contact networks, and sparse observations of colonization, we develop and validate an individual-level inference approach that estimates the colonization probability of individual hospitalized patients. For both model-simulated and historical outbreaks, the proposed method supports the more accurate identification of asymptomatic MRSA carriers than other traditional approaches. In addition, in silica control experiments indicate that interventions targeted to inpatients with a high-colonization probability outperform heuristic strategies informed by hospitalization history and contact tracing.

Antimicrobial-resistant (AMR) organisms (AMROs) remain a leading cause of healthcare-associated infections (HAIs) (1–4). Because of a lack of effective treatment and high-mortality rates, the prevalence of existing and emerging drug-resistant agents continues to impose a heavy burden on healthcare systems globally (5). The World Health Organization declared antimicrobial resistance is one of the top 10 global public health threats facing humanity (6). In the United States alone, more than 2.8 million AMR infections occur each year, resulting in over 35,000 deaths (7). In Europe, among participating countries in the European Antimicrobial Resistance Surveillance Network (EARS-Net), 29 of 30 countries reported the occurrence of antimicrobial resistance among all eight bacterial species tracked by the EARS-Net during 2019 (8). The burden of AMR infections is even higher in low- and middle-income countries (9). Currently, five AMROs (carbapenem-resistant Acinetobacter, Candida auris, and Clostridioides difficile; carbapenem-resistant Enterobacteriaceae; and drug-resistant Neisseria gonorrhoeae) are highlighted as urgent threats by the US Centers for Disease Control and Prevention (CDC) (2), with a dozen other agents listed as serious threats, including methicillin-resistant Staphylococcus aureus (MRSA) (10–12).In hospital settings, AMR infections are difficult to eliminate because of the existence of asymptomatic colonization (13–19). While most colonized patients do not experience infections, they can transmit AMROs to other patients and contaminate the environment in healthcare facilities (20). For instance, in two hospitals in the United Kingdom, undetected MRSA carriers were estimated to be the source of 75% of total transmission events in general wards (21). As a result, successful HAI control relies on the accurate and timely identification of asymptomatic AMRO spreaders (22, 23). In practice, however, sparse observations of colonization due to insufficient testing limit our ability to track transmission events, which are typically unobserved. In addition, community importation (24–26) and multiple modes of transmission in hospital [e.g., direct contact transmission (2) and environmental contamination (27, 28)] further complicate the detection of AMRO carriers. Although AMRO colonization in clinical settings has been linked to a number of risk factors, such as recent hospitalization and antibiotic use (29, 30), colonized patients without these risk factors may still be under detected and shed AMROs (31). Without improved identification methods, the asymptomatic carriage of AMROs constitutes a major barrier to effective containment of HAIs.Mathematical modeling has been widely used to investigate and understand the transmission dynamics of AMROs (32–37) and guide the development of intervention measures against HAIs in healthcare systems (22, 23, 38–42). A number of approaches have been developed to estimate population-level transmission characteristics, including nosocomial transmissibility and importation rates from the community (43–46). In addition, several studies have used individual-level observations to infer the origin of a simulated outbreak using a susceptible, infected, and recovered model in a contact network (47–49). Despite these advances, it remains challenging to efficiently estimate patient AMRO colonization probabilities at the individual level using personal diagnostic information on colonization.In this study, we develop and validate an individual-level inference method that supports the improved identification of AMRO carriers and apply this method to an outbreak of MRSA in 66 Swedish hospitals and healthcare facilities with inpatients, henceforth “Swedish healthcare facilities” (Materials and Methods). Using deidentified real-world hospitalization records, we construct an agent-based model in a time-varying patient-to-patient contact network to simulate MRSA transmission within hospitals. To better represent realistic transmission processes, we incorporate components of direct contact transmission, environmental contamination, and community importation into the model dynamics. The inference method propagates information from limited observations of colonized patients across the contact network and provides the estimates of colonization probability for each individual. For both model-generated and historical outbreaks, the proposed method more accurately identifies MRSA colonization than traditional approaches informed by hospitalization history and contract tracing. Additionally, interventions targeted to the inferred, high-probability MRSA carriers yield the greater identification of colonized patients and better control of the transmission in control simulation experiments.     

Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations

Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.

The emergence of human pathogens is one of the most concerning public health topics of modern times (1–4). According to the World Health Organization, over 300 emerging infectious diseases have been reported in the 1940 to 2004 period, a trend that has continued steadily with recent outbreaks of Ebola in West Africa, Cholera in Yemen, and the global pandemic caused by COVID-19 (3–5). Even though classical molecular approaches have advanced our understanding of bacterial pathogenesis, to date, the genetic adaptations and ecological drivers that facilitate selected strains within a species to emerge as pathogens and successfully colonize the human host remain poorly understood. Given the magnitude and complexity of this urgent threat, it is critical to develop tractable organismal model systems and theoretical frameworks that allow us to dissect the molecular adaptations and environmental factors that lead to the emergence of such human pathogens.Vibrio vulnificus, an emergent human pathogen, is one of the leading causes of non-Cholera, Vibrio-associated deaths globally (6). Despite being a natural inhabitant of estuarine, coastal, and brackish waters (7), this flesh-eating bacterium has gained particular notoriety as one of the fastest killing pathogens (8, 9). Humans are typically infected with V. vulnificus through ingestion of contaminated raw seafood or by direct exposure of open wounds to seawater (6). V. vulnificus infections often result in fulminant septicaemia with an alarming mortality rate exceeding 50% (6, 10–13). The bacterium is particularly lethal in some susceptible hosts, such as immunocompromised patients or those with alcohol-associated liver cirrhosis, diabetes mellitus, or hemochromatosis (14). The annual case counts of V. vulnificus infections have steadily increased over the past 20 y in the United States (15). An upsurge in its worldwide distribution over the past three decades, in correlation with climate change, has led to disease outbreaks in regions with no history of V. vulnificus infections (16–18). Furthermore, models predict this trend to continue resulting in a steady expansion of its geographical range and the subsequent increased risk of human infections (16, 19–21).Based on a series of biochemical and phenotypic traits, V. vulnificus strains have been historically classified into three Biotypes (BT): BT1, which is mostly associated with human infections (22, 23), BT2, which is primarily pathogenic to eels (24, 25), and BT3, which is geographically restricted to Israel and possesses hybrid characteristics from BT1 and BT2 (26, 27). In contrast to Vibrio cholerae, in which all strains capable of causing cholera belong to a single clade, genomic comparisons of V. vulnificus reveal a more complex pattern in the distribution of its clinical strains (28–30). Phylogenomic analyses indicate that the population of V. vulnificus is composed of four distinct groups or clusters (Cluster 1 to 4), which largely overlap with the classical BT classification system (23, 26, 28, 31, 32). Our analyses indicate that the two largest clusters, C1 and C2, exhibit high genomic divergence and appear to be speciating (28), with clinical strains from BT1 predominantly belonging to C1 (22, 23), whereas strains from C2 are primarily associated with BT2 (6, 24, 25). C3 is highly clonal and fully overlaps with BT3, and the rare C4 contains only four nonclonal strains and belongs to BT1 (28, 31). Interestingly, despite patients showing conserved clinical symptoms, C1 clinical strains arise from different clades within the cluster, suggesting independent emergence events of this deadly pathogen (28, 31, 32). To date, the unique genetic traits that allow certain C1 strains to cause severe septicemia remain mostly unknown, posing a daunting public health risk as it hinders our ability to detect potentially pathogenic V. vulnificus (33).Recently, using a combination of bioinformatic and phenotypic analyses that surveyed more than 100 strains of V. vulnificus, we determined that V. vulnificus C1 appears to be associated with a unique ecological lifestyle or ecotype (28). Nonetheless, to date, the ecological drivers that lead to the emergence of clinical V. vulnificus C1 and their pathogenic traits remain poorly understood. In order to start untangling the complex in-situ interactions between genotypes and the environment that underlie the emergence of clinical strains, in this study, we recently surveyed a large estuary in eastern Florida, the Indian River Lagoon (IRL), where outbreaks of the disease frequently occur (7, 34). We found endemic populations of V. vulnificus in the estuary and established two sampling locations to study the environmental dynamics of this bacterium in several natural reservoirs such as water, sediment, oysters, and cyanobacteria. Interestingly, the two sampling sites show major differences in the distribution of V. vulnificus clusters. One of them, Feller’s house (Site A), appears to be significantly enriched with C1 strains, whereas in the second sampling site, Shepard Park (Site B), we mostly recovered strains from C2. Genomic analyses of these strains indicate that, despite these major differences in distribution, high recombination rates as well as frequent exchange of mobile genetic elements and virulence factors between these V. vulnificus populations occur. Microdiversity analyses of these genomes revealed unique genomic markers among C1 strains in the form of clinical-associated alleles (CAAs) with a potential direct role in virulence. The isolated V. vulnificus strains are resistant to numerous commonly used antibiotics irrespective of cluster or site of isolation. However, phenotypic analyses indicate that strains from Site A exhibit traits associated with clinical outcomes, including the ability to resist serum and catabolize sialic acid, unlike those from Site B. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution is strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity) revealing how ecosystems might generate selective pressures that facilitate the emergence of specific strains in a population with pathogenic potential.     

A recombinant herpes virus expressing influenza hemagglutinin confers protection and induces antibody-dependent cellular cytotoxicity

Despite widespread yearly vaccination, influenza leads to significant morbidity and mortality across the globe. To make a more broadly protective influenza vaccine, it may be necessary to elicit antibodies that can activate effector functions in immune cells, such as antibody-dependent cellular cytotoxicity (ADCC). There is growing evidence supporting the necessity for ADCC in protection against influenza and herpes simplex virus (HSV), among other infectious diseases. An HSV-2 strain lacking the essential glycoprotein D (gD), was used to create ΔgD-2, which is a highly protective vaccine against lethal HSV-1 and HSV-2 infection in mice. It also elicits high levels of IgG2c antibodies that bind FcγRIV, a receptor that activates ADCC. To make an ADCC-eliciting influenza vaccine, we cloned the hemagglutinin (HA) gene from an H1N1 influenza A strain into the ΔgD-2 HSV vector. Vaccination with ΔgD-2::HA_PR8 was protective against homologous influenza challenge and elicited an antibody response against HA that inhibits hemagglutination (HAI⁺), is predominantly IgG2c, strongly activates FcγRIV, and protects against influenza challenge following passive immunization of naïve mice. Prior exposure of mice to HSV-1, HSV-2, or a replication-defective HSV-2 vaccine (dl5-29) does not reduce protection against influenza by ΔgD-2::HA_PR8. This vaccine also continues to elicit protection against both HSV-1 and HSV-2, including high levels of IgG2c antibodies against HSV-2. Mice lacking the interferon-α/β receptor and mice lacking the interferon-γ receptor were also protected against influenza challenge by ΔgD-2::HA_PR8. Our results suggest that ΔgD-2 can be used as a vaccine vector against other pathogens, while also eliciting protective anti-HSV immunity.

Influenza remains a global health threat. Seasonal strains of influenza A and B cause an estimated 5 million cases of severe infections and 500,000 deaths per year (1). Influenza pandemics have caused even greater morbidity and mortality. During the H1N1 pandemic of 1918 to 1919, 500 million people, approximately one-third of the world’s population at that time, were estimated to have been infected with this strain, leading to 50 million deaths (2). The H1N1 pandemic of 2009 is estimated to have caused up to 575,000 deaths (2). Currently, three types of influenza vaccines are offered annually in the United States: a recombinant virus expressing influenza proteins, chemically inactivated virus, and live attenuated virus (3). Regardless of the vaccine type, multiple strains are included to increase the chances of developing sufficient protection against major circulating influenza strains. However, these vaccines primarily elicit a neutralizing antibody response that is sensitive to changes in the influenza virus due to antigenic drift and shift (4). Antigenic drift results from an accumulation of random mutations in influenza antigens, like hemagglutinin (HA), altering sites recognized by the immune system (4). Influenza A strains can also undergo antigenic shift, whereby two different influenza strains infect the same cell to form a reassortant virus with new antigenic properties (4). Due to limited immunity in the population, these new strains are highly virulent, causing widespread epidemics and disease (4). With antigenic drift and shift, vaccine-mediated protection against circulating strains has been insufficient (5). Influenza vaccines that elicit more robust and long-term protection are therefore needed. Notably, if an influenza vaccine with ≥75% efficacy were to be broadly used in the United States, an estimated 19,500 deaths a year could be prevented and direct healthcare costs reduced by $3.5 billion (6).For many years, efforts to improve influenza vaccines have focused on eliciting an immune response for full, broad protection against both circulating and future strains of the virus. These studies have shown that, in general, neutralizing antibodies are sufficient for homologous protection (7). However, achieving heterologous protection may require more broadly neutralizing antibodies or nonneutralizing antibodies able to activate effector immune cells (5). Previous studies have found that passively transferred nonneutralizing monoclonal antibodies can be potently protective in a mouse influenza challenge model (8–10). Several novel strategies have attempted to generate a nonneutralizing response against influenza. For example, vaccines have been created to specifically target the conserved stem region of HA (11–13).Nonneutralizing antibodies stimulate effector cell mechanisms, including antibody-mediated phagocytosis and antibody-dependent cellular cytotoxicity (ADCC), both of which require activation of the Fcγ receptors (FcγRs) (14). Specific isotypes of IgG antibodies are associated with FcγR modulation and subsequent ADCC activation, including the IgG1 and IgG3 subtypes in humans, as well as IgG2a and IgG2c subtypes in mice (15–19). IgG2a and IgG2c isotypes are functionally equivalent and mouse strain-dependent, with IgG2c present in C57BL/6J mice (20). Recent studies have demonstrated that natural infection by influenza and vaccination elicit nonneutralizing antibodies with effector functions that contribute to protection (5, 9, 21–27). In mouse and nonhuman primate challenge models, ADCC-mediating antibodies have demonstrated protection against both homologous and heterologous influenza challenge (9, 28).Recently, we developed a single-cycle herpes simplex virus (HSV) vaccine that completely protects against vaginal, skin, and ocular challenges by HSV-1 and HSV-2 (29, 30). Protection elicited by this vaccine, designated ΔgD-2 for its lack of the essential glycoprotein D (gD) gene, is transferable via passive infusion of immune sera to naïve wild-type mice but not to mice lacking the Fcγ common chain (30). The immune response elicited by ΔgD-2 primarily elicits nonneutralizing antibodies with high levels of FcγRIV-activating function.We asked whether ΔgD-2 could be used as a vaccine platform to induce broadly protective FcγRIV-activating antibodies against a heterologous antigen, such as influenza HA. In this study, we demonstrate that our recombinant vaccine, ΔgD-2::HA_PR8, elicits protection against influenza with a high proportion of FcγRIV-activating antibodies. Additionally, anticipating the use of ΔgD-2 as a vaccine vector against other pathogens, we tested whether our construct would still be protective in mice lacking interferon (IFN) function. Many humans have inborn errors in their IFN signaling pathways, leading to more lethal outcomes in infection (31). Patients with such deficiencies are disproportionately represented among HSV encephalitis cases and are often diagnosed only after presenting with serious symptoms (32–38). This at-risk population underscores the importance of eliciting protection against HSV in the absence of a functional IFN-α/β response. Additionally, many pathogens, such as dengue virus, require mouse models lacking IFN function, and for ease of testing, an efficacious vaccine should remain functional in these mice (39–41). In this study, we demonstrate that ΔgD-2 is a versatile, immunogenic vaccine vector that provides a strong FcγRIV-activating immune response against heterologous pathogens, while maintaining its protective benefit against HSV, in both wild-type and IFN-deficient mice.     

Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.

Adaptive radiations exhibit extraordinary levels of morphological and ecological diversity (1). Although definitions of adaptive radiation vary (2–7), all center on ecological opportunity as a driver of adaptation and, ultimately, diversification (2, 8–10). Divergent selection, the primary mechanism underlying adaptive radiations, favors extreme phenotypes (11) and selects alleles that confer adaptation to unoccupied or under-utilized ecological niches. Differential adaptation results in divergence and, ultimately, reproductive isolation between populations (12). Adaptive radiations demonstrate the remarkable power of natural selection as a driver of biological diversity and provide excellent systems for studying evolutionary processes involved in diversification and speciation (13).Adaptive radiations on remote oceanic islands are especially interesting, as colonization of remote islands is expected to involve population bottlenecks that restrict genetic variation (14). Adaptive radiations in such settings are especially impressive and even paradoxical, given the generation of high species richness from an initially limited gene pool (15). Several classic examples of adaptive radiation occur on oceanic islands, such as Darwin’s finches from the Galapagos islands (16), anole lizards from the Caribbean islands (9), Hawaiian Drosophilids (17), and Hawaiian silverswords (18), to name a few.Recent advances in genome sequencing and analyses have greatly improved our ability to examine the genetics of speciation and adaptive radiation. By examining sequences of multiple individuals from their natural environment, it has become possible to “catch in the act” the speciation processes between incipient lineages (19). Genomic studies of early stage speciation show that differentiation accumulates in genomic regions that restrict the homogenizing effects of gene flow between incipient species (20). The number, size, and distribution of these genomic regions can shed light on evolutionary factors involved in speciation (19). Regions of high genomic differentiation can also form from evolutionary factors unrelated to speciation, such as linkage associated with recurrent background selection or selective sweeps on shared genomic features (21, 22).Genomic studies of lineages undergoing rapid ecological diversification have begun to reveal the evolutionary mechanisms underlying adaptive radiations. Importantly, these studies highlight the pivotal role of hybridization between populations and the consequent exchange of adaptive alleles that facilitates rapid speciation and the colonization of diverse niches (23–25). Most genomic studies of adaptive radiation involve animal systems, however, in particular, birds and fishes. In plants, genomic studies of adaptive radiation are sparse (26–28), and all examine continent-wide radiations. There are no genomics studies of plant adaptive radiations in geographically restricted systems such as remote islands. Because the eco-evolutionary scenarios associated with adaptive radiations are diverse (5, 29), whether commonalities identified in adaptive radiations in animals (23, 30) are applicable to plants is an open question. For example, the genetic architecture of animal adaptive radiations typically involves differentiation at a small number of genomic regions (31–33). In contrast, the limited insights available for plants suggest a more complex genetic architecture (26).We investigated the evolutionary genomics of adaptive radiation in Metrosideros Banks ex Gaertn. (Myrtaceae) across the Hawaiian Islands. Hawaiian Metrosideros is a landscape-dominant, hypervariable, and highly dispersible group of long-lived (possibly >650 y) (34) woody taxa that are nonrandomly distributed across Hawaii’s heterogeneous landscape, including cooled lava flows, wet forests and bogs, subalpine zones, and riparian zones (35, 36). About 25 taxa or morphotypes are distinguished by vegetative characters ranging from prostate plants that flower a few centimeters above ground to 30-m-tall trees, and leaves range dramatically in size, shape, pubescence, color, and rugosity (35, 37, 38); a majority of these forms are intraspecific varieties or races (provisional varieties) of the abundant species, Metrosideros polymorpha (35, 36, 38). Variation in leaf mass per area within the four Metrosideros taxa on Hawaii Island alone matches that observed for woody species globally (39). Common garden experiments (38, 40–44) and parent–offspring analysis (45) demonstrate heritability of taxon-diagnostic vegetative traits, indicating that taxa are distinct genetic groups and not the result of phenotypic plasticity. Metrosideros taxa display evidence of local adaptation to contrasting environments (46, 47), suggesting ecological divergent selection is responsible for diversification within the group (48). This diversification, which spans the past ∼3.1 to 3.9 million years (49, 50), has occurred despite the group’s high capacity for gene flow by way of showy bird-pollinated flowers and tiny wind-dispersed seeds (36, 51). Lastly, the presence of partial reproductive isolating barriers between taxa is consistent with the early stages of speciation (52). Here, we generated several genomic resources for Hawaiian Metrosideros and used these in population genomics analyses to gain deeper insights into the genomic architecture and evolutionary processes underlying this island adaptive radiation.     

The minor pilin PilV provides a conserved adhesion site throughout the antigenically variable meningococcal type IV pilus

Neisseria meningitidis utilizes type IV pili (T4P) to adhere to and colonize host endothelial cells, a process at the heart of meningococcal invasive diseases leading to meningitis and sepsis. T4P are polymers of an antigenically variable major pilin building block, PilE, plus several core minor pilins that initiate pilus assembly and are thought to be located at the pilus tip. Adhesion of N. meningitidis to human endothelial cells requires both PilE and a conserved noncore minor pilin PilV, but the localization of PilV and its precise role in this process remains to be clarified. Here, we show that both PilE and PilV promote adhesion to endothelial vessels in vivo. The substantial adhesion defect observed for pilV mutants suggests it is the main adhesin. Consistent with this observation, superresolution microscopy showed the abundant distribution of PilV throughout the pilus. We determined the crystal structure of PilV and modeled it within the pilus filament. The small size of PilV causes it to be recessed relative to adjacent PilE subunits, which are dominated by a prominent hypervariable loop. Nonetheless, we identified a conserved surface-exposed adhesive loop on PilV by alanine scanning mutagenesis. Critically, antibodies directed against PilV inhibit N. meningitidis colonization of human skin grafts. These findings explain how N. meningitidis T4P undergo antigenic variation to evade the humoral immune response while maintaining their adhesive function and establish the potential of this highly conserved minor pilin as a vaccine and therapeutic target for the prevention and treatment of N. meningitidis infections.

The human-restricted bacterial pathogen Neisseria meningitidis is a leading cause of meningitis and sepsis worldwide and represents a significant global public health threat (1, 2). N. meningitidis is carried asymptomatically in the protective mucus layer of the throat for 5 to 25% of the population (3–5). In some cases, N. meningitidis disseminates into the bloodstream, an environment to which this bacterium is remarkably well adapted. Meningococci possess a polysaccharide capsule that protects them against complement deposition plus several membrane associated factors that are important for survival, including factor H binding protein and iron uptake systems (6). Critical to N. meningitidis survival in the bloodstream are the type IV pili (T4P), which mediate vascular colonization; nonpiliated meningococci are rapidly cleared from the blood (7–9). T4P are long filamentous appendages displayed peritrichously on the bacterium. The major pilin protein, PilE, is the primary building block of the pilus. This and other surface-displayed N. meningitidis proteins undergo antigenic variation, allowing this pathogen to evade a protective immune response (10–12).T4P are responsible for acute colonization of human blood vessels and are thus essential in establishing invasive meningococcal diseases (7, 9, 13, 14). T4P are helical polymers of the major pilin assembled by the T4P machinery (15, 16). The conserved N terminus of the major pilin is a hydrophobic α-helix that tethers the C-terminal globular domain in the inner membrane prior to pilus assembly and forms a helical array in the core of the intact pilus, displaying the globular domain on the filament surface. Pilus assembly is initiated by a cluster of pilin-like proteins called minor pilins (17–20). These “core” minor pilins are thought to localize to the pilus tip. The major pilin, PilE, is highly conserved in amino acid sequence and structure between N. meningitidis and the urogenital pathogen Neisseria gonorrhoeae with the exception of a hypervariable β-hairpin near the C terminus that is prominent on the pilus surface (21–24). In N. meningitis, PilE has been shown to bind to sialylated N-glycans on the human endothelial cell receptor CD147 (also called EMMPRIN or Basigin) (25) and the β2-adrenergic receptor (26), two membrane proteins that form a heterotrimeric complex with cytoplasmic α-actinin 4 (27).The pathogenic Neisseria possess a set of core minor pilins, PilH (FimT), PilI (PilV), PilJ (PilW), PilK, and PilX, that are encoded within a single gene cluster and prime pilus assembly (28), plus “noncore” minor pilins PilV and ComP, which are encoded elsewhere on the genome. ComP shares the canonical T4P–pilin structure of the major pilin, PilE, with the N-terminal α-helix and C-terminal globular domain (29). ComP is involved in natural transformation of exogenous DNA (30). PilV, which is highly conserved in N. meningitidis isolates (31), participates in adhesion and signaling in host cells (13, 26, 32–34). In N. meningitidis, PilV, like PilE, directly interacts with CD147 and the β2-adrenergic receptor, suggesting that PilV colocalizes with PilE within the T4P filament (13, 26). However, another report concluded that PilV functions exclusively from within the periplasm, fine-tuning pilus surface display to regulate its interactions with host cells (35).The T4P–receptor interaction represents a key step in N. meningitidis adhesion and colonization of endothelial cells in peripheral and brain vasculature and is thus an attractive target for preventive and therapeutic approaches to tackle meningococcal infection. Interfering with piliation prevents N. meningitidis colonization of human endothelial cells and vasculature (36) and improves sepsis outcome in a mouse model grafted with human skin (9). Although both PilE and PilV are involved in adhesion, PilE exhibits considerable amino acid sequence variability in its exposed hypervariable region. This variability contributes to Neisseria immune escape. In contrast, PilV is highly conserved and has been shown to be immunogenic in humans (37). Thus, PilV may prove to be a more promising target than PilE for blocking endothelial cell adhesion. A molecular understanding of this minor pilin with respect to its structure, localization within the pilus, and interactions with host receptors will be valuable in assessing its potential as a therapeutic target. Here, we report the atomic structure of PilV and superresolution microscopy images showing that it is incorporated throughout the N. meningitidis T4P. We identify residues involved in adhesion to host cells and map these onto the PilV structure, modeled within the cryoelectron microscopy (cryoEM)-derived pilus filament structure. Finally, we show that anti-PilV antibodies inhibit meningococcal adhesion in vivo. These data provide insights into PilV-mediated adhesion and suggest that blocking its adherence functions may inhibit N. meningitidis vascular colonization and pathogenesis.     

Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese

The Beijing family is the most successful genotype of Mycobacterium tuberculosis and responsible for more than a quarter of the global tuberculosis epidemic. As the predominant genotype in East Asia, the Beijing family has been emerging in various areas of the world and is often associated with disease outbreaks and antibiotic resistance. Revealing the origin and historical dissemination of this strain family is important for understanding its current global success. Here we characterized the global diversity of this family based on whole-genome sequences of 358 Beijing strains. We show that the Beijing strains endemic in East Asia are genetically diverse, whereas the globally emerging strains mostly belong to a more homogenous subtype known as “modern” Beijing. Phylogeographic and coalescent analyses indicate that the Beijing family most likely emerged around 30,000 y ago in southern East Asia, and accompanied the early colonization by modern humans in this area. By combining the genomic data and genotyping result of 1,793 strains from across China, we found the “modern” Beijing sublineage experienced massive expansions in northern China during the Neolithic era and subsequently spread to other regions following the migration of Han Chinese. Our results support a parallel evolution of the Beijing family and modern humans in East Asia. The dominance of the “modern” Beijing sublineage in East Asia and its recent global emergence are most likely driven by its hypervirulence, which might reflect adaption to increased human population densities linked to the agricultural transition in northern China.Tuberculosis has plagued human beings since ancient times and remains a leading cause of global morbidity and mortality. The causative agent of human tuberculosis is the Mycobacterium tuberculosis complex (MTBC), a group of organisms that harbor little genetic diversity compared with other bacteria (1). MTBC most likely originated in Africa, although its age is being debated (2–4). The human-adapted MTBC is highly clonal and is classified into seven main phylogenetic groups, designated lineage 1 through lineage 7 (2). These seven lineages show strong biogeographic associations that have been proposed to result from codiversification with different human populations (2, 5). Lineage 2 that dominates in East Asia is one of the most successful MTBC variants; more than a quarter of the global tuberculosis epidemic is caused by this lineage (6, 7). Lineage 2 contains strains that mostly belong to the so-called Beijing family (8, 9). This strain family has attracted great attentions due to its global emergence in recent decades (6, 7, 10–12), its tendency to cause disease outbreak (13–17), and its association with antibiotic resistance (12, 18). Experimental and clinical evidences suggest a hypervirulent phenotype of Beijing strains (12, 19), and a higher mutation rate compared with other strains (20).According to genotyping data from previous molecular-epidemiology studies, most Beijing strains from widespread geographic areas showed a remarkable degree of genetic similarity (6, 21), suggesting this strain family might have emerged from recent expansions. It was hypothesized that vaccination with Bacille Calmette Guerin (bacillus Calmette–Guérin) that has been widely implemented in East Asian countries might be the force driving the dominance of this strain family in this area (21). Moreover, the global emergence of the Beijing family may have been due to its hypervirulence and association with drug resistance (7, 18). However, there were discrepant results regarding the relative protective effect of bacillus Calmette–Guérin vaccination against Beijing strains from animal infection experiments (19), and many epidemiological studies failed to find any association between bacillus Calmette–Guérin vaccination and Beijing strains (22–25). The link between drug resistance and the Beijing family has primarily been observed in regions where this family has emerged recently (e.g., Cuba, South Africa, countries of the former Soviet Union) but not in East Asian, where the Beijing family has been endemic for a long time (18, 26). Furthermore, more recent studies indicate that the expansion of the Beijing family may have started long before the introduction of vaccination and antibiotic treatment (2, 3, 27).With the increased availability of genotyping data, the Beijing strains were proved more heterogeneous than initially estimated, and several Beijing sublineages have been identified (28–31). However, a full understanding of the genetic diversity of Beijing family is constrained by the low amount of nucleotide variation (8, 32). Whole-genome sequencing provides an ideal tool to study the genetic diversity of MTBC, and new insights into the origin and evolution of MTBC have been gained (2, 4, 20, 33–35). The genomic diversity of Beijing family was initially studied in a most recent study, in which a general East Asian origin and recent expansions of this strain family were suggested (36). However, the details about the origin and primary dissemination of Beijing family remain unclear. Answering of these questions is important to better understand the virulence of this lineage and its global success. Here, we combined whole-genome sequencing of key strains with detailed single nucleotide polymorphism (SNP) typing of a large collection of clinical MTBC strains isolated from across China. Our results strongly support a southern East Asian origin of the MTBC Beijing family and suggest a parallel evolution of this family with modern humans in East Asia during the last 30,000 y.     

Physical evidence of predatory behavior in Tyrannosaurus rex

Feeding strategies of the large theropod, Tyrannosaurus rex, either as a predator or a scavenger, have been a topic of debate previously compromised by lack of definitive physical evidence. Tooth drag and bone puncture marks have been documented on suggested prey items, but are often difficult to attribute to a specific theropod. Further, postmortem damage cannot be distinguished from intravital occurrences, unless evidence of healing is present. Here we report definitive evidence of predation by T. rex: a tooth crown embedded in a hadrosaurid caudal centrum, surrounded by healed bone growth. This indicates that the prey escaped and lived for some time after the injury, providing direct evidence of predatory behavior by T. rex. The two traumatically fused hadrosaur vertebrae partially enclosing a T. rex tooth were discovered in the Hell Creek Formation of South Dakota.One of the most daunting tasks of paleontology is inferring the behavior and feeding habits of extinct organisms. Accurate reconstruction of the lifestyle of extinct animals is dependent on the fossil evidence and its interpretation is most confidently predicated on analogy with modern counterparts (1–6). This challenge to understanding the lifestyle of extinct animals is exemplified by the controversy over the feeding behavior of the Late Cretaceous theropod Tyrannosaurus rex (3, 7–17). Although predation and scavenging have often been suggested as distinct feeding behavior alternatives (3, 7–9, 11–17), these terms merit semantic clarification. In this study, predation is considered a subset of feeding behavior, by which any species kills what it eats. Although the term “predator” is used to distinguish such animals from obligate scavengers, it does not imply that the animal did not also scavenge.Ancient diets can be readily reconstructed on the basis of the available evidence, although their derivation (e.g., predation or scavenging behavior) often remains elusive. Speculation as to dinosaur predation has ranged from inferences based on skeletal morphology, ichnofossils such as bite marks, coprolites, stomach contents, and trackways and, by more rarely, direct predator–prey skeletal associations (3, 4, 18–23).Direct evidence of predation in nonavian dinosaurs other than tyrannosaurids has been observed in rare instances, such as the Deinonychus–Tenontosaurus kill site of the Cloverly Formation where the remains of both were found in close association along with shed teeth (9, 24), and the “fighting dinosaurs” from the Gobi Desert, in which a Velociraptor and Protoceratops were found locked in mortal combat (9, 17). The evidence on tyrannosaurids is more limited. Putative stomach contents, such as partially digested juvenile hadrosaur bones, have been reported in association with tyrannosaurid remains (3, 12, 18). This latter instance only represents physical evidence of the last items consumed before the animal’s death, an indicator of diet but not behavior.Mass death assemblages of ornithischians frequently preserve shed theropod teeth (6, 22, 24). Lockley et al. (23) suggest such shed teeth are evidence of scavenging behavior. It is widely argued that T. rex procured food through obligate scavenging rather than hunting (11, 14, 25–27) despite the fact that there is currently no modern analog for such a large bodied obligate scavenger (26). Horner (25) argued that T. rex was too slow to pursue and capture prey items (14) and that large theropods procured food solely through scavenging, rather than hunting (11, 25). Horner also suggested that the enlarged olfactory lobes in T.rex were characteristic of scavengers (25). More recent studies (28, 29) determined the olfactory lobes of modern birds are “poorly developed,” inferring that enlarged olfactory lobes in T. rex are actually a secondary adaptation for predation navigation “to track mobile, dispersed prey” (30). T. rex has a calculated bite force stronger than that of any other terrestrial predator (7), between 35,000 and 57,000 Newtons (30, 31), and possible ambulatory speeds between 20 and 40 kph (7, 15, 16), documenting that it had the capability to pursue and kill prey items.Healed injuries on potential prey animals provide the most unequivocal evidence of survival of a traumatic event (e.g., predation attempt) (3, 32, 33), and several reports attribute such damage to T. rex (4, 17, 19, 20). These include broken and healed proximal caudal vertebral dorsal spines in Edmontosaurus (17) and healed cranial lesions in Triceratops (4, 19). Although the presence of healed injuries demonstrates that an animal lived long enough after the attack to create new bone at the site of the damage (a rare occurrence in the fossil record) (19), the healing usually obliterates any clear signature linking the injury to a specific predator. Bite traces (e.g., raking tooth marks on bone and puncture wounds in the bones of possible prey animals) attributed to T. rex (2, 4, 19) are ambiguous, because the damage inflicted upon an animal during and after a successful hunt mirrors feeding during scavenging. This makes distinction between the two modes of food acquisition virtually impossible with such evidence (3, 34–38).Tooth marks, reported from dinosaur bone-bearing strata worldwide (e.g., 2–4, 8, 19, 20, 39, 40), are further direct evidence of theropod feeding behavior, attributed by some to specific theropod groups (2, 4, 19, 20). Happ (19) and Carpenter (17) identified theropods to family and genus by matching spaces to parallel marks (traces) with intertooth distance. Happ (19) described opposing conical depressions on a left supraorbital Triceratops horn that was missing its distal third (tip), attributing them to a bite by either a T. rex or a crocodilian. Happ (19) stated that the spacing of the parallel marks present on the left squamosal of the same individual matched the intertooth distance of tyrannosaurids. The presence of periosteal reaction documents healing. This contrasts with the report by Farlow and Holtz (3) and again by Hone and Rauhut (20) of the same Hypacrosaurus fibula containing a superficially embedded theropod tooth. Absence of bone reaction precludes confident attribution to predation.Two coalesced hadrosaur (compare with Edmontosaurus annectens) caudal vertebrae were discovered in the Hell Creek Formation of Harding County, South Dakota (40). Archosaur fauna identified in this site include crocodiles, dinosaurs, and birds (41). Physical evidence of dental penetration and extensive infection (osteomylitis) of the fused vertebral centra and healing (bone overgrowth) document an unsuccessful attack by a large predator. A tooth crown was discovered within the wound, permitting identification of the predator as T. rex. This is unambiguous evidence that T. rex was an active predator, fulfilling the criteria that Farlow and Holtz (3) advanced. As T. rex comprises between 1% and 16% of the Upper Cretaceous dinosaurian fauna in Western North America (41–45), its status as a predator or obligate scavenger is nontrivial and could have significant implications for paleoecological reconstructions of that time period. The present contribution provides unique information demonstrating the ecological role for T. rex as that of an active predator. Despite this documentation of predatory behavior by T. rex, we do not make the argument that T. rex was an obligate predator. Like most modern large predators (27, 45) it almost certainly did also scavenge carcasses (9, 16).     

Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection

Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug resistance profiles. Said differences usually emerge through de novo mutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ∼5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host–pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.

The Mycobacterium tuberculosis complex (MTBC) is a genetically monomorphic group of bacteria (1, 2) whose members cause tuberculosis in humans and animals. The MTBC comprises both human-associated (L1, L2, L3, L4, L5, L6, L7, L8, and L9) and animal-associated (A1, A2, A3, and A4) clades (3–7). Due to the absence of horizontal gene transfer, plasmids, and measurable recombination among strains and other species (8–10), chromosomal mutations represent the source of MTBC genetic diversity. The maximum genetic distance between any two MTBC strains is around 2,500 single-nucleotide polymorphisms (SNPs). Strikingly, studies have highlighted large phenotypic differences between strains involving traits like gene expression, drug resistance, transmissibility, and immune response, despite this limited variation. In some cases, the mutations driving phenotypic differences have been identified—for example, nonsynonymous variants in genes, such as rpoB, katG, or gyrA, cause drug-resistant phenotypes (11–13). Furthermore, single mutations in regulatory elements can induce alterations to downstream gene expression, which can foster differential virulence characteristics (14, 15). Finally, specific gene mutations may affect transmission (9), host tropism within the complex (16), and the host immune response (17). However, many of the genomic determinants of these phenotypes remain elusive, despite robust evidence that they are driven by genetic differences between strains (18, 19).Several types of evolutionary forces play crucial roles in the fixation of mutations in bacterial populations. Previous research has provided evidence for the ongoing positive selection of specific genes and regions (9, 20–23), while other studies have reported ongoing purifying selection of specific genomic regions, especially in epitopes and essential genes (24). Additionally, there exists some evidence that genetic drift may have significant functional and evolutionary consequences (25).Detecting selection in MTBC at the genome-wide level remains a challenging task due to limited genetic diversity. The significant accumulation of nonsynonymous substitutions has been previously used to characterize patterns of mutation accumulation in large categories of genes (24, 26); however, these studies employed a limited number of strains. Of note, the number of MTBC sequences has undergone a recent and rapid expansion, with studies involving hundreds to thousands of strains. The large number of available sequences has allowed, for example, the estimation of the ratio of nonsynonymous to synonymous substitutions (dN/dS) signatures in more than 10,000 strains (27), thereby allowing the identification of targets of selection with some probably related to host–pathogen interactions. Host–pathogen interaction signals are specially challenging as they are likely obscured by the force exerted by antimicrobial therapies. Weaker signals are also expected in genes related to second-line drugs related to the relative underuse of related treatments and the low abundance of associated resistant strains in genome databases (28).We reasoned that to detect signs of selection, we should focus on when and/or where they occurred in the phylogenetic tree instead of averaging signs across the phylogeny. In this study, we developed a methodology to study temporal signs of selection in MTBC genes and identified positive selection in a larger number of genes than previously described. This allowed the identification of past and currently unknown players in the MTBC evolution, particularly two-component systems (2CSs), related to host adaptation and second-line drug resistance. This methodology can be applied to other tuberculosis settings to explore signs of selection associated with changing selective pressures and could be extremely useful to unravel hidden details in the evolution of other human pathogens.     

miR-182 targeting reprograms tumor-associated macrophages and limits breast cancer progression

The protumor roles of alternatively activated (M2) tumor-associated macrophages (TAMs) have been well established, and macrophage reprogramming is an important therapeutic goal. However, the mechanisms of TAM polarization remain incompletely understood, and effective strategies for macrophage targeting are lacking. Here, we show that miR-182 in macrophages mediates tumor-induced M2 polarization and can be targeted for therapeutic macrophage reprogramming. Constitutive miR-182 knockout in host mice and conditional knockout in macrophages impair M2-like TAMs and breast tumor development. Targeted depletion of macrophages in mice blocks the effect of miR-182 deficiency in tumor progression while reconstitution of miR-182-expressing macrophages promotes tumor growth. Mechanistically, cancer cells induce miR-182 expression in macrophages by TGFβ signaling, and miR-182 directly suppresses TLR4, leading to NFκb inactivation and M2 polarization of TAMs. Importantly, therapeutic delivery of antagomiR-182 with cationized mannan-modified extracellular vesicles effectively targets macrophages, leading to miR-182 inhibition, macrophage reprogramming, and tumor suppression in multiple breast cancer models of mice. Overall, our findings reveal a crucial TGFβ/miR-182/TLR4 axis for TAM polarization and provide rationale for RNA-based therapeutics of TAM targeting in cancer.

It is well known that the nonmalignant stromal components in tumors play pivotal roles in tumor progression and therapeutic responses (1, 2). Macrophages are a major component of tumor microenvironment and display considerable phenotypic plasticity in their effects toward tumor progression (3–5). Classically activated (M1) macrophages often exert direct tumor cytotoxic effects or induce antitumor immune responses by helping present tumor-related antigens (6, 7). In contrast, tumoral cues can polarize macrophages toward alternative activation with immunosuppressive M2 properties (6–8). Numerous studies have firmly established the protumor effects of M2-like tumor-associated macrophages (TAMs) and the association of TAMs with poor prognosis of human cancer (9–11). However, how tumors induce the coordinated molecular and phenotypic changes in TAMs for M2 polarization remains incompletely understood, impeding the designing of TAM-targeting strategies for cancer intervention. In addition, drug delivery also represents a hurdle for therapeutic macrophage reprogramming.Noncoding RNAs, including microRNAs, have been shown to play vital roles in various pathological processes of cancer (12). The microRNA miR-182 has been implicated in various developmental processes and disease conditions (13–15). Particularly, it receives extensive attention in cancer studies. Prevalent chromosomal amplification of miR-182 locus and up-regulation of its expression in tumors have been observed in numerous cancer types including breast cancer, gastric cancer, lung adenocarcinoma, colorectal adenocarcinoma, ovarian carcinoma, and melanoma (16–21). miR-182 expression is also linked to higher risk of metastasis and shorter survival of patients (20, 22–24). Functional studies showed that miR-182 expression in cancer cells plays vital roles in various aspects of cancer malignancy, including tumor proliferation (25–29), migration (30, 31), invasion (16, 32, 33), epithelial-mesenchymal transition (34–36), metastasis (21, 37, 38), stemness (30, 39, 40), and therapy resistance (41, 42). A number of target genes, including FOXO1/3 (18, 21, 43–45), CYLD (46), CADM1 (47), BRCA1 (27, 48), MTSS1 (34), PDK4 (49), and SMAD7 (35), were reported to be suppressed by miR-182 in cancer cells. Our previous work also proved that tumoral miR-182 regulates lipogenesis in lung adenocarcinoma and promotes metastasis of breast cancer (34, 35, 49). Although miR-182 was established as an important regulator of cancer cell malignancy, previous studies were limited, with analyses of miR-182 in cultured cancer cells and transplanted tumors. Thus, the consequences of miR-182 regulation in physiologically relevant tumor models, such as genetically modified mice, have not been shown. More importantly, whether miR-182 also plays a role in tumor microenvironmental cell components is unknown.In this study, we show that miR-182 expression in macrophages can be induced by breast cancer cells and regulates TAM polarization in various tumor models of mice. In addition, miR-182 inhibition with TAM-targeting exosomes demonstrates promising efficacy for cancer treatment.     

From the Cover: Canine sexual dimorphism in Ardipithecus ramidus was nearly human-like

Body and canine size dimorphism in fossils inform sociobehavioral hypotheses on human evolution and have been of interest since Darwin’s famous reflections on the subject. Here, we assemble a large dataset of fossil canines of the human clade, including all available Ardipithecus ramidus fossils recovered from the Middle Awash and Gona research areas in Ethiopia, and systematically examine canine dimorphism through evolutionary time. In particular, we apply a Bayesian probabilistic method that reduces bias when estimating weak and moderate levels of dimorphism. Our results show that Ar. ramidus canine dimorphism was significantly weaker than in the bonobo, the least dimorphic and behaviorally least aggressive among extant great apes. Average male-to-female size ratios of the canine in Ar. ramidus are estimated as 1.06 and 1.13 in the upper and lower canines, respectively, within modern human population ranges of variation. The slightly greater magnitude of canine size dimorphism in the lower than in the upper canines of Ar. ramidus appears to be shared with early Australopithecus, suggesting that male canine reduction was initially more advanced in the behaviorally important upper canine. The available fossil evidence suggests a drastic size reduction of the male canine prior to Ar. ramidus and the earliest known members of the human clade, with little change in canine dimorphism levels thereafter. This evolutionary pattern indicates a profound behavioral shift associated with comparatively weak levels of male aggression early in human evolution, a pattern that was subsequently shared by Australopithecus and Homo.

A small canine tooth with little sexual dimorphism is a well-known hallmark of the human condition. The small and relatively nonprojecting deciduous canine of the first known fossil of Australopithecus, the Taung child skull, was a key feature used by Raymond Dart for his inference that the fossil represented an early stage of human evolution (1). However, recovery of additional Australopithecus fossils led to the canine of Australopithecus africanus to be characterized as large (compared to that of humans or “robust australopithecines”) and its morphology primitive, based on a projecting main cusp and crown structures lacking or hardly expressed in Homo (2). Later, the perception of a large and primitive canine was enhanced by the discovery and recognition of Australopithecus afarensis and Australopithecus anamensis (3–8), the latter species extending back in time to 4.2 million years ago (Ma). Although assessments of canine size variation and sexual dimorphism in Au. afarensis were hampered by limited sample sizes (9, 10), some suggested that the species had a more dimorphic canine than do humans, equivalent in degree to the bonobo (11) or to chimpanzees and orangutans (12). Initially, Au. anamensis was suggested to express greater canine dimorphism than did Au. afarensis (13, 14). However, based on a somewhat larger sample size, this is now considered to be the case with the tooth root but not necessarily its crown (15–17).Throughout the 1990s and 2000s, a pre-Australopithecus record of fossils spanning >6.0 to 4.4 Ma revealed that the canines of these earlier forms did not necessarily exceed those of Au. afarensis or Au. anamensis in general size (18–28). However, all these taxa apparently possessed canine crowns on average about 30% larger than in modern humans, which makes moderately high levels of sexual dimorphism potentially possible. Canine sexual dimorphism, combined with features such as body size dimorphism, inform sociobehavioral and ecological adaptations of past and present primates, and therefore have been of considerable interest since Darwin’s 1871 considerations (29–57). In particular, the relationship of canine size dimorphism (and/or male and female relative canine sizes) with reproductive strategies and aggression/competition levels in primate species have been a continued focus of interest (14, 33, 35–45, 49–56). Conspecific-directed agonistic behavior in primates related to mate and/or resource competition can be particularly intense among males both within and between groups (14, 44, 57). It is widely recognized that a large canine functions as a weapon in intra- and intergroup incidences of occasional lethal aggression (45, 58–61), and a large, tall canine has been shown or inferred to significantly enhance male fitness (50, 56). Hence, canine size and dimorphism levels in fossil species provide otherwise unavailable insights into their adaptive strategies.Here, we apply a recently developed method of estimating sexual size dimorphism from fossil assemblages of unknown sex compositions, the posterior density peak (pdPeak) method (62), and reexamine canine sexual dimorphism in Ardipithecus ramidus at ∼4.5 Ma. We include newly available fossils recovered from the Middle Awash and Gona paleoanthropological research areas in the Afar Rift, Ethiopia (26, 63, 64) in order to obtain the most reliable dimorphism estimates currently possible. We apply the same method to Australopithecus, Homo, and selected fossil apes, and evaluate canine sexual dimorphism through evolutionary time.We operationally define canine sexual dimorphism as the ratio between male and female means of basal canine crown diameters (the m/f ratio). Because the canines of Ar. ramidus, Au. anamensis, and extant and fossil apes are variably asymmetric in crown shape, we examine the maximum basal dimension of the crown. This can be either the mesiodistal crown diameter or a maximum diameter taken from the distolingual to mesiobuccal crown base (7, 27, 65). In the chronologically later Au. afarensis and all other species of Australopithecus sensu lato and Homo, we examine the more widely available conventional metric of buccolingual breadth, which corresponds to or approximates the maximum basal crown diameter. In anthropoid primates, canine height is more informative than basal canine diameter as a functional indicator of aggression and/or related display (14, 41–44). We therefore also examine available unworn and minimally worn fossil canines with reliable crown heights.     

Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis

Many insects rely on symbiotic microbes for survival, growth, or reproduction. Over evolutionary timescales, the association with intracellular symbionts is stabilized by partner fidelity through strictly vertical symbiont transmission, resulting in congruent host and symbiont phylogenies. However, little is known about how symbioses with extracellular symbionts, representing the majority of insect-associated microorganisms, evolve and remain stable despite opportunities for horizontal exchange and de novo acquisition of symbionts from the environment. Here we demonstrate that host control over symbiont transmission (partner choice) reinforces partner fidelity between solitary wasps and antibiotic-producing bacteria and thereby stabilizes this Cretaceous-age defensive mutualism. Phylogenetic analyses show that three genera of beewolf wasps (Philanthus, Trachypus, and Philanthinus) cultivate a distinct clade of Streptomyces bacteria for protection against pathogenic fungi. The symbionts were acquired from a soil-dwelling ancestor at least 68 million years ago, and vertical transmission via the brood cell and the cocoon surface resulted in host–symbiont codiversification. However, the external mode of transmission also provides opportunities for horizontal transfer, and beewolf species have indeed exchanged symbiont strains, possibly through predation or nest reuse. Experimental infection with nonnative bacteria reveals that—despite successful colonization of the antennal gland reservoirs—transmission to the cocoon is selectively blocked. Thus, partner choice can play an important role even in predominantly vertically transmitted symbioses by stabilizing the cooperative association over evolutionary timescales.Cooperation is ubiquitous in nature, yet it presents a conundrum to evolutionary biology because acts that are beneficial to the receiver but costly to the actor should not be favored by natural selection (1). In interspecific associations (i.e., symbioses), the two most important models to explain the maintenance of cooperation are partner fidelity and partner choice (2, 3). In partner-fidelity associations, host and symbiont interact repeatedly and reward cooperating individuals while punishing cheaters, thereby reinforcing mutually beneficial interactions (2, 4). In partner-choice associations, individuals may interact only once, but one member can select its partner in advance of any possible exploitation (2, 4). Partner choice appears to select for cooperative strains among environmentally acquired microbial symbionts, e.g., the bioluminescent Vibrio fischeri bacteria of squids (5), the nitrogen-fixing rhizobia of legumes (6), and mycorrhizal fungi of plants (7). By contrast, partner fidelity is generally assumed to be the major stabilizing force in the widespread and ecologically important vertically transmitted symbioses of insects (4).However, localization and transmission routes of mutualistic bacteria in insects are diverse, and the differences across symbiotic systems have important implications for the evolutionary trajectory of the associations. Symbionts with an obligate intracellular lifestyle are usually tightly integrated into the host’s metabolism (e.g., ref. 8) and development (9), and the mutual interdependence of both partners coincides with perfect vertical symbiont transmission. Over evolutionary timescales, the high degree of partner fidelity results in host–symbiont cocladogenesis, and, concordantly, phylogenies of hosts and their intracellular symbionts are often found to be congruent (10–13). Although such a pattern is also observed for some extracellular symbioses with especially tight host–symbiont integration (14, 15), the ability of many extracellularly transmitted symbionts to spend part of their life cycle outside of the host’s body is often reflected in more or less extensive horizontal transmission or de novo acquisition of symbionts from the environment (16, 17). In these cases, partner choice mechanisms are expected to ensure specificity in the establishment and maintenance of the association (18). The nature of such control mechanisms, however, remains poorly understood.Although many of the well-studied mutualistic associations in insects have a nutritional basis (19, 20), an increasing number of symbioses for the defense of the host against predators (21), parasitoids (22), or pathogens (23–25) have recently been discovered. Among defensive symbionts, Actinobacteria are particularly prevalent, probably due to their ubiquity in the soil and their ability to produce secondary metabolites with antibiotic properties (23). Antibiotic-producing actinobacterial symbionts have been discovered on the cuticle of leaf-cutting ants (26), in the fungal galleries of a bark beetle (27), and in the antennae and on cocoons of beewolf wasps (28). While in the former two cases the symbionts have been implicated in the defense of the hosts’ nutritional resources against competing fungi (26, 27), the beewolves’ bacteria protect the offspring in the cocoon against pathogenic microorganisms (28, 29).Beewolves are solitary wasps in the genera Philanthus, Trachypus, and Philanthinus (Hymenoptera, Crabronidae, Philanthini). They engage in a defensive alliance with the Actinobacterium ‘Candidatus Streptomyces philanthi’ (CaSP) (28, 30, 31), which is cultivated by female beewolves in specialized antennal gland reservoirs (32). The uniqueness and complexity of the glands suggest a long history of host adaptation towards cultivating its actinobacterial symbionts (32). From the antennae, the streptomycetes are secreted into the brood cell, taken up by the larva, and incorporated into its cocoon (33), where they provide protection against pathogenic fungi and bacteria (28) by producing at least nine different antimicrobial compounds (29). Weeks or months later, eclosing adult females acquire the bacteria from the cocoon surface (33), thus completing the vertical transmission of CaSP. However, this mode of transmission provides opportunities for the horizontal transfer of symbionts among beewolf species or the de novo uptake of bacteria from the environment. Despite these opportunities, a monophyletic clade of CaSP strains has previously been found in 31 species of beewolves, suggesting an ancient and highly coevolved relationship (30, 31, 34).Here we combine cophylogenetic analyses of beewolves and their vertically transmitted defensive symbionts with experimental manipulation of symbiont infection status and subsequent observations of transmission from female antennal gland reservoirs into the brood cell to (i) reconstruct the coevolutionary history of the symbiosis, (ii) estimate the age of the symbiosis, (iii) elucidate the ancestral lifestyle of the symbionts, and (iv) assess the importance of partner fidelity and partner choice for the long-term stability of the association.