Cholestenone functions as an antibiotic against Helicobacter pylori by inhibiting biosynthesis of the cell wall component CGL

Helicobacter pylori, a pathogen responsible for gastric cancer, contains a unique glycolipid, cholesteryl-α-D-glucopyranoside (CGL), in its cell wall. Moreover, O-glycans having α1,4-linked N-acetylglucosamine residues (αGlcNAc) are secreted from gland mucous cells of gastric mucosa. Previously, we demonstrated that CGL is critical for H. pylori survival and that αGlcNAc serves as antibiotic against H. pylori by inhibiting CGL biosynthesis. In this study, we tested whether a cholesterol analog, cholest-4-en 3-one (cholestenone), exhibits antibacterial activity against H. pylori in vitro and in vivo. When the H. pylori standard strain ATCC 43504 was cultured in the presence of cholestenone, microbial growth was significantly suppressed dose-dependently relative to microbes cultured with cholesterol, and cholestenone inhibitory effects were not altered by the presence of cholesterol. Morphologically, cholestenone-treated H. pylori exhibited coccoid forms. We obtained comparable results when we examined the clarithromycin-resistant H. pylori strain “2460.” We also show that biosynthesis of CGL and its derivatives cholesteryl-6-O-tetradecanoyl-α-D-glucopyranoside and cholesteryl-6-O-phosphatidyl-α-D-glucopyranoside in H. pylori is remarkably inhibited in cultures containing cholestenone. Lastly, we asked whether orally administered cholestenone eradicated H. pylori strain SS1 in C57BL/6 mice. Strikingly, mice fed a cholestenone-containing diet showed significant eradication of H. pylori from the gastric mucosa compared with mice fed a control diet. These results overall strongly suggest that cholestenone could serve as an oral medicine to treat patients infected with H. pylori, including antimicrobial-resistant strains.

Helicobacter pylori is a gram-negative microaerophilic pathogen that colonizes the human stomach in approximately half the world’s population. It is well established that H. pylori infection is closely associated with pathogenesis of chronic active gastritis, peptic ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue lymphoma (1–4). Thus, in 1994, H. pylori was categorized as a Group I carcinogen by the World Health Organization’s International Agency for Research on Cancer. Accordingly, eradication therapy for H. pylori is expected to decrease the incidence of gastric cancer (5–7). In fact, eradication of the bacterium has been successfully achieved in ∼90% of infected patients using a combination of three drugs, namely, a proton pump inhibitor (PPI), clarithromycin, and amoxicillin (8, 9). However, successful eradication has been challenged by emergence of drug-resistant strains, in particular, clarithromycin-resistant H. pylori (10). Thus, development of new strategies as eradication therapy for H. pylori including drug-resistant strains is needed.The cell wall of Helicobacter species, including H. pylori, characteristically contains unique glycolipid α-cholesteryl glucosides (αCGs), of which the major components are cholesteryl-α-D-glucopyranoside (CGL), cholesteryl-6-O-tetradecanoyl-α-D-glucopyranoside (CAG), and cholesteryl-6-O-phosphatidyl-α-D-glucopyranoside (CPG) (11). αCGs are synthesized by cholesterol α-glucosyltransferase (αCgT), which transfers glucose from UDP-glucose to a carbon atom at the third position of cholesterol with an α1,3-linkage (SI Appendix, Fig. S1A). On the other hand, gastric gland mucous cells secrete unique O-glycans having terminal α1,4-linked N-acetylglucosamine (αGlcNAc) attached to the scaffold protein MUC6. Previously, we revealed that αGlcNAc suppresses H. pylori growth by inhibiting αCgT activity, which forms CGL (12, 13). Because the H. pylori genome does not encode enzymes required for cholesterol biosynthesis, microbes require exogenous cholesterol to synthesize αCGs (14, 15).Cholestenone is a cholesterol analog catabolized from cholesterol by intestinal bacteria, including human-derived Escherichia coli, Eubacterium, and Bacteroides sp. that replace the steroid 3β-hydroxyl group with a keto group (16–20). Because the hydroxyl group at the cholesterol third position is critical to form CGL, we hypothesized that cholestenone cannot serve as an αCgT substrate (SI Appendix, Fig. S1B) and thus that cholestenone treatment could inhibit H. pylori growth due to defective CGL biosynthesis.In the present study, we examined growth capacity of H. pylori in vitro in the presence of cholesterol and analogs including cholestenone, β-sitosterol, and cholestanol (SI Appendix, Fig. S2). Our results clearly indicate that growth of H. pylori, including that of a clarithromycin-resistant strain, was significantly suppressed by cholestenone through inhibition of CGL biosynthesis. When cholestenone was orally administered to H. pylori-infected C57BL/6 mice, mice showed successful eradication of the microbe. Because cholestenone is safe, therapy using cholestenone could be a promising approach to eliminate H. pylori infection in humans, including infection with antibiotic-resistant strains.     

Helicobacter pylori’s historical journey through Siberia and the Americas

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

The gram-negative gastric bacterium Helicobacter pylori has shared an intimate coevolutionary relationship with humans for the last 100,000 y and possibly longer (1, 2). The greatest genetic diversity in both humans and H. pylori is found in Africa, the ancestral homeland of both species (3). After leaving Africa, H. pylori continued to differentiate in tandem with humans. Unlike its host, the bacterium evolved into multiple distinct geographic populations because it has high mutation and recombination rates, shorter generation times, and lower effective population sizes (4). Human populations expanding along the southern Asia coastal route carried the H. pylori precursors of hpSahul, a divergent, monophyletic population that continues to infect New Guinean Highlanders and Aboriginal Australians (5). The western and central parts of Paeleolithic Eurasia were dominated by hpAsia2, which has differentiated into hspIndia and hspLadakh (6, 7).A Eurasian West–East divide in H. pylori is reflected by the divergence of hpEastAsia, an ancestral East Asian population, into subpopulations hspEAsia (Southeast and East Asians), hspIndigenousAmericas (formerly known as hspAmerind, native North and South Americans), and hspMaori (Austronesian speakers). However, H. pylori’s presence, diversity, and structure in northern Eurasia are still unknown. This vast region, hereafter Siberia, extends from the Ural Mountains in the west to the Pacific Ocean in the east and the Kazakh and Mongolian Steppes in the south. Siberia is inhabited by at least 41 ethnic minorities who often live in small communities of low population densities with a total of <250,000 individuals (8). Notwithstanding often harsh environmental conditions, Siberians subsist through hunter-gathering and/or pastoralism (9), and the diversity of language families spoken in the region (Uralic, Yeniseian, Turkic, Tungusic, Mongolic, Gilyak, and Chukotko-Kamchatkan) hints at a complex history of migration and isolation.The patterns of human diversity between these ethnic groups are also largely understudied, and most genetic studies were based on traditional markers such as mitochondrial or Y chromosome DNA, whose effectiveness is compromised by relatively low mutation rates and incomplete lineage sorting (10–15). Recently, genomic studies of ancient human DNA have offered further insights, confirming that Siberia was the gateway for human migrations into northern America (16, 17) as well as into western Eurasia (18).Two important questions remain unanswered. Firstly, although anatomically modern human hunter-gatherers first appeared in Siberia 45,000 y ago (kya) in the Upper Paleolithic (16), their continued presence in the region throughout the last glacial maximum (LGM, 26.5 to 19 kya) is controversial. One argument suggests that ancient northern Eurasian [ANE (19)] metapopulations in Siberia had already developed adaptive mechanisms that allowed them to persist throughout the LGM, at least in sheltered locations with favorable environments (20). The presence of genetically similar human remains in central Siberia at 24 kya (Ma’lta boy, MA1) and 17 kya (AG2) (17) also hints that the region may have been continuously inhabited by ANEs during the LGM. Conversely, other scientists propose that the LGM paleoclimate resulted in the complete depopulation of central Siberia, driving humans into refugia to the south where they persisted for thousands of years before repopulating northern Siberia during the Holocene (9, 21, 22). Secondly, the peopling of the Americas by anatomically modern humans has long attracted scientific attention. Recent genomic evidence suggests that a single genetically diverse human population migrated across the Bering land bridge into the Americas, followed by subsequent post-LGM gene flow (23, 24). However, the dates of colonization by these migrants, the size of their founder population, and their relationships to other human groups remain unclear.To help answer these and other questions about human movements through Eurasia and the Americas, we undertook large-scale sampling of H. pylori from ethnically diverse aboriginal human populations across Siberia and Mongolia. Genotyping and sequence data were combined with a large reference database of Asian strains to provide an overview of the population structure of their genetic diversity and to infer the demographic and evolutionary histories of the peoples of Siberia and the Americas.     

CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left–right symmetry breaking

Proper left–right symmetry breaking is essential for animal development, and in many cases, this process is actomyosin-dependent. In Caenorhabditis elegans embryos active torque generation in the actomyosin layer promotes left–right symmetry breaking by driving chiral counterrotating cortical flows. While both Formins and Myosins have been implicated in left–right symmetry breaking and both can rotate actin filaments in vitro, it remains unclear whether active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength of C. elegans genetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counterrotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counterrotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin–dependent manner. Altogether, we conclude that CYK-1/Formin–dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left–right symmetry breaking in the nematode worm.

The emergence of left–right asymmetry is essential for normal animal development and, in the majority of animal species, one type of handedness is dominant (1). The actin cytoskeleton plays an instrumental role in establishing the left–right asymmetric body plan of invertebrates like fruit flies (2–6), nematodes (7–11), and pond snails (12–15). Moreover, an increasing number of studies showed that vertebrate left–right patterning also depends on a functional actomyosin cytoskeleton (13, 16–22). Actomyosin-dependent chiral behavior has even been reported in isolated cells (23–28) and such cell-intrinsic chirality has been shown to promote left–right asymmetric morphogenesis of tissues (29, 30), organs (21, 31), and entire embryonic body plans (12, 13, 32, 33). Active force generation in the actin cytoskeleton is responsible for shaping cells and tissues during embryo morphogenesis. Torques are rotational forces with a given handedness and it has been proposed that in plane, active torque generation in the actin cytoskeleton drives chiral morphogenesis (7, 8, 34, 35).What could be the molecular origin of these active torques? The actomyosin cytoskeleton consists of actin filaments, actin-binding proteins, and Myosin motors. Actin filaments are polar polymers with a right-handed helical pitch and are therefore chiral themselves (36, 37). Due to the right-handed pitch of filamentous actin, Myosin motors can rotate actin filaments along their long axis while pulling on them (33, 38–42). Similarly, when physically constrained, members of the Formin family rotate actin filaments along their long axis while elongating them (43). In both cases the handedness of this rotation is determined by the helical nature of the actin polymer. From this it follows that both Formins and Myosins are a potential source of molecular torque generation that could drive cellular and organismal chirality. Indeed, chiral processes across different length scales, and across species, are dependent on Myosins (19), Formins (13–15, 26), or both (7, 8, 21, 44). It is, however, unclear how Formins and Myosins contribute to active torque generation and the emergence chiral processes in developing embryos.In our previous work we showed that the actomyosin cortex of some Caenorhabditis elegans embryonic blastomeres undergoes chiral counterrotations with consistent handedness (7, 35). These chiral actomyosin flows can be recapitulated using active chiral fluid theory that describes the actomyosin layer as a thin-film, active gel that generates active torques (7, 45, 46). Chiral counterrotating cortical flows reorient the cell division axis, which is essential for normal left–right symmetry breaking (7, 47). Moreover, cortical counterrotations with the same handedness have been observed in Xenopus one-cell embryos (32), suggesting that chiral counterrotations are conserved among distant species. Chiral counterrotating actomyosin flow in C. elegans blastomeres is driven by RhoA signaling and is dependent on Non-Muscle Myosin II motor proteins (7). Moreover, the Formin CYK-1 has been implicated in actomyosin flow chirality during early polarization of the zygote as well as during the first cytokinesis (48, 49). Despite having identified a role for Myosins and Formins, the underlying mechanism by which active torques are generated remains elusive.Here we show that the Diaphanous-like Formin, CYK-1/Formin, is a critical determinant for the emergence of actomyosin flow chirality, while Non-Muscle Myosin II (NMY-2) plays a permissive role. Our results show that cortical CYK-1/Formin is recruited by active RhoA signaling foci and promotes active torque generation, which in turn tends to locally rotate the actomyosin cortex clockwise. In the highly connected actomyosin meshwork, a gradient of these active torques drives the emergence of chiral counterrotating cortical flows with uniform handedness, which is essential for proper left–right symmetry breaking. Together, these results provide mechanistic insight into how Formin-dependent torque generation drives cellular and organismal left–right symmetry breaking.     

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history

Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.

Animal gastrointestinal tracts contain microbial communities that are integral to host metabolism, immunity, and development (1, 2). Symbioses between animals and their gut microbiome have deep evolutionary origins (1, 2), often exhibit phylosymbiosis (3), and can serve as a physiological buffer to heterogeneous environments (2). Despite the necessity of the gastrointestinal tract and benefits of the gut microbiome (3), species in various phyla have lost a functional digestive system (4, 5). Loss of a functional gut should, in theory, cascade into a reduction in microbial diversity and the loss of diet-induced shifts in microbiome composition. These nutritional shifts may then provide a niche for functionally important endosymbionts, such as the chemoautotrophic bacteria commonly associated with gutless invertebrates (6, 7).Major life history transitions are driven by tradeoffs in reproduction and development that, in turn, impact fitness (8). These tradeoffs are particularly evident in benthic marine invertebrates whose developmental stages broadly group into two alternative nutritional strategies (4, 9). The first—planktotrophy—typically includes the production of a high number of small, energy-poor eggs that develop into larvae with feeding structures used to collect and process exogenous resources required to reach metamorphic competency (4, 9). The second—lecithotrophy—involves the production of fewer large, energy-rich eggs and nonfeeding larvae that undergo metamorphosis without the requirement of external nutrients through feeding (4, 9). Life history transitions between these developmental modes have occurred in several major animal lineages, with rapid evolutionary shifts from planktotrophy to lecithotrophy being well documented in echinoderms (4, 5, 10–13). It is thought that an increase in the eggs energetic content relaxes the selective pressure maintaining the feeding structures (e.g., the larval arms and a functional gastrointestinal tract) and that development to metamorphosis is accelerated once these are lost (5).One of the most comprehensively studied systems for life history transitions among marine invertebrates involves species in the sea urchin genus Heliocidaris. A speciation event ∼5 Mya resulted in two sister species with alternative life history strategies: Heliocidaris tuberculata is planktotrophic while Heliocidaris erythrogramma is lecithotrophic (14). Typical of planktotrophs, H. tuberculata develops from small eggs into feeding larvae that exhibit morphological plasticity in response to food limitation (15), which is correlated with compositional shifts in the microbiome (16, 17). H. erythrogramma, on the other hand, develops from eggs ∼53× to 86× the volume of H. tuberculata (18), lacks the morphological structures required for feeding, and has a reduced, nonfunctional digestive tract (11). This life history switch and heterochronic shift in development (11) corresponds with a rewiring of the gene regulatory network (19), reorganization of cell fates (20), and modification to gametogenesis (21).Here, we compare the bacterial communities of these Heliocidaris species and test two hypotheses. First, we test whether the loss of gut function coincides with a reduction in microbial symbiont diversity, and second, by simulating the natural range in food availability, we also test that the loss in gut function coincides with a loss in diet-related shifts in the microbiome. We report major reductions in microbiome diversity and abundance as well as the absence of bacterial communities correlated with food availability for the lecithotrophic H. erythrogramma. Moreover, we find that this species vertically transmits a Rickettsiales that encodes pathways for the biosynthesis of essential amino acids, proteins with pivotal roles in host reproduction, and enzymes to metabolize diacylglycerol ethers, the major lipid group responsible for the increase in egg size in H. erythrogramma and that is used to fuel growth and development (18, 22).     

Wild-type α-synuclein inherits the structure and exacerbated neuropathology of E46K mutant fibril strain by cross-seeding

Heterozygous point mutations of α-synuclein (α-syn) have been linked to the early onset and rapid progression of familial Parkinson’s diseases (fPD). However, the interplay between hereditary mutant and wild-type (WT) α-syn and its role in the exacerbated pathology of α-syn in fPD progression are poorly understood. Here, we find that WT mice inoculated with the human E46K mutant α-syn fibril (hE46K) strain develop early-onset motor deficit and morphologically different α-syn aggregation compared with those inoculated with the human WT fibril (hWT) strain. By using cryo-electron microscopy, we reveal at the near-atomic level that the hE46K strain induces both human and mouse WT α-syn monomers to form the fibril structure of the hE46K strain. Moreover, the induced hWT strain inherits most of the pathological traits of the hE46K strain as well. Our work suggests that the structural and pathological features of mutant strains could be propagated by the WT α-syn in such a way that the mutant pathology would be amplified in fPD.

α-Synuclein (α-Syn) is the main component of Lewy bodies, which serve as the common histological hallmark of Parkinson’s disease (PD) and other synucleinopathies (1, 2). α-Syn fibrillation and cell-to-cell transmission in the brain play essential roles in disease progression (3–5). Interestingly, WT α-syn could form fibrils with distinct polymorphs, which exhibit disparate seeding capability in vitro and induce distinct neuropathologies in mouse models (6–10). Therefore, it is proposed that α-syn fibril polymorphism may underlie clinicopathological variability of synucleinopathies (6, 9). In fPD, several single-point mutations of SNCA have been identified, which are linked to early-onset, severe, and highly heterogeneous clinical symptoms (11–13). These mutations have been reported to influence either the physiological or pathological function of α-syn (14). For instance, A30P weakens while E46K strengthens α-syn membrane binding affinity that may affect its function in synaptic vesicle trafficking (14, 15). E46K, A53T, G51D, and H50Q have been found to alter the aggregation kinetics of α-syn in different manners (15–17). Recently, several cryogenic electron microscopy (cryo-EM) studies revealed that α-syn with these mutations forms diverse fibril structures that are distinct from the WT α-syn fibrils (18–26). Whether and how hereditary mutations induced fibril polymorphism contributes to the early-onset and exacerbated pathology in fPD remains to be elucidated. More importantly, most fPD patients are heterozygous for SNCA mutations (12, 13, 27, 28), which leads to another critical question: could mutant fibrils cross-seed WT α-syn to orchestrate neuropathology in fPD patients?E46K mutation is one of the eight disease-causing mutations on SNCA originally identified from a Spanish family with autosomal-dominant PD (11). E46K-associated fPD features early-onset motor symptoms and rapid progression of dementia with Lewy bodies (11). Studies have shown that E46K mutant has higher neurotoxicity than WT α-syn in neurons and mouse models overexpressing α-syn (29–32). The underlying mechanism is debatable. Some reported that E46K promotes the formation of soluble species of α-syn without affecting the insoluble fraction (29, 30), while others suggested that E46K mutation may destabilize α-syn tetramer and induce aggregation (31, 32). Our previous study showed that E46K mutation disrupts the salt bridge between E46 and K80 in the WT fibril strain and rearranges α-syn into a different polymorph (33). Compared with the WT strain, the E46K fibril strain is prone to be fragmented due to its smaller and less stable fibril core (33). Intriguingly, the E46K strain exhibits higher seeding ability in vitro, suggesting that it might induce neuropathology different from the WT strain in vivo (33).In this study, we found that human E46K and WT fibril strains (referred to as hE46K and hWT strains) induced α-syn aggregates with distinct morphologies in mice. Mice injected with the hE46K strain developed more α-syn aggregation and early-onset motor deficits compared with the mice injected with the hWT strain. Notably, the hE46K strain was capable of cross-seeding both human and mouse WT (mWT) α-syn to form fibrils (named as hWT_cs and mWT_cs). The cross-seeded fibrils replicated the structure and seeding capability of the hE46K template both in vitro and in vivo. Our results suggest that the hE46K strain could propagate its structure as well as the seeding properties to the WT monomer so as to amplify the α-syn pathology in fPD.     

Cell type-specific lipid storage changes in Parkinson’s disease patient brains are recapitulated by experimental glycolipid disturbance

Neurons are dependent on proper trafficking of lipids to neighboring glia for lipid exchange and disposal of potentially lipotoxic metabolites, producing distinct lipid distribution profiles among various cell types of the central nervous system. Little is known of the cellular distribution of neutral lipids in the substantia nigra (SN) of Parkinson’s disease (PD) patients and its relationship to inflammatory signaling. This study aimed to determine human PD SN neutral lipid content and distribution in dopaminergic neurons, astrocytes, and microglia relative to age-matched healthy subject controls. The results show that while total neutral lipid content was unchanged relative to age-matched controls, the levels of whole SN triglycerides were correlated with inflammation-attenuating glycoprotein non-metastatic melanoma protein B (GPNMB) signaling in human PD SN. Histological localization of neutral lipids using a fluorescent probe (BODIPY) revealed that dopaminergic neurons and midbrain microglia significantly accumulated intracellular lipids in PD SN, while adjacent astrocytes had a reduced lipid load overall. This pattern was recapitulated by experimental in vivo inhibition of glucocerebrosidase activity in mice. Agents or therapies that restore lipid homeostasis among neurons, astrocytes, and microglia could potentially correct PD pathogenesis and disease progression.

Both neurons and glia depend on tight regulation and exchange of lipids for proper function. Typically through lipid transport mechanisms (1, 2), the continuous exchange of lipids is essential for maintaining physiological function as brain lipid content, transport, and distribution are complex and critical aspects of neuropathology. Recently, both clinical findings and experimental studies have implicated lipid storage and trafficking in the pathogenesis of Parkinson’s disease (PD) and related disorders (3, 4). Reduced function of lysosomal hydrolases that are associated with lysosomal storage disorders increases the risk for PD and results in brain pathology similar to that seen in most sporadic and genetic forms of the disease (5–11).One of the strongest genetic risk factors for PD is heterozygous loss-of-function mutations in GBA1, encoding the lysosomal hydrolase glucocerebrosidase (GCase) (12–14), a deficiency that causes systemic accumulation of its glycolipid substrate glucosylceramide (GlcCer). GCase activity is reduced with aging of both the human and murine brain (6, 15), and age is the overall greatest risk factor for developing PD (16). In contrast, the more severe loss of GCase activity in homozygous GBA1 mutant carriers causes the lysosomal storage disease Gaucher disease (GD) (17). Conduritol beta epoxide (CBE), an irreversible inhibitor of GCase, causes widespread accumulation of GlcCer and related glycosphingolipids in mice. In this model, there is marked increase of high molecular weight alpha-synuclein (aSYN) and deposition of proteinase K-resistant aSYN resembling that seen in PD (18–20). aSYN is a constituent of the classical Lewy bodies and Lewy neurites (21) found in surviving dopaminergic neurons in postmortem PD materials as a standard pathological criterion for PD (22). aSYN has a lipid-binding domain, and aSYN protein–lipid interactions are potentially perturbed in PD (reviewed in refs. 17, 23, 24). We recently demonstrated that excessive aSYN can deposit into lipid compartments, and that this process is reversible under increased lysosomal β-hexosaminidase expression (25).Several in vitro physiological studies have demonstrated that a reduction in neuronal neutral lipid storage or knockdown of fatty acid desaturases protects cultured neurons from degeneration (26–28). However, as neurons exhibit limited capacity to synthesize, metabolize, and transport lipid species under physiological conditions (29), other resident cells of the substantia nigra (SN), such as glial cells, are required to maintain lipid homeostasis in the brain. Astrocyte health and lipid exchange function—and microglial activation—are potentially central to PD pathogenesis and other age-dependent neurodegenerative diseases (30–33). Brain resident microglia can accumulate and generate lipids, which may propagate inflammatory processes through, for example, TREM2 binding of apolipoproteins (34–38). Proinflammatory cytokines present in chronic conditions are attenuated by the binding of glycoprotein nonmetastatic melanoma protein B (GPNMB) to the CD44 receptor on astrocytes (39). In GD patient serum, GPNMB level is significantly correlated with disease severity (40), and GPNMB is increased in human PD SN and following CBE-induced glycolipid accumulation in mice (41).There are surprisingly little data on lipid distribution patterns in PD-affected cell types given the relevance of lipid homeostasis, aSYN–lipid interactions, and lipidopathy-associated inflammatory signatures as they relate to PD (17, 41). In this study, we measured the differences in total lipid content and cellular distribution between PD and healthy subject (HS) SN and compared them with a lipid-associated neuroinflammatory signal, GPNMB. To quantify cell type-specific intracellular lipid content, colocalization analysis was performed on human postmortem SN sections that were costained for neutral lipids and markers of dopaminergic neurons, astrocytes, and microglia. Compared with HS SN, the lipid content of PD dopaminergic neurons and microglia was significantly higher, and that of astrocytes was significantly lower. To understand a possible mechanistic reason for this lipid distribution pattern, we used an in vivo mouse model of glycolipid dysregulation and attendant aSYN accumulation through GCase inhibition by CBE. This in vivo model recapitulated the lipid distribution pattern that we observed in human PD SN. Based on these data, we propose that PD is characterized by a unique neutral lipid distribution signature in neurons, astrocytes, and microglia that can be recapitulated experimentally by glycolipid dysregulation.     

Mesoscale networks and corresponding transitions from self-assembly of block copolymers

A series of cubic network phases was obtained from the self-assembly of a single-composition lamellae (L)-forming block copolymer (BCP) polystyrene-block-polydimethylsiloxane (PS-b-PDMS) through solution casting using a PS-selective solvent. An unusual network phase in diblock copolymers, double-primitive phase (DP) with space group of Im3¯m, can be observed. With the reduction of solvent evaporation rate for solution casting, a double-diamond phase (DD) with space group of Pn3¯m can be formed. By taking advantage of thermal annealing, order–order transitions from the DP and DD phases to a double-gyroid phase (DG) with space group of Ia3¯d can be identified. The order–order transitions from DP (hexapod network) to DD (tetrapod network), and finally to DG (trigonal planar network) are attributed to the reduction of the degree of packing frustration within the junction (node), different from the predicted Bonnet transformation from DD to DG, and finally to DP based on enthalpic consideration only. This discovery suggests a new methodology to acquire various network phases from a simple diblock system by kinetically controlling self-assembling process.

From constituted molecules to polymers, finally ordered hierarchical superstructures, self-assembled solids cover a vast area of nanostructures where the characters of building blocks direct the progress of self-assembly (1, 2). In nature, fascinating periodic network structures and morphologies from different species are appealing in nanoscience and nanotechnology due to their superior properties, especially for photonic crystal structures (3–7). For gyroid, trigonal planar network with chirality demonstrates its potential as chiropitc metamaterial (8–10). Beyond the splendid colors, networks either in macroscale or mesoscale mechanically strengthen their skeletons and protect those fragile but vital organs from impact (11, 12). Inspired by nature, biomimicking materials with mesoscale network may exceed the limitation of the intrinsic properties (13). The topology of networks could further improve their adaptability, allowing extreme deformation for energy dissipation (14). Moreover, network materials from hybridization of self-assembled block copolymers (BCPs) have been exploited to the design of mesoscale quantum metamaterials (15, 16). With the desire to acquire network textures for biomimicking nanomaterials, BCPs with immiscible constituted segments covalently joined together give the accessibility to the formation of nanonetwork morphologies via balancing enthalpic penalty from the repulsive interaction of constituted blocks and entropic penalty from the stretching of polymer chains (17–21). By taking advantage of precise synthesis procedures, it is feasible to obtain the aimed network phases from the self-assembly of BCPs such as Fddd (O⁷⁰) (22–24), gyroid (Q²¹⁴, Q²³⁰) (20, 21, 25–27), and diamond (Q²²⁴, Q²²⁷) (28–31) experimentally and theoretically. On the basis of theoretical prediction, the junction points (nodes) in the network phases could be coordinated with three, four, or six neighbors in three-dimensional space, resulting in the enhancement of packing frustration (31). Topologically, all these phases match the coordination number to neighbors (n = 3, 4, 6), showing no special case of quasicrystal. Accordingly, an order–order transition from double-diamond phase (DD, tetrapod) to double-gyroid phase (DG, trigonal planar network) has been observed (29). Yet, there is no DP phase being found in simple diblock systems except for liquid crystals (32, 33) or organic–inorganic nanocomposites from the mixtures of BCP with inorganic precursors (34, 35). Searching the rare occurrence of network phases and the corresponding phase transitions among phases will be essential to the demands for application by considering the deliberate structuring effects on aimed properties but the approaches remain challenging (8, 36–40). For instance, viewing the narrow window for network morphologies in diblock copolymer phase diagram, it demands harsh requirements for syntheses (2, 41). Recently, by taking advantage of using selective solvent for solution casting, it is feasible to acquire DG phase and even inverted DG phase from the self-assembly of lamellae (L)-forming polystyrene-block-polydimethylsiloxane (PS-b-PDMS) (42). Apart from that, a triclinic DG phase was recently discovered from the PS-b-PDMS which is commonly believed nonexisting in the conventional phase diagram (43). As a result, the phase diagram of BCPs with high interaction parameter is worthy of study for searching the metastable phases with unique network textures (44). Herein, we aim to acquire network phases from a simple diblock system by kinetically controlling the transformation mechanisms of self-assembly. As exemplified by using the PS-b-PDMS for solution casting, with the use of a PS-selective solvent (chloroform), a DP phase and a DD phase could be formed through controlled self-assembly, giving unique network phases simply from solution casting. Moreover, a DG phase can be also acquired from phase transformation. Consequently, a series of network phases with hexapod, tetrapod, and trigonal planar building units could be successfully obtained by using a single-composition L-forming PS-b-PDMS for self-assembly. The corresponding order–order transitions among these network phases examined by temperature-resolved in situ small-angle X-ray scattering (SAXS) combining with electron tomography results provide insights of network phase formation and the corresponding phase transformation mechanisms in the self-assembly of BCPs.     

The β-encapsulation cage of rearrangement hotspot (Rhs) effectors is required for type VI secretion

Bacteria deploy rearrangement hotspot (Rhs) proteins as toxic effectors against both prokaryotic and eukaryotic target cells. Rhs proteins are characterized by YD-peptide repeats, which fold into a large β-cage structure that encapsulates the C-terminal toxin domain. Here, we show that Rhs effectors are essential for type VI secretion system (T6SS) activity in Enterobacter cloacae (ECL). ECL rhs⁻ mutants do not kill Escherichia coli target bacteria and are defective for T6SS-dependent export of hemolysin-coregulated protein (Hcp). The RhsA and RhsB effectors of ECL both contain Pro−Ala−Ala−Arg (PAAR) repeat domains, which bind the β-spike of trimeric valine−glycine repeat protein G (VgrG) and are important for T6SS activity in other bacteria. Truncated RhsA that retains the PAAR domain is capable of forming higher-order, thermostable complexes with VgrG, yet these assemblies fail to restore secretion activity to ∆rhsA ∆rhsB mutants. Full T6SS-1 activity requires Rhs that contains N-terminal transmembrane helices, the PAAR domain, and an intact β-cage. Although ∆rhsA ∆rhsB mutants do not kill target bacteria, time-lapse microscopy reveals that they assemble and fire T6SS contractile sheaths at ∼6% of the frequency of rhs⁺ cells. Therefore, Rhs proteins are not strictly required for T6SS assembly, although they greatly increase secretion efficiency. We propose that PAAR and the β-cage provide distinct structures that promote secretion. PAAR is clearly sufficient to stabilize trimeric VgrG, but efficient assembly of T6SS-1 also depends on an intact β-cage. Together, these domains enforce a quality control checkpoint to ensure that VgrG is loaded with toxic cargo before assembling the secretion apparatus.

Bacteria use many strategies to compete against other microorganisms in the environment. Research over the past 15 y has uncovered several distinct mechanisms by which bacteria deliver inhibitory toxins directly into neighboring competitors (1–8). Cell contact-dependent competition systems have been characterized most extensively in Gram-negative bacteria, and the most widespread mechanism is mediated by the type VI secretion system (T6SS) (9). T6SSs are multiprotein complexes related in structure and function to the contractile tails of Myoviridae bacteriophages. T6SS loci vary considerably between bacterial species, but all encode 13 core type VI secretion (Tss) proteins that are required to build a functional apparatus. TssJ, TssL, and TssM form a multimeric complex that spans the cell envelope and serves as the secretion conduit. The phage-like baseplate is composed of TssE, TssF, TssG, and TssK proteins, which form a sixfold symmetrical array surrounding a central “hub” of trimeric valine−glycine repeat protein G (VgrG/TssI). VgrG is structurally homologous to the gp27−gp5 tail spike of phage T4 (10, 11). The T4 tail spike is further acuminated with gp5.4, a small protein that forms a sharpened apex at the tip of the gp5 spike (12). Proline−alanine−alanine−arginine (PAAR) repeat proteins form an orthologous structure on VgrG; and PAAR is thought to facilitate penetration of the target cell outer membrane (13). The T6SS duty cycle begins when the baseplate docks onto TssJLM at the cytoplasmic face of the inner membrane (14). The baseplate then serves as the assembly origin for the contractile sheath and inner tube. The sheath is built from TssB−TssC subunits, and the tube is formed by stacked hexameric rings of hemolysin-coregulated protein (Hcp/TssD). TssA coordinates this assembly process to ensure that the sheath and tube are polymerized at equivalent rates (15). After elongating across the width of the cell, the sheath undergoes rapid contraction to expel the PAAR•VgrG-capped Hcp tube through the transenvelope complex. The ejected tube impales neighboring cells and delivers a variety of toxic effector proteins into the target. After firing, the contracted sheath is disassembled by the ClpV (TssH) ATPase (16), and the recycled TssBC subunits are used to support additional rounds of sheath assembly and contraction.T6SSs were originally identified through their ability to intoxicate eukaryotic host cells (17), and VgrG proteins were the first effectors to be recognized. VgrG-1 from Vibrio cholerae V52 carries a C-terminal domain that cross-links actin and blocks macrophage phagocytosis (10). Similarly, the VgrG1 protein from Aeromonas hydrophila American Type Culture Collection (ATCC) 7966 carries a C-terminal actin adenosine 5′-diphosphate (ADP) ribosyltransferase domain that disrupts the host cytoskeleton (18). Although the T6SS clearly plays a role in pathogenesis, most of the systems characterized to date deliver toxic effectors into competing bacteria. Because antibacterial effectors are potentially autoinhibitory, these latter toxins are invariably encoded with specific immunity proteins. Antibacterial effectors commonly disrupt the integrity of the bacterial cell envelope. VgrG-3 from V. cholerae carries a lysozyme-like domain that degrades the peptidoglycan cell wall (19, 20). Other peptidoglycan-cleaving amidase toxins are packaged within the lumen of Hcp hexamers for T6SS-mediated delivery (21–24). Phospholipase toxins collaborate with peptidoglycan degrading enzymes to lyse target bacteria (25–27). Other T6SS effectors act in the cytosol to degrade nucleic acids and nicotinamide adenine dinucleotide cofactors (3, 28, 29). Most recently, Whitney and coworkers described a novel T6SS effector that produces the inhibitory nucleotide ppApp (30). These latter toxins are commonly delivered through noncovalent interactions with VgrG. Many effectors contain PAAR domains, which enable direct binding to the C-terminal β-spike of VgrG (13), whereas others are indirectly tethered to VgrG through adaptor proteins (31–33). This combinatorial strategy allows multiple different toxins to be delivered with each firing event.Rearrangement hotspot (Rhs) proteins are potent effectors deployed by many T6SS⁺ bacteria (3, 34–37). T6SS-associated Rhs effectors range from ∼150 kDa to 180 kDa in mass and carry highly variable C-terminal toxin domains. The N-terminal region of Rhs proteins often contains two predicted transmembrane (TM) helix regions followed by a PAAR domain. The central region is composed of many Rhs/YD-peptide repeats, which form a β-cage structure that fully encapsulates the toxin domain (38). Genes coding for Rhs were first identified in Escherichia coli K-12 as elements that promote chromosomal duplication (39, 40). This genomic rearrangement was the result of unequal recombination between the rhsA and rhsB loci, which share 99.4% sequence identity over some 3,700 nucleotides. Subsequently, Hill and coworkers recognized that rhs genes are genetic composites (41), and that the variable C-terminal extension domains inhibit cell growth (42). Although E. coli K-12 encodes four full-length Rhs proteins, it lacks a T6SS, and there is no evidence that it deploys Rhs in competition. However, other Rhs/YD-peptide repeat proteins are known to deliver toxins in a T6SS-independent manner. Gram-positive bacteria export antibacterial YD-repeat proteins through the Sec pathway (3), and the tripartite insecticidal toxin complexes released by Photorhabdus and Yersinia species contain subunits with Rhs/YD repeats (38, 43). Thus, the Rhs encapsulation structure has been incorporated into at least three different toxin delivery platforms.Here, we report that Rhs effectors are critical for the activity of the T6SS-1 locus of Enterobacter cloacae ATCC 13047 (ECL). ECL encodes two Rhs effectors—RhsA and RhsB—which are each exported in a constitutive manner by T6SS-1 (35). Deletion of either rhs gene has little effect on T6SS-1 activity, but mutants lacking both rhsA and rhsB are defective for Hcp1 secretion and no longer inhibit target bacteria. Although ∆rhsA ∆rhsB mutants lose T6SS-1−mediated inhibition activity, they still assemble and fire contractile sheaths at a significantly reduced frequency. We further show that truncated RhsA that retains the PAAR domain still interacts with cognate VgrG2, but the resulting complex does not support Hcp1 secretion or target-cell killing. Full T6SS-1 function requires wild-type Rhs effectors that retain the N-terminal TM helices and PAAR domain together with an intact β-cage. These findings suggest that the Rhs β-cage mediates a quality control checkpoint on T6SS-1 assembly to ensure that VgrG is loaded with a toxic effector prior to export.     

Isolation and characterization of Helicobacter suis from human stomach

Helicobacter suis, a bacterial species naturally hosted by pigs, can colonize the human stomach in the context of gastric diseases such as gastric mucosa-associated lymphoid tissue (MALT) lymphoma. Because H. suis has been successfully isolated from pigs, but not from humans, evidence linking human H. suis infection to gastric diseases has remained incomplete. In this study, we successfully in vitro cultured H. suis directly from human stomachs. Unlike Helicobacter pylori, the viability of H. suis decreases significantly on neutral pH; therefore, we achieved this using a low-pH medium for transport of gastric biopsies. Ultimately, we isolated H. suis from three patients with gastric diseases, including gastric MALT lymphoma. Successful eradication of H. suis yielded significant improvements in endoscopic and histopathological findings. Oral infection of mice with H. suis clinical isolates elicited gastric and systemic inflammatory responses; in addition, progression of gastric mucosal metaplasia was observed 4 mo postinfection. Because H. suis could be isolated from the stomachs of infected mice, our findings satisfied Koch’s postulates. Although further prospective clinical studies are needed, H. suis, like H. pylori, is likely a gastric pathogen in humans. Furthermore, comparative genomic analysis of H. suis using complete genomes of clinical isolates revealed that the genome of each H. suis isolate contained highly plastic genomic regions encoding putative strain-specific virulence factors, including type IV secretion system–associated genes, and that H. suis isolates from humans and pigs were genetically very similar, suggesting possible pig-to-human transmission.

Non-Helicobacter pylori Helicobacters (NHPH), which have a corkscrew-like spiral morphology very different from that of H. pylori, have been known to be present in human stomachs since the 1980s (1). NHPH infection has been observed in patients with gastric diseases, including peptic ulcers, chronic gastritis, gastric cancers, and gastric mucosa-associated lymphoid tissue (MALT) lymphoma (2–4).Because routine diagnostic methods based on the urease activity of H. pylori, such as the urea breath test and rapid urease test, often yield negative results for NHPH (5), and the bacteria is uncultivable, NHPH infection in individual patients could be missed. Thus, in the post-H. pylori era, NHPH could become an important gastric pathogen in people of all ages.The primary human pathogenic NHPH species is Helicobacter suis, which is naturally hosted by pigs (6). H. suis infects 60 to 95% of livestock pigs, in which it causes gastritis, ulcers, and a reduced rate of weight gain (6, 7). Humans are frequently infected by H. pylori in childhood but rarely in adulthood (8); by contrast, the route and period of H. suis infection in humans is completely unknown. In some cases, H. suis was observed in patients with gastric diseases after H. pylori eradication therapy (9). It is not known whether only H. pylori was eradicated in individuals coinfected by H. pylori and H. suis or if instead H. suis arose after H. pylori eradication.Successful isolation and in vitro culture of H. pylori has dramatically contributed to elucidating the causal relationships between bacterial infection and gastric diseases as well as the molecular and cellular mechanisms of gastric cancer pathogenesis (10, 11). Successful isolation and in vitro culture of H. suis from pig stomach were reported in 2008 (12), and animal infection experiments using H. suis isolates from pigs demonstrated its pathogenicity. In addition, previous reports strongly suggested that H. suis infection contributes to gastric diseases in humans (SI Appendix, Table S1). However, studies on H. suis have been hindered because H. suis has not been successfully isolated from humans. In other words, the first and third of Koch’s postulates (13) (“association of the microbe with symptoms and presence of the microbe at the site of infection” and “reproduction of the disease by inoculation of a susceptible host with the microbe”) have been partially achieved for H. suis, whereas the remaining two postulates (“isolation of the microbe from lesions” and “re-isolation of the microbe from experimentally infected individuals”) have not.We developed a modified culture method for a human isolate, H. suis strain SNTW101c (14), which was isolated in 2008 from a patient with nodular gastritis and has been passaged in mouse stomach for 12 y by repeated inoculations of uninfected mice with gastric mucosal homogenates from infected mice (15). In this study, we succeeded in culturing H. suis directly from human gastric biopsies and demonstrated H. suis virulence in humans based on Koch’s postulates using an experimental animal model of H. suis infection. We also determined the complete genomes of H. suis isolates from humans and pigs and compared their genetic features.     

Structural insights into α-synuclein monomer–fibril interactions

Protein aggregation into amyloid fibrils is associated with multiple neurodegenerative diseases, including Parkinson’s disease. Kinetic data and biophysical characterization have shown that the secondary nucleation pathway highly accelerates aggregation via the absorption of monomeric protein on the surface of amyloid fibrils. Here, we used NMR and electron paramagnetic resonance spectroscopy to investigate the interaction of monomeric α-synuclein (α-Syn) with its fibrillar form. We demonstrate that α-Syn monomers interact transiently via their positively charged N terminus with the negatively charged flexible C-terminal ends of the fibrils. These intermolecular interactions reduce intramolecular contacts in monomeric α-Syn, yielding further unfolding of the partially collapsed intrinsically disordered states of α-Syn along with a possible increase in the local concentration of soluble α-Syn and alignment of individual monomers on the fibril surface. Our data indicate that intramolecular unfolding critically contributes to the aggregation kinetics of α-Syn during secondary nucleation.

Synucleinopathies, including Parkinson’s disease (PD), are associated with the accumulation of intracellular neuronal aggregates termed as Lewy bodies and Lewy neuritis, which contain high concentration of the protein α-synuclein (α-Syn) in an aggregated state (1, 2). The disease-relevant role of α-Syn is further highlighted by mutations in the α-Syn gene (SNCA) causing familial PD [i.e., A30P (3), E46K (4), H50Q (5), G51D (6), A53E (7), and A53T (8)] and the duplication or triplication of the SNCA leading to early-onset PD in affected families (9, 10). α-Syn is a 140-residue intrinsically disordered protein (IDP) in solution (11) but adopts a helical structure in the presence of acidic lipid surfaces (12, 13). The positively charged N terminus (residues 1 to 60) is rich in lysine residues and contains KTKEGV binding repeats associated with vesicle binding (14). Moreover, the N-terminal domain includes all known SNCA familial PD mutations. The central region (residues 61 to 95) defines the non-amyloid-β component (NAC) (15), which is essential for α-Syn aggregation (16), while the C terminus (residues 96 to 140) is highly negatively charged.In vitro, α-Syn forms polymorphic amyloid fibrils (17–19) with unique arrangements of cross-β-sheet motifs (20–22). When injected into model animals, these fibrils induce a PD-like pathology (23) where the aggregation pathway of α-Syn plays a key role in the development of the disease (24). A detailed analysis of the aggregation kinetics of α-Syn into amyloids is therefore important toward understanding the toxic mechanisms relevant for synucleinopathies.Amyloid formation of α-Syn is very sensitive to solution conditions, including pH (25), temperature (26), and salt concentration (27). It further requires the presence of an air–water interface (28) or negatively charged lipid membranes (29) for which α-Syn has a high affinity. Previous studies suggest that amyloid fibril growth of α-Syn occurs via a nucleation-dependent polymerization reaction (30). Following a fairly slow primary nucleus formation, α-Syn fibrils are elongated by addition of single monomers. In a next step, the amyloid fibrils multiply by fragmentation or can catalyze the formation of new amyloids from monomers on their surface—a process known as secondary nucleation that was first described for sickle cell anemia 40 y ago (31). Fragmentation and secondary nucleation critically depend on the fibril mass and accelerate the aggregation kinetics (30). In the case of α-Syn aggregation under quiescent condition fragmentation does not exist and only the described secondary nucleation process occurs. While detailed kinetic experiments showed no significant secondary nucleation at pH 7, it strongly contributes at pH values lower than 6 (25, 30). However, mechanistic or structural information of the secondary nucleation process in α-Syn aggregation has been lacking so far.In this study we investigated the structural properties of α-Syn monomer–fibril interactions by NMR and electron paramagnetic resonance (EPR) spectroscopy. Our results provide insights into how monomeric α-Syn transiently interacts in vitro via its positively charged N terminus with the negatively charged C-terminal residues of the α-Syn fibrils, giving detailed insights into the mechanism of the secondary nucleation process.     

Orthosteric–allosteric dual inhibitors of PfHT1 as selective antimalarial agents

Artemisinin-resistant malaria parasites have emerged and have been spreading, posing a significant public health challenge. Antimalarial drugs with novel mechanisms of action are therefore urgently needed. In this report, we exploit a “selective starvation” strategy by inhibiting Plasmodium falciparum hexose transporter 1 (PfHT1), the sole hexose transporter in P. falciparum, over human glucose transporter 1 (hGLUT1), providing an alternative approach to fight against multidrug-resistant malaria parasites. The crystal structure of hGLUT3, which shares 80% sequence similarity with hGLUT1, was resolved in complex with C3361, a moderate PfHT1-specific inhibitor, at 2.3-Å resolution. Structural comparison between the present hGLUT3-C3361 and our previously reported PfHT1-C3361 confirmed the unique inhibitor binding-induced pocket in PfHT1. We then designed small molecules to simultaneously block the orthosteric and allosteric pockets of PfHT1. Through extensive structure–activity relationship studies, the TH-PF series was identified to selectively inhibit PfHT1 over hGLUT1 and potent against multiple strains of the blood-stage P. falciparum. Our findings shed light on the next-generation chemotherapeutics with a paradigm-shifting structure-based design strategy to simultaneously target the orthosteric and allosteric sites of a transporter.

Plasmodium falciparum is the deadliest species of Plasmodium, responsible for around 50% of human malaria cases and nearly all malarial death (1). Despite intensive malaria-eradication efforts to control the spread of this disease, malaria prevalence remains alarmingly high, with 228 million cases and a fatality tally of 405,000 in 2018 alone (2). The situation has become even more daunting as resistance to the first-line antimalarial agents has emerged and is rapidly spreading. For instance, artemisinin resistance, primarily mediated by P. falciparum Kelch13 (PF3D7_1343700) propeller domain mutations (3, 4), severely compromises the campaign of antimalarial chemotherapy (5–9). Novel antimalarial agents overcoming the drug resistance are therefore urgently needed (10).The blood-stage malaria parasites depend on a constant glucose supply as their primary source of energy (11). P. falciparum hexose transporter 1 (PfHT1; PF3D7_0204700) (12) is transcribed from a single-copy gene with no close paralogue (13) and has been genetically validated as essential for the survival of the blood-stage parasite (14). A possible approach to kill the parasite is to “starve it out” by the chemical intervention of the parasite hexose transporter (13, 15). The feasibility of this approach would depend on the successful development of selective PfHT1 inhibitors that do not affect the activities of human hexose transporter orthologs (e.g., human glucose transporter 1 [hGLUT1]).Previously, Compound 3361 (C3361) (15), a glucose analog, has been reported to moderately inhibit PfHT1 and suppress the growth of blood-stage parasites in vitro (16). Nonetheless, the modest potency and selectivity of C3361 had limited its further development. Structural determination of PfHT1 and human glucose transporters provides an unprecedented opportunity for rational design of PfHT1-specific inhibitors (17–20). While hGLUT1 is the primary glucose transporter in erythrocyte, its structure was determined only in the inward-open state (17). Fortunately, the neuronal glucose transporter hGLUT3, which shares over 80% sequence similarity with hGLUT1, was captured in both outward-open and outward-occluded conformations (18). A reliable homology model of outward-facing hGLUT1 could thus be generated based on the structure of hGLUT3.Comparing the structures of PfHT1 (19, 20) and hGLUT1, we identified an additional pocket adjacent to the substrate-binding site. Coadministration of allosteric and orthosteric drugs is generally applied to tackle drug resistance when these two pockets were spatially separated (21). However, this discovery led to a hypothesis that simultaneously targeting the orthosteric and allosteric sites by tethering a pharmacophore to the carbohydrate core might render selective inhibitors for PfHT1. Based on this hypothesis, we designed a class of small molecules containing a sugar moiety and an allosteric pocket-occupying motif connected by a flexible linker. Among them, TH-PF01, TH-PF02, and TH-PF03 have exhibited selective biophysical and antiplasmodial activities with moderate cytotoxicity. Furthermore, in silico computational simulations also confirmed their binding mode, lending further support to the dual-inhibitor design. Taken together, our studies validated an antimalaria development strategy that simultaneously targets the orthosteric and allosteric sites of PfHT1.     

Heterozygous germline BLM mutations increase susceptibility to asbestos and mesothelioma

Rare biallelic BLM gene mutations cause Bloom syndrome. Whether BLM heterozygous germline mutations (BLM^+/−) cause human cancer remains unclear. We sequenced the germline DNA of 155 mesothelioma patients (33 familial and 122 sporadic). We found 2 deleterious germline BLM^+/− mutations within 2 of 33 families with multiple cases of mesothelioma, one from Turkey (c.569_570del; p.R191Kfs*4) and one from the United States (c.968A>G; p.K323R). Some of the relatives who inherited these mutations developed mesothelioma, while none with nonmutated BLM were affected. Furthermore, among 122 patients with sporadic mesothelioma treated at the US National Cancer Institute, 5 carried pathogenic germline BLM^+/− mutations. Therefore, 7 of 155 apparently unrelated mesothelioma patients carried BLM^+/− mutations, significantly higher (P = 6.7E-10) than the expected frequency in a general, unrelated population from the gnomAD database, and 2 of 7 carried the same missense pathogenic mutation c.968A>G (P = 0.0017 given a 0.00039 allele frequency). Experiments in primary mesothelial cells from Blm^+/− mice and in primary human mesothelial cells in which we silenced BLM revealed that reduced BLM levels promote genomic instability while protecting from cell death and promoted TNF-α release. Blm^+/− mice injected intraperitoneally with asbestos had higher levels of proinflammatory M1 macrophages and of TNF-α, IL-1β, IL-3, IL-10, and IL-12 in the peritoneal lavage, findings linked to asbestos carcinogenesis. Blm^+/− mice exposed to asbestos had a significantly shorter survival and higher incidence of mesothelioma compared to controls. We propose that germline BLM^+/− mutations increase the susceptibility to asbestos carcinogenesis, enhancing the risk of developing mesothelioma.

In the United States, the incidence rate of mesothelioma varies between fewer than one case per 100,000 persons in states with no asbestos industry to two to three cases per 100,000 persons in states with an asbestos industry (1, 2). Asbestos causes DNA damage and apoptosis (3) and promotes a chronic inflammatory reaction that supports the emergence of malignant cells (4). Fortunately, only a small fraction of exposed individuals develop mesothelioma; for example, 4.6% of deaths in miners who worked in asbestos mines for over 10 y were caused by mesothelioma (1). Therefore, multiple cases of mesothelioma in the same family are rare and suggest genetic predisposition (5). In 2001, we discovered that susceptibility to mesothelioma was transmitted in a Mendelian fashion across multiple generations in some Turkish families exposed to the carcinogenic fiber erionite, pointing to gene × environment interaction (G×E) as the cause (6). In 2011, we discovered that carriers of heterozygous germline BRCA1-associated protein–1 (BAP1) mutations (BAP1^+/−) developed mesothelioma and uveal melanoma (5), findings expanded and confirmed by us and by multiple research teams (reviewed in refs. 1, 7, 8). Moreover, heterozygous germline Bap1 mutations (Bap1^+/−) significantly increased susceptibility to asbestos-induced mesothelioma in mice (9, 10), evidence of G×E. Reduced BAP1 levels impair DNA repair (11) as well as different forms of cell death (3, 12) and induce metabolic alterations (13–15) that together favor cancer development and growth.Recent studies revealed that mesothelioma may also develop among carriers of germline mutations of additional tumor-suppressor genes that cause well-defined cancer syndromes, including MLH1 and MLH3 (Lynch syndrome), TP53 (Li–Fraumeni syndrome), and BRCA1-2 (Breast and Ovarian Cancer syndrome) (16, 17). When all germline mutations are combined, it has been estimated that about 12% of mesotheliomas occur in carriers of heterozygous germline mutations of BAP1, the most frequent mutation among patients with mesothelioma, or of other tumor suppressors. Some of these mutations may sensitize the host to asbestos carcinogenesis, according to a G×E scenario (17). Thus, presently, mesothelioma is considered an ideal model to study G×E in cancer (17). As part of the Healthy Nevada Project (HNP), we are studying G×E in northern Nevada, a region with an unusually high risk of exposure to carcinogenic minerals and arsenic, which may be related to the high cancer rates in this region (18). We are investigating genetic variants that may increase cancer risk upon exposure to carcinogens to implement preventive strategies.Biallelic mutations of the Bloom syndrome gene (BLM) cause Bloom syndrome, an autosomal-recessive tumor predisposition syndrome characterized by pre- and postnatal growth deficiency, photosensitivity, type 2 diabetes, and greatly increased risk of developing various types of cancers. BLM is a RecQ helicase enzyme that modulates DNA replication and repair of DNA damage by homologous recombination (19). In patients affected by Bloom syndrome, the absence of the BLM protein causes chromosomal instability, increased number of sister chromatid exchanges, and increased numbers of micronuclei (20–22). In addition, BLM is required for p53-mediated apoptosis (23), a process critical to eliminate cells that have accumulated DNA damage. Impaired DNA repair together with altered apoptosis resulted in increased cancer incidence (17, 24). Of course, inactivating germline BLM heterozygous (BLM^+/−) mutations are much more common than biallelic BLM (BLM^−/−) mutations, with an estimated frequency in the general population of 1 in 900 based on data from the Exome Aggregation Consortium (25). BLM^+/− mutation carriers do not show an obvious phenotype; however, some studies have suggested that carriers of these mutations may have an increased cancer risk (17, 24). Mice carrying Blm^+/− mutations are prone to develop a higher rate of malignancies in the presence of contributing factors, such as concurrent heterozygous mutations of the adenomatous polyposis coli (Apc) gene, or upon infection with murine leukemia virus (26). However, in studies in which Blm^+/− mice were crossed with tuberous sclerosis 1-deficient (Tsc1^+/−) mice that are predisposed to renal cystadenomas and carcinomas, Wilson et al. found that Tsc1^+/− Blm^+/− mice did not show significantly more renal cell carcinomas compared with Tsc1^+/− Blm^WT mice (27). In humans, a large study involving 1,244 patients with colon cancer and 1,839 controls of Ashkenazi Jewish ancestry, in which BLM^+/− frequency is as high as 1 in 100 individuals (28), suggested that carriers of germline BLM^+/− mutations might have a twofold increase in colorectal cancer (CRC) (29). A smaller study did not confirm these results, but reported a trend of increasing incidence of adenomas—premalignant lesions—among BLM^+/− mutation carriers (30). In addition, BLM^+/− mutations were found overrepresented among early-onset (<45 y old) CRC patients (25). Other studies associated BLM^+/− mutations to an increased risk of breast (31, 32) and prostate cancer (33), but the low power of these studies hampered definite conclusions. In summary, it appears possible that BLM^+/− mutations may increase cancer risk in the presence of contributing factors.     

LGI1–ADAM22–MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention

Physiological functioning and homeostasis of the brain rely on finely tuned synaptic transmission, which involves nanoscale alignment between presynaptic neurotransmitter-release machinery and postsynaptic receptors. However, the molecular identity and physiological significance of transsynaptic nanoalignment remain incompletely understood. Here, we report that epilepsy gene products, a secreted protein LGI1 and its receptor ADAM22, govern transsynaptic nanoalignment to prevent epilepsy. We found that LGI1–ADAM22 instructs PSD-95 family membrane-associated guanylate kinases (MAGUKs) to organize transsynaptic protein networks, including NMDA/AMPA receptors, Kv₁ channels, and LRRTM4–Neurexin adhesion molecules. Adam22^ΔC5/ΔC5 knock-in mice devoid of the ADAM22–MAGUK interaction display lethal epilepsy of hippocampal origin, representing the mouse model for ADAM22-related epileptic encephalopathy. This model shows less-condensed PSD-95 nanodomains, disordered transsynaptic nanoalignment, and decreased excitatory synaptic transmission in the hippocampus. Strikingly, without ADAM22 binding, PSD-95 cannot potentiate AMPA receptor-mediated synaptic transmission. Furthermore, forced coexpression of ADAM22 and PSD-95 reconstitutes nano-condensates in nonneuronal cells. Collectively, this study reveals LGI1–ADAM22–MAGUK as an essential component of transsynaptic nanoarchitecture for precise synaptic transmission and epilepsy prevention.

Epilepsy, characterized by unprovoked, recurrent seizures, affects 1 to 2% of the population worldwide. Many genes that cause inherited epilepsy when mutated encode ion channels, and dysregulated synaptic transmission often causes epilepsy (1, 2). Although antiepileptic drugs have mainly targeted ion channels, they are not always effective and have adverse effects. It is therefore important to clarify the detailed processes for synaptic transmission and how they are affected in epilepsy.Recent superresolution imaging of the synapse reveals previously overlooked subsynaptic nano-organizations and pre- and postsynaptic nanodomains (3–6), and mathematical simulation suggests their nanometer-scale coordination in individual synapses for efficient synaptic transmission: presynaptic neurotransmitter release machinery and postsynaptic receptors precisely align across the synaptic cleft to make “transsynaptic nanocolumns” (7, 8).So far, numerous transsynaptic cell-adhesion molecules have been identified (9–12), including presynaptic Neurexins and type IIa receptor protein tyrosine phosphatases (PTPδ, PTPσ, and LAR) and postsynaptic Neuroligins, LRRTMs, NGL-3, IL1RAPL1, Slitrks, and SALMs. Neurexins–Neuroligins have attracted particular attention because of their synaptogenic activities when overexpressed and their genetic association with neuropsychiatric disorders (e.g., autism). Another type of transsynaptic adhesion complex mediated by synaptically secreted Cblns (e.g., Neurexin–Cbln1–GluD2) promotes synapse formation and maintenance (13–15). Genetic studies in Caenorhabditis elegans show that secreted Ce-Punctin, the ortholog of the mammalian ADAMTS-like family, specifies cholinergic versus GABAergic identity of postsynaptic domains and functions as an extracellular synaptic organizer (16). However, the molecular identity and in vivo physiological significance of transsynaptic nanocolumns remain incompletely understood.LGI1, a neuronal secreted protein, and its receptor ADAM22 have recently emerged as major determinants of brain excitability (17) as 1) mutations in the LGI1 gene cause autosomal dominant lateral temporal lobe epilepsy (18); 2) mutations in the ADAM22 gene cause infantile epileptic encephalopathy with intractable seizures and intellectual disability (19, 20); 3) Lgi1 or Adam22 knockout mice display lethal epilepsy (21–24); and 4) autoantibodies against LGI1 cause limbic encephalitis characterized by seizures and amnesia (25–28). Functionally, LGI1–ADAM22 regulates AMPA receptor (AMPAR) and NMDA receptor (NMDAR)-mediated synaptic transmission (17, 22, 29) and Kv₁ channel-mediated neuronal excitability (30, 31). Recent structural analysis shows that LGI1 and ADAM22 form a 2:2 heterotetrameric assembly (ADAM22–LGI1–LGI1–ADAM22) (32), suggesting the transsynaptic configuration.In this study, we identify ADAM22-mediated synaptic protein networks in the brain, including pre- and postsynaptic MAGUKs and their functional bindings to transmembrane proteins (NMDA/AMPA glutamate receptors, voltage-dependent ion channels, cell-adhesion molecules, and vesicle-fusion machinery). ADAM22 knock-in mice lacking the MAGUK-binding motif show lethal epilepsy of hippocampal origin. In this mouse, postsynaptic PSD-95 nano-assembly as well as nano-scale alignment between pre- and postsynaptic proteins are significantly impaired. Importantly, PSD-95 is no longer able to modulate AMPAR-mediated synaptic transmission without binding to ADAM22. These findings establish that LGI1–ADAM22 instructs MAGUKs to organize transsynaptic nanocolumns and guarantee the stable brain activity.