Genome-wide enhancer RNA profiling adds molecular links between genetic variation and human cancers.

BACKGROUND: Dysregulation of enhancer transcription occurs in multiple cancers. Enhancer RNAs (eRNAs) are transcribed products from enhancers that play critical roles in transcriptional control. Characterizing the genetic basis of eRNA expression may elucidate the molecular mechanisms underlying cancers. METHODS: Initially, a comprehensive analysis of eRNA quantitative trait loci (eRNAQTLs) was performed in The Cancer Genome Atlas (TCGA), and functional features were characterized using multi-omics data. To establish the first eRNAQTL profiles for colorectal cancer (CRC) in China, epigenomic data were used to define active enhancers, which were subsequently integrated with transcription and genotyping data from 154 paired CRC samples. Finally, large-scale case-control studies (34,585 cases and 69,544 controls) were conducted along with multipronged experiments to investigate the potential mechanisms by which candidate eRNAQTLs affect CRC risk. RESULTS: A total of 300,112 eRNAQTLs were identified across 30 different cancer types, which exert their influence on eRNA transcription by modulating chromatin status, binding affinity to transcription factors and RNA-binding proteins. These eRNAQTLs were found to be significantly enriched in cancer risk loci, explaining a substantial proportion of cancer heritability. Additionally, tumor-specific eRNAQTLs exhibited high responsiveness to the development of cancer. Moreover, the target genes of these eRNAs were associated with dysregulated signaling pathways and immune cell infiltration in cancer, highlighting their potential as therapeutic targets. Furthermore, multiple ethnic population studies have confirmed that an eRNAQTL rs3094296-T variant decreases the risk of CRC in populations from China (OR = 0.91, 95%CI 0.88-0.95, P = 2.92 × 10-7) and Europe (OR = 0.92, 95%CI 0.88-0.95, P = 4.61 × 10-6). Mechanistically, rs3094296 had an allele-specific effect on the transcription of the eRNA ENSR00000155786, which functioned as a transcriptional activator promoting the expression of its target gene SENP7. These two genes synergistically suppressed tumor cell proliferation. Our curated list of variants, genes, and drugs has been made available in CancereRNAQTL ( http://canernaqtl.whu.edu.cn/#/ ) to serve as an informative resource for advancing this field. CONCLUSION: Our findings underscore the significance of eRNAQTLs in transcriptional regulation and disease heritability, pinpointing the potential of eRNA-based therapeutic strategies in cancers.

The lgi-miR-2d is Potentially Involved in Shell Melanin Synthesis by Targeting mitf in Manila Clam Ruditapes philippinarum.

Shell color as an important economic trait is also the crucial target trait for breeding and production. MicroRNA (miRNA) is an endogenous small non-coding RNA that can post-transcriptionally regulate the expression of target genes, it plays important roles in many life activities and physiological processes, such as shell color, stress response, and disease traits. In this study, we investigated the function of lgi-miR-2d in shell melanin formation and the expression patterns of lgi-miR-2d and target gene Rpmitf in Manila clam Ruditapes philippinarum. We further explored and verified the relationship between Rpmitf and lgi-miR-2d and identified the expression level of shell color-related gene changes by RNAi and injecting the antagomir of lgi-miR-2d, respectively. Our results indicated that lgi-miR-2d antagomir affected the expression of its target gene Rpmitf. In addition, the dual-luciferase reporter assay was conducted to confirm the direct interaction between lgi-miR-2d and Rpmitf. The results showed that the expression levels of melanin-related genes such as Rpmitf and tyr were significantly decreased in the positive treatment group compared with the blank control group after the Rpmitf dsRNA injection, indicating Rpmitf plays a crucial role in the melanin synthesis pathway. Taken together, we speculated that lgi-miR-2d might be negatively modulating Rpmitf, which might regulate other shell color-related genes, thereby affecting melanin synthesis in R. philippinarum.

Create your own path: social cerebellum in sequence-based self-guided navigation.

Spatial trajectory planning and execution in a social context play a vital role in our daily lives. To study this process, participants completed a goal-directed task involving either observing a sequence of preferred goals and self-planning a trajectory (Self Sequencing) or observing and reproducing the entire trajectory taken by others (Other Sequencing). The results indicated that in the observation phase, witnessing entire trajectories created by others (Other Sequencing) recruited cerebellar mentalizing areas (Crus 2 and 1) and cortical mentalizing areas in the precuneus, ventral and dorsal medial prefrontal cortex and temporo-parietal junction more than merely observing several goals (Self Sequencing). In the production phase, generating a trajectory by oneself (Self Sequencing) activated Crus 1 more than merely reproducing the observed trajectories from others (Other Sequencing). Additionally, self-guided observation and planning (Self Sequencing) activated the cerebellar lobules IV and VIII more than Other Sequencing. Control conditions involving non-social objects and non-sequential conditions where the trajectory did not have to be (re)produced revealed no differences with the main Self and Other Sequencing conditions, suggesting limited social and sequential specificity. These findings provide insights into the neural mechanisms underlying trajectory observation and production by the self or others during social navigation.

Large flour aggregates containing ordered B + V starch crystals significantly improved the digestion resistance of starch in pretreated multigrain flour.

The starch digestibility of flour is influenced by both physicochemical treatment and flour particle size, but the interactive effect of these two factors is still unclear. In this study, the effect of pullulanase debranching, combined with heat-moisture treatment (P-HMT), on starch digestibility of multi-grain flours (including oat, buckwheat and wheat) differing in particle size was investigated. The results showed that the larger-size flour always resulted in a higher resistant starch (RS) content either in natural or treated multi-grain flour (NMF or PHF). P-HMT doubled the RS content in NMFs and the large-size PHF yielded the highest RS content (78.43 %). In NMFs, the cell wall integrity and flour particle size were positively related to starch anti-digestibility. P-HMT caused the destruction of cell walls and starch granules, as well as the formation of rigid flour aggregates with B + V starch crystallite. The largest flour aggregates with the most ordered B + V starch were found in large-size PHF, which contributed to its highest RS yield, while the medium- and small-size PHFs with smaller aggregates were sensitive to P-HMT, resulting in the lower ordered starch but stronger interactions between starch and free lipid or monomeric proteins, eventually leading to their lower RS but higher SDS yield.

One step too far: social cerebellum in norm-violating navigation.

Social norms are pivotal in guiding social interactions. The current study investigated the potential contribution of the posterior cerebellum, a critical region involved in perceiving and comprehending the sequential dynamics of social actions, in detecting actions that either conform to or deviate from social norms. Participants engaged in a goal-directed task in which they observed others navigating towards a goal. The trajectories demonstrated either norm-violating (trespassing forbidden zones) or norm-following behaviors (avoiding forbidden zones). Results revealed that observing social norm-violating behaviors engaged the bilateral posterior cerebellar Crus 2 and the right temporoparietal junction (TPJ) from the mentalizing network, and the parahippocampal gyrus (PHG) to a greater extent than observing norm-following behaviors. These mentalizing regions were also activated when comparing social sequences against non-social and non-sequential control conditions. Reproducing norm-violating social trajectories observed earlier, activated the left cerebellar Crus 2 and the right PHG compared to reproducing norm-following trajectories. These findings illuminate the neural mechanisms in the cerebellum associated with detecting norm transgressions during social navigation, emphasizing the role of the posterior cerebellum in detecting and signaling deviations from anticipated sequences.

Genome-wide association analysis of left ventricular imaging-derived phenotypes identifies 72 risk loci and yields genetic insights into hypertrophic cardiomyopathy.

Left ventricular regional wall thickness (LVRWT) is an independent predictor of morbidity and mortality in cardiovascular diseases (CVDs). To identify specific genetic influences on individual LVRWT, we established a novel deep learning algorithm to calculate 12 LVRWTs accurately in 42,194 individuals from the UK Biobank with cardiac magnetic resonance (CMR) imaging. Genome-wide association studies of CMR-derived 12 LVRWTs identified 72 significant genetic loci associated with at least one LVRWT phenotype (P < 5 × 10-8), which were revealed to actively participate in heart development and contraction pathways. Significant causal relationships were observed between the LVRWT traits and hypertrophic cardiomyopathy (HCM) using genetic correlation and Mendelian randomization analyses (P < 0.01). The polygenic risk score of inferoseptal LVRWT at end systole exhibited a notable association with incident HCM, facilitating the identification of high-risk individuals. The findings yield insights into the genetic determinants of LVRWT phenotypes and shed light on the biological basis for HCM etiology.

Two is company: The posterior cerebellum and sequencing for pairs versus individuals during social preference prediction.

Previous studies have identified that the posterior cerebellum, which plays a role in processing temporal sequences in social events, is consistently and robustly activated when we predict future action sequences based on personality traits (Haihambo Haihambo et al. Social Cognitive and Affective Neuroscience 17(2), 241-251, 2022) and intentions (Haihambo et al. Cognitive, Affective, and Behavioral Neuroscience 23(2), 323-339, 2023). In the current study, we investigated whether these cerebellar areas are selectively activated when we predict the sequences of (inter)actions based on protagonists' preferences. For the first time, we also compared predictions based on person-to-person interactions or single person activities. Participants were instructed to predict actions of one single or two interactive protagonists by selecting them and putting them in the correct chronological order after being informed about one of the protagonists' preferences. These conditions were contrasted against nonsocial (involving objects) and nonsequencing (prediction without generating a sequence) control conditions. Results showed that the posterior cerebellar Crus 1, Crus 2, and lobule IX, alongside the temporoparietal junction and dorsal medial prefrontal cortex were more robustly activated when predicting sequences of behavior of two interactive protagonists, compared to one single protagonist and nonsocial objects. Sequence predictions based on one single protagonist recruited lobule IX activation in the cerebellum and more ventral areas of the medial prefrontal cortex compared to a nonsocial object. These cerebellar activations were not found when making predictions without sequences. Together, these findings suggest that cerebellar mentalizing areas are involved in social mentalizing processes which require temporal sequencing, especially when they involve social interactions, rather than behaviors of single persons.

A Functional Atlas of the Cerebellum Based on NeuroSynth Task Coordinates.

Although the human cerebellum has a surface that is about 80% of that of the cerebral cortex and has about four times as many neurons, its functional organization is still very much uncharted. Despite recent attempts to provide resting-state and task-based parcellations of the cerebellum, these two approaches lead to large discrepancies. This article describes a comprehensive task-based functional parcellation of the human cerebellum based on a large-scale functional database, NeuroSynth, involving an unprecedented diversity of tasks, which were reliably associated with ontological key terms referring to psychological functions. Involving over 44,500 participants from this database, we present a parcellation that exhibits replicability with earlier resting-state parcellations across cerebellar and neocortical structures. The functional parcellation of the cerebellum confirms the major networks revealed in prior work, including sensorimotor, directed (dorsal) attention, divided (ventral) attention, executive control, mentalizing (default mode) networks, tiny patches of a limbic network, and also a unilateral language network (but not the visual network), and the association of these networks with underlying ontological key terms confirms their major functionality. The networks are revealed at locations that are roughly similar to prior resting-state cerebellar parcellations, although they are less symmetric and more fragmented across the two hemispheres. This functional parcellation of the human cerebellum and associated key terms can provide a useful guide in designing studies to test specific functional hypotheses and provide a reference for interpreting the results.

Glutenin-gliadin ratio changes combining heat-moisture treatment significantly influences the in vitro digestibility of starch in recombinant wheat flours.

This study aimed to investigate the effect of heat-moisture treatment (HMT) on the in vitro digestibility of recombinant wheat flours characterizing by gluten proteins differ in glutenin-gliadin ratio. Compared with the untreated flours in our previous study, HMT improved the digestion resistance of starch in flours with different glutenin-gliadin ratios. For the HMT strong-gluten flour, the proportional increase of glutenin led to an excessively strong and fragile gluten network that unstable under HMT, which weakened the wrapping of gluten network around starch granules and reduced the long- and short-range order of starch, resulting in the conversion of resistant starch (RS) and slowly digestible starch (SDS) to rapidly digestible starch (RDS); however, the quantitative increase of gliadin induced the conversion of SDS to RS due to the enhanced protein-starch interactions as well as the improved long- and short-range order of starch during HMT. For the HMT weak-gluten flour, the changes of glutenin-gliadin ratio aggravated the broken of protein network and starch granules during HMT, thus improving the starch digestibility in varying degrees. In conclusion, the relative crystallinity of starch mainly affected the content of resistant starch, while the content of slowly digestible starch was more influenced by protein-starch interactions.

To Do or Not to Do: The cerebellum and neocortex contribute to predicting sequences of social intentions.

Humans read the minds of others to predict their actions and efficiently navigate social environments, a capacity called mentalizing. Accumulating evidence suggests that the cerebellum, especially Crus 1 and 2, and lobule IX are involved in identifying the sequence of others' actions. In the current study, we investigated the neural correlates that underly predicting others' intentions and how this plays out in the sequence of their actions. We developed a novel intention prediction task, which required participants to put protagonists' behaviors in the correct chronological order based on the protagonists' honest or deceitful intentions (i.e., inducing true or false beliefs in others). We found robust activation of cerebellar lobule IX and key mentalizing areas in the neocortex when participants ordered protagonists' intentional behaviors compared with not ordering behaviors or to ordering object scenarios. Unlike a previous task that involved prediction based on personality traits that recruited cerebellar Crus 1 and 2, and lobule IX (Haihambo et al., 2021), the present task recruited only the cerebellar lobule IX. These results suggest that cerebellar lobule IX may be generally involved in social action sequence prediction, and that different areas of the cerebellum are specialized for distinct mentalizing functions.

Effective cerebello-cerebral connectivity during implicit and explicit social belief sequence learning using dynamic causal modeling.

To study social sequence learning, earlier functional magnetic resonance imaging (fMRI) studies investigated the neural correlates of a novel Belief Serial Reaction Time task in which participants learned sequences of beliefs held by protagonists. The results demonstrated the involvement of the mentalizing network in the posterior cerebellum and cerebral areas (e.g. temporoparietal junction, precuneus and temporal pole) during implicit and explicit social sequence learning. However, little is known about the neural functional interaction between these areas during this task. Dynamic causal modeling analyses for both implicit and explicit belief sequence learning revealed that the posterior cerebellar Crus I & II were effectively connected to cerebral mentalizing areas, especially the bilateral temporoparietal junction, via closed loops (i.e. bidirectional functional connections that initiate and terminate at the same cerebellar and cerebral areas). There were more closed loops during implicit than explicit learning, which may indicate that the posterior cerebellum may be more involved in implicitly learning sequential social information. Our analysis supports the general view that the posterior cerebellum receives incoming signals from critical mentalizing areas in the cerebrum to identify sequences of social actions and then sends signals back to the same cortical mentalizing areas to better prepare for others' social actions and one's responses to it.

The posterior cerebellum and social action sequences in a cooperative context.

Recent research has suggested that the posterior cerebellum encodes predictions and sequences of social actions, and also supports detecting inconsistent trait-implying actions of individuals as discussed by Pu et al. (2020, 2021). However, little is known about the role of the posterior cerebellum in detecting sequencing and inconsistencies by a group of individuals during social interaction. Therefore, the present study investigates these cerebellar functions during inconsistent trait-implying actions in a cooperative context. We presented scenarios in which two fictitious protagonists work together to accomplish a common (positive or negative) goal, followed by six sentences describing actions that implied a personality trait of the protagonists. Participants had to memorize the sequence of these actions. Crucially, the implied trait of the actions of the first protagonist contributed to achieving the goal, whereas the implied trait of the second protagonist was either consistent or inconsistent with that goal. As comparison, we added control conditions where participants had to memorize sequences of nonsocial events (implying the same characteristic of two objects), or simply read the social actions without memorizing their order. We found that the posterior cerebellum was activated while memorizing the sequence of social actions compared to simply reading these actions. More importantly, the cerebellar Crus was more strongly activated when detecting inconsistent (as opposed to consistent) actions, especially when inconsistent negative actions impeded a positive goal, relative to consistent negative actions that supported a negative goal. In conclusion, these findings confirm the crucial role of the posterior cerebellum in memorizing social action sequences and extend the cerebellar function in identifying inconsistencies in an individual's actions in a social collaborative context.

Dynamic causal modeling of cerebello-cerebral connectivity when sequencing trait-implying actions.

Prior studies suggest that the cerebellum contributes to the prediction of action sequences as well as the detection of social violations. In this dynamic causal modeling study, we explored the effective connectivity of the cerebellum with the cerebrum in processing social action sequences. A first model aimed to explore functional cerebello-cerebral connectivity when learning trait/stereotype-implying action sequences. We found many significant bidirectional connectivities between mentalizing areas of the cerebellum and the cerebrum including the temporo-parietal junction (TPJ) and medial prefrontal cortex (mPFC). Within the cerebrum, we found significant connectivity between the right TPJ and the mPFC, and between the TPJ bilaterally. A second model aimed to investigate cerebello-cerebral connectivity when conflicting information arises. We found many significant closed loops between the cerebellum and cerebral mentalizing (e.g. dorsal mPFC) and executive control areas (e.g. medial and lateral prefrontal cortices). Additional closed loops were found within the cerebral mentalizing and executive networks. The current results confirm prior research on effective connectivity linking the cerebellum with mentalizing areas in the cerebrum for predicting social sequences, and extend it to cerebral executive areas for social violations. Overall, this study emphasizes the critical role of cerebello-cerebral connectivity in understanding social sequences.

Can transcranial direct current stimulation (tDCS) of the cerebellum improve implicit social and cognitive sequence learning?

Accumulating evidence shows that the posterior cerebellum is involved in mentalizing inferences of social events by detecting sequence information in these events, and building and updating internal models of these sequences. By applying anodal and sham cerebellar transcranial direct current stimulation (tDCS) on the posteromedial cerebellum of healthy participants, and using a serial reaction time (SRT) task paradigm, the current study examined the causal involvement of the cerebellum in implicitly learning sequences of social beliefs of others (Belief SRT) and non-social colored shapes (Cognitive SRT). Apart from the social or cognitive domain differences, both tasks were structurally identical. Results of anodal stimulation (i.e., 2 mA for 20 min) during the social Belief SRT task, did not show significant improvement in reaction times, however it did reveal generally faster responses for the Cognitive SRT task. This improved performance could also be observed after the cessation of stimulation after 30 min, and up to one week later. Our findings suggest a general positive effect of anodal cerebellar tDCS on implicit non-social Cognitive sequence learning, supporting a causal role of the cerebellum in this learning process. We speculate that the lack of tDCS modulation of the social Belief SRT task is due to the familiar and overlearned nature of attributing social beliefs, suggesting that easy and automatized tasks leave little room for improvement through tDCS.

The novel HLA-B*55:131 allele, identified by Sanger dideoxy nucleotide sequencing in a Chinese individual.

HLA-B*55:131 differs from HLA-B*55:02:01:01 by one nucleotide in exon 4.

Effects of HMW-GSs at Glu-B1 locus on starch-protein interaction and starch digestibility during thermomechanical processing of wheat dough.

BACKGROUND: The composition of glutenin protein significantly affects protein-starch interactions and starch digestion characteristics in wheat dough matrices. To elucidate the effects of high molecular weight glutenin subunits at the Glu-B1 locus on dough processing quality, the detailed structural changes of protein, starch, and their complexes were compared in Mixolab dough samples of two near isogenic lines 7 + 8 and 7 + 9. RESULTS: The results showed that the degree of protein aggregation increased continuously during dough processing, as did the destruction and rearrangement of the gluten network. Compared to 7 + 8, the stronger and more stable protein network formed in 7 + 9 dough induced intensive interactions between protein and starch, primarily through hydrogen bonds and isomeric glycosidic bonds. In 7 + 9 dough, the more compact and extensive protein-starch network significantly inhibited starch gelatinization during dough pasting, while during the dough cooling stage [from C4 (82.8 °C) to C5 (52.8 °C)], more protein-starch complexes composed of monomeric proteins and short-chain starch were generated, which remarkably inhibited starch retrogradation. All protein-starch interactions in the 7 + 9 dough improved the starch digestion resistance, as reflected by the high content of resistant starch. CONCLUSION: The more extensive and intensive protein-starch interactions in the 7 + 9 dough inhibited the gelatinization and enzymatic hydrolysis of starch, thereby producing more slowly digestible starch and resistant starch. These findings demonstrate the feasibility of optimizing the texture and digestibility of wheat-based food products by regulating the behavior and interactions of proteins and starch during dough processing. © 2022 Society of Chemical Industry.

Pre-baking-steaming of oat induces stronger macromolecular interactions and more resistant starch in oat-buckwheat noodle.

Pre-hydrothermal treatment is widely used to improve the quality of oat or buckwheat noodles. Noodle preparations containing pre-baked-steamed oat and untreated buckwheat (BUN) exhibited the highest sensory score (45.2) among six oat-buckwheat noodle preparations produced with different pre-hydrothermal treatments. Further comparison between the BUN and the noodle prepared with untreated oat and buckwheat showed that, the pre-baking-steaming of oat not only produced a more extended and thermally stable protein network involving rearranged gluten and oat globulins in cooked BUN, but also enhanced the short-range molecular order of gelatinized starch through the formation of nascent double helixes and binary/ternary complexes (starch-lipid, starch-protein and starch-lipid-protein). Overall, these stronger macromolecular interactions in cooked BUN led to an extensive and compact protein-starch network that promoted the formation of more resistant starch (41%). Our findings elucidated the molecular mechanism that underpin the positive effect of oat pretreatment on noodle quality and digestibility.

Effects of Composition and Strength of Wheat Gluten on Starch Structure, Digestion Properties and the Underlying Mechanism.

To understand the effect of gluten on starch digestion characteristics, the structural characteristics of protein, starch, and starch digestion attributes were explored by using flours of four wheat near-isogenic lines. Protein and starch fractions from the four flours were used to form so-called recombinant flours where glutenin and gliadin protein fractions, in different ratios, were combined with starch and heated in a water slurry at 80 °C for 5 min. We found that starch digestibility of the recombinant flours could be reproducibly modified by altering the long- and short-range molecular order of starch through varying the attributes of the gluten protein by virtue of the gluten strength as well as the proportions of glutenin and gliadins. The gluten composition changes of strong-gluten flour did not improve the starch digestion resistibility, however, for the moderate- and weak-gluten flours, the proportional increase of glutenin improved the resistance of starch to digestion through the increased long- and short-range molecular order of starch. The resistance of starch to digestion could also be enhanced with increasing gliadin, and was associated with the modified short-range molecular order of starch. We propose that flour mixtures can be optimized for specified product quality by manipulating the amounts of both gliadin and glutenin.

Impaired sequence generation: a preliminary comparison between high functioning autistic and neurotypical adults.

Earlier research demonstrated robust cerebellar involvement in sequencing, including high-level social information sequencing that requires mental state attributions, termed mentalizing. Earlier research also found cerebellar deficiencies in autism spectrum disorders (ASD) which are characterized by social difficulties. However, studies on high-level social sequencing functionality by persons with ASD are almost non-existent. In this study, we, therefore, perform a comparison between behavioral performances of high-functioning ASD and neurotypical participants on the Picture and Verbal Sequencing Tasks. In these tasks, participants are requested to put separate events (depicted in cartoon-like pictures or behavioral sentences, respectively) in their correct chronological order. To do so, some of these events require understanding of high-level social beliefs, of social routines (i.e., scripts), or nonsocial mechanical functionality. As expected, on the Picture Sequencing task, we observed longer response times for persons with ASD (in comparison with neurotypical controls) when ordering sequences requiring an understanding of social beliefs and social scripts, but not when ordering nonsocial mechanical events. This confirms our hypotheses that social sequence processing is impaired in ASD. The verbal version of this task did not reveal differences between groups. Our results are the first step toward new theoretical insights for social impairments of persons with ASD. They highlight the importance of taking into account sequence processing, and indirectly the cerebellum when investigating ASD difficulties.