Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity.

Long-read RNA sequencing has shed light on transcriptomic complexity, but questions remain about the functionality of downstream protein products. We introduce Biosurfer, a computational approach for comparing protein isoforms, while systematically tracking the transcriptional, splicing, and translational variations that underlie differences in the sequences of the protein products. Using Biosurfer, we analyzed the differences in 32,799 pairs of GENCODE annotated protein isoforms, finding a majority (70%) of variable N-termini are due to the alternative transcription start sites, while only 9% arise from 5' UTR alternative splicing. Biosurfer's detailed tracking of nucleotide-to-residue relationships helped reveal an uncommonly tracked source of single amino acid residue changes arising from the codon splits at junctions. For 17% of internal sequence changes, such split codon patterns lead to single residue differences, termed "ragged codons". Of variable C-termini, 72% involve splice- or intron retention-induced reading frameshifts. We found an unusual pattern of reading frame changes, in which the first frameshift is closely followed by a distinct second frameshift that restores the original frame, which we term a "snapback" frameshift. We analyzed long read RNA-seq-predicted proteome of a human cell line and found similar trends as compared to our GENCODE analysis, with the exception of a higher proportion of isoforms predicted to undergo nonsense-mediated decay. Biosurfer's comprehensive characterization of long-read RNA-seq datasets should accelerate insights of the functional role of protein isoforms, providing mechanistic explanation of the origins of the proteomic diversity driven by the alternative splicing. Biosurfer is available as a Python package at https://github.com/sheynkman-lab/biosurfer.

Patronin regulates presynaptic microtubule organization and neuromuscular junction development in Drosophila.

Synapses are fundamental components of the animal nervous system. Synaptic cytoskeleton is essential for maintaining proper neuronal development and wiring. Perturbations in neuronal microtubules (MTs) are correlated with numerous neuropsychiatric disorders. Despite discovering multiple synaptic MT regulators, the importance of MT stability, and particularly the polarity of MT in synaptic function, is still under investigation. Here, we identify Patronin, an MT minus-end-binding protein, for its essential role in presynaptic regulation of MT organization and neuromuscular junction (NMJ) development. Analyses indicate that Patronin regulates synaptic development independent of Klp10A. Subsequent research elucidates that it is short stop (Shot), a member of the Spectraplakin family of large cytoskeletal linker molecules, works synergistically with Patronin to govern NMJ development. We further raise the possibility that normal synaptic MT polarity contributes to proper NMJ morphology. Overall, this study demonstrates an unprecedented role of Patronin, and a potential involvement of MT polarity in synaptic development.

The difference in volumetric alternations of the orbitofrontal-limbic-striatal system between major depressive disorder and anxiety disorders: A systematic review and voxel-based meta-analysis.

BACKGROUND: Major depressive disorder (MDD) and anxiety disorders (ANX) are psychiatric disorders with high mutual comorbidity rates that might indicate some shared neurobiological pathways between them, but they retain diverse phenotypes that characterize themselves specifically. However, no consistent evidence exists for common and disorder-specific gray matter volume (GMV) alternations between them. METHODS: A systematic review and meta-analysis on voxel-based morphometry studies of patients with MDD and ANX were performed. The effect of comorbidity was explicitly controlled during disorder-specific analysis and particularly investigated in patient with comorbidity. RESULTS: A total of 45 studies with 54 datasets comprising 2196 patients and 2055 healthy participants met the inclusion criteria. Deficits in the orbitofrontal cortex, striatum, and limbic regions were found in MDD and ANX. The disorder-specific analyses showed decreased GMV in the bilateral anterior cingulate cortex, right striatum, hippocampus, and cerebellum in MDD, while decreased GMV in the left striatum, amygdala, insula, and increased cerebellar volume in ANX. A totally different GMV alternation pattern was shown involving bilateral temporal and parietal gyri and left fusiform gyrus in patients with comorbidity. LIMITATIONS: Owing to the design of included studies, only partial patients in the comorbid group had a secondary comorbidity diagnosis. CONCLUSION: Patients with MDD and ANX shared a structural disruption in the orbitofrontal-limbic-striatal system. The disorder-specific effects manifested their greatest severity in distinct lateralization and directionality of these changes that differentiate MDD from ANX. The comorbid group showed a totally different GMV alternation pattern, possibly suggesting another illness subtype that requires further investigation.

CT hyperdense lesions after endovascular therapy in acute ischemic stroke: imaging findings and clinical significance.

Background The hyperdense lesion on non-contrast CT (NCCT) is a common postoperative phenomenon in acute ischemic stroke (AIS) patients who are treated with endovascular therapy (EVT). Both contrast extravasation and hemorrhagic transformation presented hyperdense lesions on NCCT, which are sometimes difficult to distinguish them. Summary of Review Radiographic findings are important for identifying contrast extravasation and hemorrhagic transformation. We recommended a standardized follow-up protocol involving imaging and clinical evaluation as it will allow neurologists and neuroradiologists to reveal the relationships between these hyperdensities and various clinical outcomes. Key Messages Dual-energy CT and susceptibility weighted imaging are capable of distinguishing contrast extravasation and hemorrhagic transformation at an early stage after EVT. However, in institutions without access to such technology, a follow-up protocol based on NCCT is crucial.

Linked patterns of interhemispheric functional connectivity and microstructural characteristics of the corpus callosum in antipsychotic-naive first-episode schizophrenia.

OBJECTIVE: Many magnetic resonance imaging (MRI) studies have showed significant structural abnormalities of the corpus callosum (CC) and dysregulated interhemispheric functional connectivity (FC) in schizophrenia. Although the hemispheres are mainly linked through CC, few studies directly examined the relationship between aberrant interhemispheric FC and the white matter deficits of the CC in schizophrenia. METHODS: One hundred and sixty-nine antipsychotic-naive first-episode schizophrenia patients (AN-FES) and 214 healthy controls (HCs) were recruited. Diffusional and functional MRI data were obtained for each participant, and fractional anisotropy (FA) values of the five CC subregions and interhemispheric FC for each participant were acquired. Between-group differences in these metrics were compared using multivariate analysis of covariance (MANCOVA). Moreover, sparse canonical correlation analysis (sCCA) was conducted to explore correlations of fibers integrity of the CC subregions with dysregulated interhemispheric FC in patients. RESULTS: Compared with HCs, the patients with schizophrenia showed significantly reduced FA values of the CC subregions and dysregulated connectivity between two cerebral hemispheres. The canonical correlation coefficients identified five significant sCCA modes between FA and FC (r > 0.75, p < 0.001), suggesting strong relationships between FA values of the CC subregions and interhemispheric FC in patients. CONCLUSION: Our findings support a key role of CC in maintaining ongoing functional communication between two cerebral hemispheres, and suggest that microstructural changes of white matter fibers crossing different CC subregions may affect special interhemispheric FC in schizophrenia.

The whole-brain connectome landscape in patients with schizophrenia: A systematic review and meta-analysis of graph theoretical characteristics.

The alterations of connectome in schizophrenia have been reported, but the results remain inconsistent. We conducted a systematic review and random-effects meta-analysis on structural or functional connectome MRI studies comparing global graph theoretical characteristics between schizophrenia and healthy controls. Meta-regression and subgroup analyses were performed to examine confounding effects. Based on the included 48 studies, structural connectome in schizophrenia showed a significant decrease in segregation (lower clustering coefficient and local efficiency, Hedge's g= -0.352 and -0.864, respectively) and integration (higher characteristic path length and lower global efficiency, Hedge's g= 0.532 and -0.577 respectively). The functional connectome showed no difference between groups except γ. Moderator analysis indicated that clinical and methodological factors exerted a potential effect on the graph theoretical characteristics. Our analysis revealed a weaker small-worldization trend in structural connectome of schizophrenia. For the relatively unchanged functional connectome, more homogenous and high-quality studies are warranted to elucidate whether the change was blurred by heterogeneity or the presentation of pathophysiological reconfiguration.

A specific anti-cyclin D1 intrabody represses breast cancer cell proliferation by interrupting the cyclin D1-CDK4 interaction.

BACKGROUND: Cyclin D1 overexpression may contribute to development of various cancers, including breast cancer, and thus may serve as a key cancer diagnostic marker and therapeutic target. In our previous study, we generated a cyclin D1-specific single-chain variable fragment antibody (ADκ) from a human semi-synthetic single-chain variable fragment library. ADκ specifically interacted with recombinant and endogenous cyclin D1 proteins through an unknown molecular basis to inhibit HepG2 cell growth and proliferation. RESULTS: Here, using phage display and in silico protein structure modeling methods combined with cyclin D1 mutational analysis, key residues that bind to ADκ were identified. Notably, residue K112 within the cyclin box was required for cyclin D1-ADκ binding. In order to elucidate the molecular mechanism underlying ADκ anti-tumor effects, a cyclin D1-specific nuclear localization signal-containing intrabody (NLS-ADκ) was constructed. When expressed within cells, NLS-ADκ interacted specifically with cyclin D1 to significantly inhibit cell proliferation, induce G1-phase arrest, and trigger apoptosis of MCF-7 and MDA-MB-231 breast cancer cells. Moreover, the NLS-ADκ-cyclin D1 interaction blocked binding of cyclin D1 to CDK4 and inhibited RB protein phosphorylation, resulting in altered expression of downstream cell proliferation-related target genes. CONCLUSION: We identified amino acid residues in cyclin D1 that may play key roles in the ADκ-cyclin D1 interaction. A nuclear localization antibody against cyclin D1 (NLS-ADκ) was constructed and successfully expressed in breast cancer cells. NLS-ADκ exerted tumor suppressor effects via blocking the binding of CDK4 to cyclin D1 and inhibiting phosphorylation of RB. The results presented here demonstrate anti-tumor potential of intrabody-based cyclin D1-targeted breast cancer therapy.

Establishment of a novel axon pruning model of Drosophila motor neuron.

Developmental neuronal pruning is a process by which neurons selectively remove excessive or unnecessary neurite without causing neuronal death. Importantly, this process is widely used for the refinement of neural circuits in both vertebrates and invertebrates, and may also contribute to the pathogenesis of neuropsychiatric disorders, such as autism and schizophrenia. In the peripheral nervous system (PNS), class IV dendritic arborization (da) sensory neurons of Drosophila, selectively remove the dendrites without losing their somas and axons, while the dendrites and axons of mushroom body (MB) γ neuron in the central nervous system (CNS) are eliminated by localized fragmentation during metamorphosis. Alternatively, dendrite pruning of ddaC neurons is usually investigated via live-cell imaging, while dissection and fixation are currently used for evaluating MB γ neuron axon pruning. Thus, an excellent model system to assess axon specific pruning directly via live-cell imaging remains elusive. Here, we report that the Drosophila motor neuron offers a unique advantage for studying axon pruning. Interestingly, we uncover that long-range projecting axon bundle from soma at ventral nerve cord (VNC), undergoes degeneration rather than retraction during metamorphosis. Strikingly, the pruning process of the motor axon bundle is straightforward to investigate via live imaging and it occurs approximately at 22 h after pupal formation (APF), when axon bundles are completely cleared. Consistently, the classical axon pruning regulators in the Drosophila MB γ neuron, including TGF-ß signaling, ecdysone signaling, JNK signaling, and the ubiquitin-proteasome system are also involved in governing motor axon pruning. Finally, our findings establish an unprecedented axon pruning mode that will serve to systematically screen and identify undiscovered axon pruning regulators. This article has an associated First Person interview with the first author of the paper.

Radiomic features of gray matter in never-treated first-episode schizophrenia.

Alterations of radiomic features (RFs) in gray matter are observed in schizophrenia, of which the results may be limited by small study samples and confounding effects of drug therapies. We tested for RFs alterations of gray matter in never-treated first-episode schizophrenia (NT-FES) patients and examined their associations with known gene expression profiles. RFs were examined in the first sample with 197 NT-FES and 178 healthy controls (HCs) and validated in the second independent sample (90 NT-FES and 74 HCs). One-year follow-up data were available from 87 patients to determine whether RFs were associated with treatment outcomes. Associations between identified RFs in NT-FES and gene expression profiles were evaluated. NT-FES exhibited alterations of 30 RFs, with the greatest involvement of microstructural heterogeneity followed by measures of brain region shape. The identified RFs were mainly located in the central executive network, frontal-temporal network, and limbic system. Two baseline RFs with the involvement of microstructural heterogeneity predicted treatment response with moderate accuracy (78% for the first sample, 70% for the second sample). Exploratory analyses indicated that RF alterations were spatially related to the expression of schizophrenia risk genes. In summary, the present findings link brain abnormalities in schizophrenia with molecular features and treatment response.

The Extent of Edgetic Perturbations in the Human Interactome Caused by Population-Specific Mutations.

Until recently, efforts in population genetics have been focused primarily on people of European ancestry. To attenuate this bias, global population studies, such as the 1000 Genomes Project, have revealed differences in genetic variation across ethnic groups. How many of these differences can be attributed to population-specific traits? To answer this question, the mutation data must be linked with functional outcomes. A new "edgotype" concept has been proposed, which emphasizes the interaction-specific, "edgetic", perturbations caused by mutations in the interacting proteins. In this work, we performed systematic in silico edgetic profiling of ~50,000 non-synonymous SNVs (nsSNVs) from the 1000 Genomes Project by leveraging our semi-supervised learning approach SNP-IN tool on a comprehensive set of over 10,000 protein interaction complexes. We interrogated the functional roles of the variants and their impact on the human interactome and compared the results with the pathogenic variants disrupting PPIs in the same interactome. Our results demonstrated that a considerable number of nsSNVs from healthy populations could rewire the interactome. We also showed that the proteins enriched with interaction-disrupting mutations were associated with diverse functions and had implications in a broad spectrum of diseases. Further analysis indicated that distinct gene edgetic profiles among major populations could shed light on the molecular mechanisms behind the population phenotypic variances. Finally, the network analysis revealed that the disease-associated modules surprisingly harbored a higher density of interaction-disrupting mutations from healthy populations. The variation in the cumulative network damage within these modules could potentially account for the observed disparities in disease susceptibility, which are distinctly specific to certain populations. Our work demonstrates the feasibility of a large-scale in silico edgetic study, and reveals insights into the orchestrated play of population-specific mutations in the human interactome.

[Effect of origin species, body weight, and gender on quality of Bufonis Venenum].

Based on standard sampling for Bufonis Venenum, this study analyzed the effect of the origin, and body weight and gender of Bufo bufo gargarizans on the quality of Bufonis Venenum. To be specific, mass spectrometry(MS) and the content determination methods in Chinese Pharmacopoeia(2020) were adopted. First, MS was performed on 76 Bufonis Venenum samples collected from 40 cities/counties in 17 provinces/autonomous regions which were derived from B. bufo gargarizans and B. melanostictus. Based on content determination, the body weight and gender of B. bufo gargarizans, which influenced the quality of Bufonis Venenum, were evaluated. Multivariate statistical analysis suggested huge difference in the material basis of the medicinal material derived from B. bufo gargarizans and B. melanostictus, and 9 differential compounds were identified. The content of components specified in Chinese Pharmacopoeia was higher in the medicinal material derived from B. bufo gargarizans than in the medicinal material derived from B. melanostictus. The content of the components specified in Chinese Pharmacopoeia was low in Bufonis Venenum derived from heavy B. bufo gargarizans, and higher in the Bufonis Venenum produced by male B. bufo gargarizans than in that produced by female B. bufo gargarizans irrespective of time and geographic location. In summary, this study provide new ideas and reference for the quality control of Bufonis Venenum, collection and processing of Bufonis Venenum, artificial breeding of B. bufo gargarizans, and biosynthesis mechanism of Bufonis Venenum.

Uterine artery embolization combined with ultrasound-guided dilation and curettage for the treatment of cesarean scar pregnancy: Efficacy and 5-8-year follow-up study.

Objective: To evaluate the efficacy and safety of uterine artery embolization (UAE) combined with dilation and curettage (D&C) using ultrasound as a treatment for cesarean scar pregnancy (CSP) and assess its effect on ovarian and reproductive function. Methods: A total of 54 patients with uterine CSP between January 2011 and December 2015 were included in this retrospective study. The patients were treated with UAE combined with D&C using ultrasound for the treatment of CSP and followed up for 5-8 years. Their medical records, medical histories, clinical manifestations, treatment courses, and treatment results were analyzed. Results: The 54 patients were initially treated without severe complications. ß-Human chorionic gonadotropin (ß-hCG) normalization took 36.11 â€‹± â€‹10.73 days (range, 25-84 days), length of hospitalization was 6.6 â€‹± â€‹1.5 days (range, 4-10 days), and total blood loss was 18.48 â€‹± â€‹8.41 â€‹mL (range, 5-33 â€‹mL). All patients resumed normal menstruation after 33.48 â€‹± â€‹8.71 days (range, 26-70 days). At the 5-8-year follow-up after UAE combined with D&C by ultrasound for the treatment of uterine CSP, the menstrual volume in 32 (59.3%) patients decreased versus before the operation. Compared with pretreatment, the menstrual cycle was prolonged in two (3.7%) cases, shortened in 10 (18.5%) cases, irregular in one (1.9%) case, and unchanged in 39 (72.2%) cases. Three patients conceived naturally and successfully gave birth to healthy children. Seven (12.96%) patients with accidental natural pregnancies chose induced abortion with no significant change in their sex lives. Conclusion: UAE combined with D&C using ultrasound for the treatment of uterine CSP is safe and effective and may not affect the fertility of patients aged <40 years. However, menstrual volume may be reduced in some patients.

Comparisons of resting-state brain activity between insomnia and schizophrenia: a coordinate-based meta-analysis.

Growing evidence shows that insomnia is closely associated with schizophrenia (SCZ), but the neural mechanism under the association remains unclear. A direct comparison of the patterns of resting-state brain activities would help understand the above question. Using meta-analytic approach, 11 studies of insomnia vs. healthy controls (HC) and 39 studies of SCZ vs. HC were included to illuminate the common and distinct patterns between insomnia and SCZ. Results showed that SCZ and insomnia shared increased resting-state brain activities in frontolimbic structures including the right medial prefrontal gyrus (mPFC) and left parahippocampal gyrus. SCZ additionally revealed greater increased activities in subcortical areas including bilateral putamen, caudate and right insula and greater decreased activities in precentral gyrus and orbitofrontal gyrus. Our study reveals both shared and distinct activation patterns in SCZ and insomnia, which may provide novel insights for understanding the neural basis of the two disorders and enlighten the possibility of the development of treatment strategies for insomnia in SCZ in the future.

[Distribution characteristics of Bufo bufo gargarizans resources in China based on quality evaluation of Bufonis Venenum].

On the premise of strictly controlling the harvesting conditions of Bufonis Venenum, we studied the relationship between the quality and resource distribution of Bufonis Venenum in China, aiming to provide the data for comprehensively understanding the geographical distribution and characteristics of Bufonis Venenum in China. In this study, 105 samples of Bufonis Venenum were collected from 42 counties and cities in 19 provinces in China, and the material basis and index components were determined by mass spectrometry and high performance liquid chromatography. The obtained data formed the quality database of Bufonis Venenum from different producing areas in China. The analysis of the material basis showed that Bufonis Venenum was mainly produced in two characteristic regions(north area and south area) divided by Qinling Mountains, northern edge of Huaiyang hills and the connecting area of Huang-Huai Plain, Huangshan Mountains, and Tianmu Mountains. Eight differential components were identified in the Bufonis Venenum samples from the south area and the north area. All the Bufonis Venenum samples from the north area showed the content of index components above the requirements of Chinese Pharmacopoeia(2020 edition), while those from the south area had the content of index components lower than the standards of Chinese Pharmacopoeia(2020 edition). The quality evaluation showed uneven distribution of Bufonis Venenum quality, which was high in the north and low in the south. The results provided a research basis for the breeding base selection of Bufo bufo gargarizans.

Formononetin Protects LPS-Induced Mastitis Through Suppressing Inflammation and Enhancing Blood-Milk Barrier Integrity via AhR-Induced Src Inactivation.

Formononetin (FOR), a natural flavonoid derived from Radix Astragali, has been reported to have anti-inflammatory and anti-oxidative effects. However, its protective mechanism against mastitis is still unknown. Nuclear factor kappa-B (NF-κB) signaling pathway plays an important role in inflammation, especially mastitis. Aryl hydrocarbon receptor (AhR) is involved in inflammatory regulation and defense against diseases. We investigated the protective effect of FOR on LPS-induced mastitis in mice and the effect of Ahr and NF-κB signaling pathways on the development of mastitis. In this study, mastitis model was induced by LPS injection through the nipple duct. Protective effect of FOR on LPS-induced mastitis was assessed by FOR pretreatment. The protective mechanism of FOR against mastitis was further investigated using LPS stimulation on mouse mammary epithelial cells EpH4-Ev. The results showed that LPS-induced mammary histological injury was inhibited by FOR. FOR significantly inhibited LPS-induced MPO activity. FOR administration enhanced the integrity of blood-milk barrier. In vitro and in vivo experiments showed that FOR inhibited LPS-induced NF-κB signaling pathway activation and the production of inflammatory factors TNF-α and IL-1ß. Moreover, FOR increased the expression of tight junction protein and enhanced blood-milk barrier integrity. LPS activated AhR and Src expression. But FOR induced significant increase in AhR inhibited Src phosphorylation to exert anti-inflammatory effects. In addition, AhR antagonist CH223191 reversed the inhibition of FOR on Src expression. And the inhibition of FOR on NF-κB activation and inflammatory cytokine production were reversed by AhR antagonist CH223191. In conclusion, FOR had protective effects against LPS-induced mastitis via suppressing inflammation and enhancing blood-milk barrier integrity via AhR-induced Src inactivation.

Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins.

During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge, we leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.

Comparative oral and intravenous pharmacokinetics of phlorizin in rats having type 2 diabetes and in normal rats based on phase II metabolism.

Phlorizin (PHZ), a type of dihydrochalcone widely found in Rosaceae such as apples, is the first compound discovered as a sodium-glucose cotransporter (SGLT) inhibitor. It has been confirmed to improve the symptoms of diabetes and diabetic complications effectively. Like other flavonoids, the bioavailability challenge of PHZ is the wide phase I and II metabolism in the digestive tract. In this study, we investigated the pharmacokinetics and contribution of phase II metabolism after the oral and intravenous administrations of PHZ in rats having type 2 diabetes (T2D) and in normal rats. The phase II metabolism characteristics of PHZ were investigated by treating plasma samples with ß-glucuronidase/sulfatase. The contribution ratio of phase II metabolism of PHZ ranged from 41.9% to 69.0% after intravenous injection with three doses of PHZ in normal rats. Compared with the observations for normal rats, AUC0-t and Cmax of PHZ significantly increased and T1/2 of PHZ significantly decreased in T2D rats. PHZ was converted into phloretin (PHT) through an enzyme-catalyzed hydrolysis reaction, and PHT was further transformed into conjugates with glycose after both oral and intravenous administrations. Moreover, it was found that the bioavailability of PHZ was about 5% in T2D rats, which was significantly higher than that in normal rats (0%). In conclusion, compared with the observations for normal rats, the pharmacokinetic characteristics of PHZ significantly changed in T2D rats through oral and intravenous administrations. The bioavailability of PHZ significantly increased in T2D rats. Besides, the phase II metabolites of PHT were the major existing forms in blood after oral and intravenous administrations. Our results indicated that the phase II metabolism characteristics of PHZ should be considered when PHZ is applied for the treatment of diabetes as a drug or functional food.

Architecture, substructures, and dynamic assembly of STRIPAK complexes in Hippo signaling.

Striatin-interacting phosphatases and kinases (STRIPAKs) are evolutionarily conserved supramolecular complexes, which have been implicated in the Hippo signaling pathway. Yet the topological structure and dynamic assembly of STRIPAK complexes remain elusive. Here, we report the overall architecture and substructures of a Hippo kinase-containing STRIPAK complex. PP2Aa/c-bound STRN3 directly contacts the Hippo kinase MST2 and also controls the loading of MST2 via two "arms" in a phosphorylation-dependent manner, one arm being STRIP1 and the other SIKE1-SLMAP. A decreased cell density triggered the dissociation of the STRIP1 arm from STRIPAK, reflecting the dynamic assembly of the complex upon sensing upstream signals. Crystallographic studies defined at atomic resolution the interface between STRN3 and SIKE1, and that between SIKE1 and SLMAP. Disrupting the complex assembly abrogated the regulatory effect of STRIPAK towards Hippo signaling. Collectively, our study revealed a "two-arm" assembly of STRIPAK with context-dependent dynamics, offering a framework for further studies on Hippo signaling and biological processes involving MST kinases.

Microbiota of Inflammatory Bowel Disease Models.

Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.

Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids.

Organoids are three-dimensional cell cultures that mimic organ functions and structures. The organoid model has been developed as a versatile in vitro platform for stem cell biology and diseases modeling. Tumor organoids are shown to share ~ 90% of genetic mutations with biopsies from same patients. However, it's not clear whether tumor organoids recapitulate the cellular heterogeneity observed in patient tumors. Here, we used single-cell RNA-Seq to investigate the transcriptomics of tumor organoids derived from human colorectal tumors, and applied machine learning methods to unbiasedly cluster subtypes in tumor organoids. Computational analysis reveals cancer heterogeneity sustained in tumor organoids, and the subtypes in organoids displayed high diversity. Furthermore, we treated the tumor organoids with a first-line cancer drug, Oxaliplatin, and investigated drug response in single-cell scale. Diversity of tumor cell populations in organoids were significantly perturbed by drug treatment. Single-cell analysis detected the depletion of chemosensitive subgroups and emergence of new drug tolerant subgroups after drug treatment. Our study suggests that the organoid model is capable of recapitulating clinical heterogeneity and its evolution in response to chemotherapy.