Miracle-dz/UniFAR-FTUs huggingface dataset:
Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell lines

Numerous aspects of cellular signaling are regulated by the kinome – the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of kinases organized into functional subnetworks leads to kinome dysregulation being a key driver of many diseases, particularly cancer. In the case of pancreatic ductal adenocarcinoma (PDAC), a variety of kinases and associated signaling pathways have been identified for their key role in the establishment of disease as well as its progression. However, the identification of additional relevant therapeutic targets has been slow and is further confounded by interactions between the tumor and the surrounding tumor microenvironment. Fundamentally, it is an open question as to the degree to which knowledge of the state of the kinome at the protein level is able to provide insight into the downstream phenotype of the cell. In this work, we attempt to link the state of the kinome, or kinotype, with cell viability in representative PDAC tumor and stroma cell lines. Through the application of both regression and classification models to independent kinome perturbation and kinase inhibitor cell screen data, we find that the inferred kinotype of a cell has a significant and predictive relationship with cell viability. While regression models perform poorly, we find that classification approaches are able to predict drug viability effects. We further find that models are able to identify a set of kinases whose behavior in response to perturbation drive the majority of viability responses in these cell lines. Using the models to predict new compounds with cell viability effects and not in the initial data set, we conducted a validation screen that confirmed the accuracy of the models. These results suggest that characterizing the state of the protein kinome provides significant opportunity for better understanding signaling behavior and downstream cell phenotypes, as well as providing insight into the broader design of potential therapy design for PDAC.
E-cadherin regulates the stability and transcriptional activity of β-catenin in embryonic stem cells

E-CADHERIN is abundantly expressed in embryonic stem cells (ESCs) and plays an important role in the maintenance of cell-cell adhesions. However, the exact function of this molecule beyond cell adhesion, in the context of cell fate decisions is largely unknown. Using mouse ESCs (mESCs), we demonstrate that E-CADHERIN and β- CATENIN interact at the membrane and continue to do so upon internalization within the cell. Knockout of the gene encoding E-CADHERIN, Cdh1, in mESCs resulted in a failure to form tight colonies, accompanied by altered expression of differentiation markers, and retention of pluripotency factor expression during differentiation. Interestingly, Cdh1-/- mESCs showed a dramatic reduction in β-CATENIN levels. Transcriptional profiling of Cdh1-/- mESCs displayed a significant alteration in the expression of a subset of β-CATENIN targets, in a cell-state dependent manner. While treatment with a pharmacological inhibitor against GSK3β could rescue levels of β-CATENIN in Cdh1-/- mESCs, expression of downstream targets were altered in a context-dependent manner, indicating an additional layer of regulation within this subset. Together, our results reveal the existence of a cell-state-dependent regulation of β-CATENIN and its transcriptional targets in an E-CADHERIN dependent manner. Our findings hint at hitherto unknown roles played by E- CADHERIN in regulating the activity of β-CATENIN in ESCs. Significance Statement Are cell adhesions only responsible for maintaining tissue architecture, or do they also regulate cell fate decisions during early embryonic stages by modulating the output of specific signalling pathways? In this study, we study the role of E- CADHERIN, a crucial component of cell-cell adhesions in the context of mouse embryonic stem cells (mESCs). We find that E-CADHERIN regulates the stability and activity of β-CATENIN in mESCs through physical interactions. However, the loss of E-CADHERIN affected the expression of only a subset of downstream targets of β-CATENIN in a cell-state dependent manner. This study highlights a critical cross-talk between molecules involved in cell-cell adhesion and the underlying signalling network critical for establishing cell fate during early mammalian development.
Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequence complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome, which demonstrate that many genes are absent from the reference genomes whose analysis has dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and investigated network topology and differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable “occupancy” in the pan-genome – genes which are either present in all studied genotypes or missing in some genotypes – show different distributions among co-expression modules. Co-expression analysis united drought genes expressed in drought-stressed plants into 9 modules covering 343 hub genes (440 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 724 hub genes (911 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low- occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
GIV/Girdin binds BRCA1 and links trimeric G-proteins to DNA damage response

Upon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DNA damage hinges on two functions of GIV/Girdin, a guanine nucleotide-exchange modulator of heterotrimeric G-protein, Giα•βγ. First, GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1’s BRCT-modules via both phospho-dependent and -independent mechanisms. Second, GIV promotes NHEJ, and binds and activates Gi and enhances the ‘free’ Gβγ→PI-3-kinase→Akt pathway, thus revealing the enigmatic origin of prosurvival Akt signals during dsDNA repair. Absence of GIV, or the loss of either of its two functions impaired DNA repair, and induced cell death when challenged with numerous cytotoxic agents. That GIV selectively binds few other BRCT-containing proteins suggests convergent signaling such that heterotrimeric G-proteins may finetune sensing, repair, and outcome after DNA damage. GRAPHIC ABSTRACT HIGHLIGHTS Non-receptor G protein modulator, GIV/Girdin binds BRCA1 Binding occurs in both canonical and non-canonical modes GIV sequesters BRCA1 away from dsDNA breaks, suppresses HR Activation of Gi by GIV enhances Akt signals, favors NHEJ IN BRIEF In this work, the authors show that heterotrimeric G protein signaling that is triggered by non-receptor GEF, GIV/Girdin, in response to double-stranded DNA breaks is critical for decisive signaling events which favor non-homologous end-joining (NHEJ) and inhibit homologous recombination (HR).
Transcriptome wide association study of coronary artery disease identifies novel susceptibility genes

Transcriptome-wide association studies (TWAS) explore genetic variants affecting gene expression for association with a trait. Here we studied coronary artery disease (CAD) using this approach by first determining genotype-regulated expression levels in nine CAD relevant tissues by EpiXcan in two genetics-of-gene-expression panels, the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET) and the Genotype-Tissue Expression (GTEx). Based on these data we next imputed gene expression in respective nine tissues from individual level genotype data on 37,997 CAD cases and 42,854 controls for a subsequent gene-trait association analysis. Transcriptome-wide significant association (P < 3.85e-6) was observed for 114 genes, which by genetic means were differentially expressed predominately in arterial, liver, and fat tissues. Of these, 96 resided within previously identified GWAS risk loci and 18 were novel (CAND1, EGFLAM, EZR, FAM114A1, FOCAD, GAS8, HOMER3, KPTN, MGP, NLRC4, RGS19, SDCCAG3, STX4, TSPAN11, TXNRD3, UFL1, WASF1, and WWP2). Gene set analyses showed that TWAS genes were strongly enriched in CAD-related pathways and risk traits. Associations with CAD or related traits were also observed for damaging mutations in 67 of these TWAS genes (11 novel) in whole-exome sequencing data of UK Biobank. Association studies in human genotype data of UK Biobank and expression-trait association statistics of atherosclerosis mouse models suggested that newly identified genes predominantly affect lipid metabolism, a classic risk factor for CAD. Finally, CRISPR/Cas9-based gene knockdown of RGS19 and KPTN in a human hepatocyte cell line resulted in reduced secretion of APOB100 and lipids in the cell culture medium. Taken together, our TWAS approach was able to i) prioritize genes at known GWAS risk loci and ii) identify novel genes which are associated with CAD.
3D Collagen-Nanocellulose Matrices Model the Tumour Microenvironment of Pancreatic Cancer

Three-dimensional (3D) cancer models are invaluable tools designed to study tumour biology and new treatments. Pancreatic ductal adenocarcinoma (PDAC), one of the deadliest types of cancer, has been progressively explored with bioengineered 3D approaches by deconstructing elements of its tumour microenvironment. Here, we investigated the suitability of collagen-nanocellulose hydrogels to mimic the extracellular matrix of PDAC and to promote the formation of tumour spheroids and multicellular 3D cultures with stromal cells. Blending of type I collagen fibrils and cellulose nanofibres formed a matrix of controllable stiffness, which resembled the lower profile of pancreatic tumour tissues. Collagen-nanocellulose hydrogels supported the growth of tumour spheroids and multicellular 3D cultures, with increased metabolic activity and matrix stiffness. To validate our 3D cancer model, we tested the individual and combined effects of the anti-cancer compound triptolide and the chemotherapeutics gemcitabine and paclitaxel, resulting in differential cell responses. Our blended 3D matrices with tuneable mechanical properties consistently maintain the growth of PDAC cells and its cellular microenvironment and allow the screening of anti-cancer treatments.
Cathelicidin-WA Protects Against LPS-Induced Gut Damage Through Enhancing Survival and Function of Intestinal Stem Cells

Preservation of intestinal stem cells (ISCs) plays a critical role in initiating epithelial regeneration after intestinal injury. Cathelicidin peptides have been shown to participate in regulating intestinal damage repair. However, it is not known how exactly Cathelicidin-WA (CWA) exert its function after tissue damage. Using a gut injury model in mice involving Lipopolysaccharide (LPS), we observed that CWA administration significantly improved intestinal barrier function, preserved ISCs survival, and augmented ISCs viability within the small intestine (SI) under LPS treatment. In addition, CWA administration effectively prevented proliferation stops and promoted the growth of isolated crypts. Mechanistically, our results show that the appearance of γH2AX was accompanied by weakened expression of SETDB1, a gene that has been reported to safeguard genome stability. Notably, we found that CWA significantly rescued the decreased expression of SETDB1 and reduced DNA damage after LPS treatment. Taken together, CWA could protect against LPS-induced gut damage through enhancing ISCs survival and function. Our results suggest that CWA may become an effective therapeutic regulator to treat intestinal diseases and infections.
Lovastatin Alleviates α-Synuclein Aggregation and Phosphorylation in Cellular Models of Synucleinopathy

Parkinson’s disease (PD) is one of the most common neurodegenerative diseases. Pathologically, it is characterized by the aberrant aggregation of α-synuclein (α-syn) in neurons. Clinical evidence shows that patients with hypercholesterolemia are more likely to get PD, while lovastatin users have a lower risk of suffering from it. In this study, we investigated the effects of lovastatin on the aggregation and phosphorylation of α-syn in vitro. Our results demonstrate that α-syn preformed fibrils induce the phosphorylation and aggregation of α-syn in HEK293 cells stably transfected with α-syn-GFP and SH-SY5Y cells as well, which could be attenuated by in a concentration-dependent manner. Besides, lovastatin inhibited oxidative stress, histone acetylation, and the activation of casein kinase 2 (CK2). Collectively, lovastatin alleviates α-syn aggregation and phosphorylation in cellular models of synucleinopathy, indicating its potential value of being adopted in the management of PD.
Invasive Electrophysiology for Circuit Discovery and Study of Comorbid Psychiatric Disorders in Patients With Epilepsy: Challenges, Opportunities, and Novel Technologies

Intracranial electroencephalographic (iEEG) recordings from patients with epilepsy provide distinct opportunities and novel data for the study of co-occurring psychiatric disorders. Comorbid psychiatric disorders are very common in drug-resistant epilepsy and their added complexity warrants careful consideration. In this review, we first discuss psychiatric comorbidities and symptoms in patients with epilepsy. We describe how epilepsy can potentially impact patient presentation and how these factors can be addressed in the experimental designs of studies focused on the electrophysiologic correlates of mood. Second, we review emerging technologies to integrate long-term iEEG recording with dense behavioral tracking in naturalistic environments. Third, we explore questions on how best to address the intersection between epilepsy and psychiatric comorbidities. Advances in ambulatory iEEG and long-term behavioral monitoring technologies will be instrumental in studying the intersection of seizures, epilepsy, psychiatric comorbidities, and their underlying circuitry.
Phonetically Grounded Structural Bias in Learning Tonal Alternations

This study investigates the hypothesis that tone alternation directionality becomes a basis of structural bias for tone alternation learning, where “structural bias” refers to a tendency to prefer uni-directional tone deletions to bi-directional ones. Two experiments were conducted. In the first, Mandarin speakers learned three artificial languages, with bi-directional tone deletions, uni-directional, left-dominant deletions, and uni-directional, right-dominant deletions, respectively. The results showed a learning bias toward uni-directional, right-dominant patterns. As Mandarin tone sandhi is right-dominant while Cantonese tone change is lexically restricted and does not have directionality asymmetry, a follow-up experiment trained Cantonese speakers either on left- or right-dominant deletions to see whether the right-dominant preference was due to L1 transfer from Mandarin. The results of the experiment also showed a learning bias toward right-dominant patterns. We argue that structural simplicity affects tone deletion learning but the simplicity should be grounded on phonetics factors, such as syllables’ contour-tone bearing ability. The experimental results are consistent with the findings of a survey on other types of tone alternation’s directionality, i.e., tone sandhi across 17 Chinese varieties. This suggests that the directionality asymmetry found across different tone alternations reflects a phonetically grounded structural learning bias.
Chaperonin Abundance Enhances Bacterial Fitness

The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that their abundance should be evolutionarily advantageous. Here, we investigate the effect of chaperonin overproduction on cellular fitness in Escherichia coli. We demonstrate that chaperonin abundance confers 1) an ability to tolerate higher temperatures, 2) improved cellular fitness, and 3) enhanced folding of metabolic enzymes, which is expected to lead to enhanced energy harvesting potential.
Investigating the Youth Sports Development Pathway Within a South African Context

The past two decades witnessed increased participation in professional as well as amateur sport, giving impetus to concomitant amplified interest in long-term athlete development (LTAD). LTAD has been described as the structured and progressive growth of an athlete through different stages of development resulting in some athletes achieving elite sport status. Furthermore, the interest in athletic career development from a holistic perspective has contributed to management approaches underscoring sustainable talent development and participation in sport. The current study investigated youth sports development pathways through both models of development within a South African context. A descriptive quantitative cross-sectional design was used to generate a convenient sample of athletes (N = 267). The Talent Development Environment Questionnaire (TDEQ) was administered, which in previous studies produced acceptable psychometric properties. Principal factor analysis, confirmatory factor analysis, Monte Carlo parallel simulation, MANOVA, and hierarchical regression were performed to analyze the data. The TDEQ was validated for the South African context and was found to measure four components, namely supportive and challenging environment, development fundamentals, support networks, and long-term development. Respondents in the various developmental categories of novice, advanced and elite student-athletes were not statistically significantly influenced by any of the four factors. Controlling for the talent developmental phase, the model proposed did not statistically significantly predict the development pathway of youth athletes. The results provide evidence with some practical significance as supportive and challenging environment and long-term development focus reported a small effect. Further research is warranted to develop a more suitable measuring instrument to measure the talent development pathway within the investigated athlete environment.
Effects of Vessel Interruption Sequence During Lobectomy for Non-small Cell Lung Cancer: A Systematic Review and Meta-Analysis

Background: For lobectomy in non-small cell lung cancer (NSCLC), whether interrupting the pulmonary vein first (Vein-first) achieves better perioperative and survival outcomes than interrupting the pulmonary artery first (Artery-first) remains controversial. We conducted this meta-analysis to compare outcomes between the two groups to facilitate better surgical decision-making. Methods: Web of Science, EMBASE, Cochrane Library, Ovid MEDLINE, PubMed, ScienceDirect, and Scopus were searched for eligible studies comparing Vein-first and Artery-first procedures. The primary endpoints were survival indicators [overall survival (OS), disease-free survival (DFS), and lung cancer-specific survival (LCSS)]. Secondary endpoints included intraoperative indicators, hospitalization, and follow-up indicators. Results: After screening 2,505 studies, 8 studies involving 1,714 patients (Vein-First group: 881 patients; Artery-first group: 833 patients) were included. The vein-first group achieved better OS [HR (hazard ratio): 1.46, 95% confidence interval (CI): 1.12–1.91, p = 0.005], DFS (HR: 1.60, 95% CI: 1.23–2.08, p < 0.001), and LCSS (HR: 1.64, 95% CI: 1.16–2.31, p = 0.005). The survival rates of OS at 2–5 years, DFS at 1–5 years, and LCSS at 3–5 years were also higher in the Vein-First group. Subgroup analyses suggested that the advantages of survival in the Vein-First group were primarily embodied in the subgroups of squamous cell carcinoma (SCC) and earlier pathological TNM stage (I–II). Operative time, intraoperative blood loss, total complications, and total recurrences were comparable between the two groups. Conclusions: The Vein-first sequence is the suitable choice of vessel interruption sequence during lobectomy for NSCLC with better survival and similar perioperative outcomes, especially for stage I–II SCC.
PHF6 Mutations in Hematologic Malignancies

Next generation sequencing has uncovered several genes with associated mutations in hematologic malignancies that can serve as potential biomarkers of disease. Keeping abreast of these genes is therefore of paramount importance in the field of hematology. This review focuses on PHF6, a highly conserved epigenetic transcriptional regulator that is important for neurodevelopment and hematopoiesis. PHF6 serves as a tumor suppressor protein, with PHF6 mutations and deletions often implicated in the development of T-lymphoblastic leukemia and less frequently in acute myeloid leukemia and other myeloid neoplasms. PHF6 inactivation appears to be an early event in T-lymphoblastic leukemogenesis, requiring cooperating events, including NOTCH1 mutations or overexpression of TLX1 and TLX3 for full disease development. In contrast, PHF6 mutations tend to occur later in myeloid malignancies, are frequently accompanied by RUNX1 mutations, and are often associated with disease progression. Moreover, PHF6 appears to play a role in lineage plasticity within hematopoietic malignancies, with PHF6 mutations commonly present in mixed phenotype acute leukemias with a predilection for T-lineage marker expression. Due to conflicting data, the prognostic significance of PHF6 mutations remains unclear, with a subset of studies showing no significant difference in outcomes compared to malignancies with wild-type PHF6, and other studies showing inferior outcomes in certain patients with mutated PHF6. Future studies are necessary to elucidate the role PHF6 plays in development of T-lymphoblastic leukemia, progression of myeloid malignancies, and its overall prognostic significance in hematopoietic neoplasms.
The Vicious Cycle: Problematic Family Relations, Substance Abuse, and Crime in Adolescence: A Narrative Review

Despite the copiousness of studies on the risky behaviors of adolescents, we cannot establish with certainty the leading aspects involved in teens’ substance abuse and criminal actions. This review aims to explore the interplay among the family system, substance abuse, and criminal behavior. An analysis of the main results of the 61 articles published between 2010 and 2020 shows that adolescents whose parents are justice-involved and often absent from home are more likely to perceive lower cohesion, support, and poor family communication. These factors can involve them in criminal acts and substance abuse. Moreover, these conducts are often linked to a form of uneasiness and a search of autonomy. Indeed, risky behaviors could have more than one meaning. Our findings also suggest that the most diffused drug-related crimes in adolescence are economic crimes, weapon carrying, robberies, dealing, and drug possession. Considering these results, future clinical implications might be based on multidimensional approaches, focusing more on the family context to promote interventions for at-risk adolescents.