Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.

Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.

CBP Is Required for Establishing Adaptive Gene Programs in the Adult Mouse Brain.

Environmental factors and life experiences impinge on brain circuits triggering adaptive changes. Epigenetic regulators contribute to this neuroadaptation by enhancing or suppressing specific gene programs. The paralogous transcriptional coactivators and lysine acetyltransferases CREB binding protein (CBP) and p300 are involved in brain plasticity and stimulus-dependent transcription, but their specific roles in neuroadaptation are not fully understood. Here we investigated the impact of eliminating either CBP or p300 in excitatory neurons of the adult forebrain of mice from both sexes using inducible and cell type-restricted knock-out strains. The elimination of CBP, but not p300, reduced the expression and chromatin acetylation of plasticity genes, dampened activity-driven transcription, and caused memory deficits. The defects became more prominent in elderly mice and in paradigms that involved enduring changes in transcription, such as kindling and environmental enrichment, in which CBP loss interfered with the establishment of activity-induced transcriptional and epigenetic changes in response to stimulus or experience. These findings further strengthen the link between CBP deficiency in excitatory neurons and etiopathology in the nervous system.SIGNIFICANCE STATEMENT How environmental conditions and life experiences impinge on mature brain circuits to elicit adaptive responses that favor the survival of the organism remains an outstanding question in neurosciences. Epigenetic regulators are thought to contribute to neuroadaptation by initiating or enhancing adaptive gene programs. In this article, we examined the role of CREB binding protein (CBP) and p300, two paralogous transcriptional coactivators and histone acetyltransferases involved in cognitive processes and intellectual disability, in neuroadaptation in adult hippocampal circuits. Our experiments demonstrate that CBP, but not its paralog p300, plays a highly specific role in the epigenetic regulation of neuronal plasticity gene programs in response to stimulus and provide unprecedented insight into the molecular mechanisms underlying neuroadaptation.

Soluble urokinase-type plasminogen activator receptor (suPAR) in patients with acute pancreatitis (AP) - Progress in prediction of AP severity.

BACKGROUND: Soluble urokinase-type plasminogen activator receptor (suPAR) is a glycoprotein secreted during inflammation and infections. Moreover, increased levels of suPAR are observed after hypoxia and ischaemia. The aim of the study was to assess whether suPAR could represent a useful marker of acute pancreatitis (AP) severity. PATIENTS AND METHODS: We have observed a cohort of 126 prospectively enrolled patients. Based on the presence of persistent organ failure (more than 48 h) and local complications (diagnosis of moderate AP [MSAP]), patients were classified into three groups: mild AP (MAP), moderate and severe AP (SAP). The blood samples were taken on admission for detecting suPAR concentrations. RESULTS: AP was considered severe in 33 patients (26.2%), MSAP was found in 37 patients (29.4%), and MAP was found in 56 patients (44,4%). The AUC for SAP predicted by suPAR was 0.993. The calculated cut-off point for prognosis SAP is 4.75 ng/mL. The BISAP score of ≥3 for detection of SAP had sensitivity and specificity of 94.6% and 63.6%, respectively. The AUC for severity predicted by BISAP amounted to 0.916. Additionally, suPAR turned out to be a good predictor of fatal AP: for the cut-off point 7.05 ng/mL, the AUC was 0.917. The AUC for death prediction in AP patients based on the BISAP score ≥3 was 0.894. CONCLUSIONS: suPAR concentration is a promising new diagnostic and prognostic indicator in SAP obtainable in the early stage of disease. Larger studies are recommended to evaluate this role further.

Autophosphorylation of alpha isoform of calcium/calmodulin-dependent kinase II regulates alcohol addiction-related behaviors.

The development of addiction is associated with a dysregulation of glutamatergic transmission in the brain reward circuit. α isoform of calcium/calmodulin-dependent kinase II (αCaMKII) is one of the key proteins that regulates structural and functional plasticity of glutamatergic synapses. αCaMKII activity can be controlled by the autophosphorylation of threonine 286. The role of this autophosphorylation in the regulation of addiction-related behaviors has been proposed but is still poorly understood. Here, using αCaMKII autophosphorylation-deficient mutant mice (T286A), we show that, in comparison with wild-type animals, they are less resistant to high doses of alcohol and do not show psychostimulant response neither to alcohol injections nor during voluntary alcohol drinking. T286A mutants are also less prone to develop alcohol addiction-related behaviors including an increased motivation for alcohol, persistent alcohol seeking during withdrawal and alcohol consumption on relapse. Finally, we demonstrate that αCaMKII autophosphorylation regulates also alcohol-induced remodeling of glutamatergic synapses in the hippocampus and amygdala. In conclusion, our data suggest that αCaMKII autophosphorylation-dependent remodeling of glutamatergic synapses is a plausible mechanism for the regulation of the alcohol addiction-related behaviors.

Mechanism for long-term memory formation when synaptic strengthening is impaired.

Long-term memory (LTM) formation has been linked with functional strengthening of existing synapses and other processes including de novo synaptogenesis. However, it is unclear whether synaptogenesis can contribute to LTM formation. Here, using α-calcium/calmodulin kinase II autophosphorylation-deficient (T286A) mutants, we demonstrate that when functional strengthening is severely impaired, contextual LTM formation is linked with training-induced PSD95 up-regulation followed by persistent generation of multiinnervated spines, a type of synapse that is characterized by several presynaptic terminals contacting the same postsynaptic spine. Both PSD95 up-regulation and contextual LTM formation in T286A mutants required signaling by the mammalian target of rapamycin (mTOR). Furthermore, we show that contextual LTM resists destabilization in T286A mutants, indicating that LTM is less flexible when synaptic strengthening is impaired. Taken together, we suggest that activation of mTOR signaling, followed by overexpression of PSD95 protein and synaptogenesis, contributes to formation of invariant LTM when functional strengthening is impaired.

Early changes in serum creatinine level and estimated glomerular filtration rate predict pancreatic necrosis and mortality in acute pancreatitis: Creatinine and eGFR in acute pancreatitis.

AIM: The aim of the study was to evaluate the significance of serum creatinine level (SCL) and estimated glomerular filtration rate (eGFR) measured in an early phase of acute pancreatitis (AP) for prediction of pancreatic necrosis (PNec) and mortality. METHODS: One hundred and forty-seven patients with AP were retrospectively reviewed in the study. Serum creatinine level and estimated glomerular filtration rate (calculated using the abbreviated Modification of Diet in Renal Disease equation) on admission and 48 h thereafter were analyzed for each patient. These parameters were compared with contrast-enhanced computed tomography images performed within 96 h from admission (n = 103). Usefulness of SCL and eGFR for prediction of PNec and fatal outcome of AP was evaluated using a receiver operator characteristic curve analysis and comparison of average parameter values. RESULTS: We confirmed pancreatic necrosis in 41 (39.8%) of 103 patients using computed tomography examination. Both creatinine and estimated glomerular filtration rate measured on admission (p < 0.001, p < 0.001 respectively) and 48 h later (p = 0.001, p < 0.001 respectively) were significantly associated with the presence of pancreatic necrosis. Moreover, serum creatinine level and eGFR measured on the 1st day proved to be a good predictor of fatal outcome. Both, mortality and presence of pancreatic necrosis were significantly higher in the group with elevated serum creatinine level and low eGFR values. CONCLUSIONS: SCL and eGFR on admission are useful indicators of PNec and mortality.

Conley-Morse-Forman theory for generalized combinatorial multivector fields on finite topological spaces.

We generalize and extend the Conley-Morse-Forman theory for combinatorial multivector fields introduced in Mrozek (Found Comput Math 17(6):1585-1633, 2017). The generalization is threefold. First, we drop the restraining assumption in Mrozek (Found Comput Math 17(6):1585-1633, 2017) that every multivector must have a unique maximal element. Second, we define the dynamical system induced by the multivector field in a less restrictive way. Finally, we also change the setting from Lefschetz complexes to finite topological spaces. Formally, the new setting is more general, because every Lefschetz complex is a finite topological space, but the main reason for switching to finite topologcial spaces is because the latter better explain some peculiarities of combinatorial topological dynamics. We define isolated invariant sets, isolating neighborhoods, Conley index and Morse decompositions. We also establish the additivity property of the Conley index and the Morse inequalities.

Rifaximin in gut microbiota modification in acute pancreatitis: 15 years of retrospective clinical study.

BACKGROUND: Gut decontamination could have some benefits in preventing infectious complications in acute pancreatitis (AP). OBJECTIVES: To investigate whether the administration of rifaximin could have an impact on the outcomes of AP. MATERIAL AND METHODS: We conducted a retrospective study on 373 patients with a median age of 50 years that were admitted to our Department of Gastroenterology in the years 2001-2016 with a diagnosis of AP. Patients were subclassified according to the revised Atlanta criteria: mild acute pancreatitis (MAP), moderately severe acute pancreatitis (MSAP) and severe acute pancreatitis (SAP). Thereafter, all the patients were divided into 2 groups: in the 1st group (R0) with MSAP and SAP, patients did not receive rifaximin, and in the 2nd group (R1), in the cases of MSAP and SAP, rifaximin was administered to patients at a dose of 3 × 400 mg (for at least 5 days and up to 7 days). There was no other difference in the treatment between the groups. The median duration of hospital stay, the number of infectious complications and the mortality rate were recorded for both groups. RESULTS: A significant difference was observed between median durations of hospitalization between the groups with (R1) and without (R0) rifaximin treatment (14 days compared to 24 days, p = 0.001) and in the number of patients infected with pancreatic necrosis (7 compared to 1, p = 0.0487). However, there was no statistically significant difference between the R1 and R0 group in terms of mortality rate. CONCLUSIONS: The results indicate that rifaximin seems to be a promising novel therapeutic option in MSAP and SAP.

Pancreatic cystic lesions in diabetes mellitus patients.

INTRODUCTION: According to the literature exocrine pancreatic insufficiency is relatively common among patients with diabetes mellitus (DM). Pseudocysts are the most common cystic lesions and may be formed in the setting of acute or chronic pancreatitis. However, whether DM is involved or not in pancreatic cyst formation is still not well established. AIM: To investigate the frequency and risk factors of cystic lesions in diabetic patients. MATERIAL AND METHODS: One hundred and sixty-one patients with DM, with no previous history of pancreatic diseases, were prospectively included in the study. Endosonography followed by fine needle aspiration biopsy was then performed. RESULTS: Finally, 33 of 161 patients (20.5%) were recognized with cystic lesions of the pancreas. Among them 5 patients were classified as cystic neoplasms, and 28 as pseudocysts. In the group of patients with pseudocysts, cystic lesions were significantly more prevalent in individuals with DM lasting less than 3 years. Prevalence of cystic lesions was significantly higher in metformin users in comparison to other diabetic patients (p < 0.05). Cystic lesions were more frequent in patients above 50 years of age (p < 0.05). CONCLUSIONS: The prevalence of cystic lesions in the diabetic population is higher than in the general population. DM seems to play a major role in the process of cyst development, especially in patients without previous history of pancreatitis. Higher prevalence of cystic lesions in early diabetes seems to be the first stage of pancreatic injury. The exact role of diabetes duration and type of treatment should be established.

Acute pancreatitis and the weekend effect: does weekend admission affect patient outcome?

INTRODUCTION: When a patient is admitted to a hospital for acute pancreatitis (AP), the day of the week on which the admission occurs may influence the outcome of care. The link between reduced weekend staffing practices and outcomes for patients hospitalised for AP, however, has been inadequately studied. AIM: To evaluate the relationship between weekend admission and AP outcome. MATERIAL AND METHODS: One hundred and twenty-six patients were prospectively included, assessed according to the revised Atlanta criteria, and observed until discharge or death. Weekend and weekday admissions were compared in terms of severity, aetiology, length of hospital stay, and in-hospital mortality. RESULTS: Patients were divided into two groups according to the timing of admission (weekday, n = 99, 78.6%; or weekend, n = 27, 21.4%). AP was considered severe in 33 (26.2%) patients, moderately severe AP in 37 (29.4%) patients, and mild in 56 (44.4%) patients. No significant differences were found with regard to the distribution of AP severity between the two groups. The impact of weekend admission was not significant for aetiology or for the length of hospital stay (median of 9 vs. 10 days). In-hospital mortality rates were not significantly different for weekday and weekend admissions. CONCLUSIONS: Patients admitted for hospitalisation during a weekend received the same level and quality of care at the facility under study as AP patients admitted during the week. Additionally, the rate of favourable outcomes for patients admitted during the weekend was found to be similar to the outcomes of patients admitted on a weekday.

Methods for prevention of acute post-endoscopic retrograde cholangiopancreatography pancreatitis.

Acute pancreatitis is the most common complication of endoscopic retrograde cholangiopancreatography (ERCP), with incidence rates ranging between 2% and 16%. In addition to being experienced in endoscopic procedures and having knowledge of the patient qualification criteria, physicians should also be aware of the patient and procedure-related risk factors responsible for post-ERCP pancreatitis (PEP). Intrarectal administration of nonsteroidal anti-inflammatory drugs and pancreatic duct stenting were demonstrated to be efficient in high-risk patients. This review provides a broader summary of pharmacological methods and techniques aimed at reducing the risk of PEP.

KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain.

The lysine acetyltransferases type 3 (KAT3) family members CBP and p300 are important transcriptional co-activators, but their specific functions in adult post-mitotic neurons remain unclear. Here, we show that the combined elimination of both proteins in forebrain excitatory neurons of adult mice resulted in a rapidly progressing neurological phenotype associated with severe ataxia, dendritic retraction and reduced electrical activity. At the molecular level, we observed the downregulation of neuronal genes, as well as decreased H3K27 acetylation and pro-neural transcription factor binding at the promoters and enhancers of canonical neuronal genes. The combined deletion of CBP and p300 in hippocampal neurons resulted in the rapid loss of neuronal molecular identity without de- or transdifferentiation. Restoring CBP expression or lysine acetylation rescued neuronal-specific transcription in cultured neurons. Together, these experiments show that KAT3 proteins maintain the excitatory neuron identity through the regulation of histone acetylation at cell type-specific promoter and enhancer regions.

CBP/p300 in brain development and plasticity: disentangling the KAT's cradle.

The paralogous transcriptional co-activators CBP and p300 (aka KAT3A and KAT3B, respectively) contain a characteristic and promiscuous lysine acetyltransferase (KAT) domain and multiple independent protein-binding domains that enable them to interact with hundreds of proteins, possibly promoting the acetylation of thousands of target lysine residues. Both proteins play critical roles during the development of the nervous system and may also regulate stimuli-driven transcription and plasticity in postmitotic neurons. The multiplicity of functions, substrates, and molecular partners, together with the redundancy and singularity of the two KAT3 paralogs, define a complex cat's cradle of relationships. In this review, we discuss the role of the KAT3 proteins in neurons and integrate recent information regarding their function and mode of action.

CBP and SRF co-regulate dendritic growth and synaptic maturation.

The CREB-binding protein (CBP) exerts tight control of developmental processes. Here, we investigated the consequences of its selective ablation in newborn neurons. Mice in which CBP was eliminated during neuronal differentiation showed perinatal death and defective diaphragm innervation. Adult-born neurons also showed impaired growth and maturation after inducible and restricted CBP loss in dentate gyrus neuroprogenitors. Consistent with these in vivo findings, cultured neurons displayed impaired outgrowth, immature spines, and deficient activity-dependent synaptic remodeling after CBP ablation. These deficits coincided with broad transcriptional changes affecting genes involved in neuronal growth and plasticity. The affected gene set included many predicted targets of both CBP and the serum response factor (SRF), an activity-regulated transcription factor involved in structural plasticity. Notably, increasing SRF activity in a CBP-independent manner ameliorated the transcriptional, synaptic, and growth defects. These results underscore the relevance of CBP-SRF interactions during neuronal outgrowth and synaptic maturation, and demonstrate that CBP plays an essential role in supporting the gene program underlying the last steps of neuronal differentiation, both during development and in the adult brain.

Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus.

Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here we combine genetic tagging of nuclei and ribosomes with RNA sequencing, chromatin immunoprecipitation with sequencing, assay for transposase-accessible chromatin using sequencing and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different time points after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions and the formation of gene loops that bring together the transcription start site and transcription termination site of induced genes and may sustain the fast reloading of RNA polymerase complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.

Cystic fluid neutrophil gelatinase-associated lipocalin (NGAL) concentration in differential diagnosis of pancreatic cystic lesions: a new factor enters the scene?

INTRODUCTION: Neutrophil gelatinase-associated lipocalin - 25 kDa peptide - is at present one of the most fascinating and unrecognised proteins implicated in the process of tumour development. Precise assessment of pancreatic cystic lesions is crucial for selecting available treatment options, such as conservative therapy or surgical resection. AIM: To determine the utility of NGAL concentration in cyst fluid obtained by endoscopic ultrasound (EUS) with EUS-guided fine-needle aspiration (EUS-FNA) to distinguish neoplastic pancreatic cysts from pseudocysts. MATERIAL AND METHODS: Twenty-two patients underwent EUS and FNA of a pancreatic cystic lesion; 9 of these patients underwent surgical resection, providing a histologic diagnosis of the cystic lesion. Furthermore, the final diagnosis was based on cyst fluid cytology, cyst fluid tumour markers (CEA, CA 72-4, CA 19-9), and medical history. Patients were divided in two groups: cystic neoplasms and inflammatory cysts (pseudocysts). RESULTS: The final diagnosis was pseudocyst in 7 patients, serous cystadenoma in 4, mucinous cystadenoma in 3, intraductal papillary mucinous neoplasms in 6 patients, and cystic form of pancreatic adenocarcinoma in 2. Cyst fluid analysis of these patients showed that median cyst fluid NGAL for the cystic neoplasm group (211 ng/ml; n = 15) was significantly lower (p = 0.02) than the inflammatory cystic group (4689 ng/ml; n = 7). Correlation analysis showed that only fluid CA 72-4 was positively related to NGAL (r = 0.8, p < 0.01). CONCLUSIONS: In this single-centre study, pancreatic cyst fluid NGAL concentration appeared to be useful in distinguishing neoplastic pancreatic cysts from pseudocysts. Larger studies are recommended to evaluate this role further.

Guidelines on the management of irritable bowel syndrome: In memory of Professor Witold Bartnik.

These guidelines constitute an update of the previous "Recommendations on the management of irritable bowel syndrome" issued in 2008. They have been developed by a Task Force organized by the Governing Board of the Polish Society of Gastroenterology. They discuss, with particular emphasis on new scientific data covering papers published since 2008, the aetiology, epidemiology, clinical presentation, diagnostic principles and criteria for the diagnosis, and recommendations for the treatment of irritable bowel syndrome (IBS). The English-language acronym for the syndrome (IBS) has become popular in medical and popular scientific language. It is also widely recognized by patients who identify with this diagnosis. Therefore, in the discussed guidelines, this is what we will use.

Diagnostic and therapeutic recommendations for chronic pancreatitis. Recommendations of the Working Group of the Polish Society of Gastroenterology and the Polish Pancreas Club.

This article describes the latest diagnostic and therapeutic recommendations in chronic pancreatitis, developed by the Working Group of the Polish Society of Gastroenterology and the Polish Pancreas Club. The recommendations refer to the diagnosis of chronic pancreatitis, autoimmune pancreatitis, conservative management, treatment of pain, and exocrine and endocrine pancreatic insufficiency, treatment of chronic pancreatitis by endoscopic and surgical methods, and oncological surveillance of chronic pancreatitis. This paper refers to the Polish recommendations published in 2011, which have been updated and supplemented. All recommendations were voted by experts of the Polish Society of Gastroenterology and the Polish Pancreas Club, who evaluated them each time on a five-degree scale, where I meant full acceptance, II - acceptance with some reservation, III - acceptance with serious reservation, IV - rejection with some reservation and V - full rejection. The results of the voting, together with a brief commentary, have been included with each recommendation put to the vote. In addition, the expert group assessed the value of clinical studies on which the statements are based, on a scale where A means high (based on meta-analyses and randomised clinical trials), B means medium (based on clinical trials and observational studies), and C means low (based mainly on expert opinion).

Immature granulocytes predict severe acute pancreatitis independently of systemic inflammatory response syndrome.

INTRODUCTION: Early prediction of severity of acute pancreatitis (AP) by a simple parameter that positively correlates with the activation stage of the immune system would be very helpful because it could influence the management and improve the outcome. Tumor necrosis factor α (TNF-α) and interleukin-1 (IL-1) play a critical role in the pathogenesis systemic inflammatory response syndrome (SIRS) and severity of AP. One of the effects of IL-1 and TNF-α is an increase in the number of immature granulocytes (IGs) in the peripheral blood. AIM: To assess whether the IGs% in plasma could be an independent marker of AP severity. MATERIAL AND METHODS: A cohort of 77 patients with AP were prospectively enrolled in the study. The IGs were measured from whole blood samples obtained from the first day of hospitalization using an automated analyser. RESULTS: We observed 44 (57%) patients with mild AP, 21 (27%) patients with moderate severe AP (SAP) and 12 (16%) patients with SAP. The cut-off value of IGs was 0.6%. The IGs > 0.6% had a sensitivity, specificity, and positive and negative predictive value of 100%, 96%, 85.7%, and 100%, respectively (area under the curve (AUC) = 0.98). On admission, SIRS was present in 25 (32%) patients. We found that in patients who fulfilled at least two criteria for SIRS, SAP could be predicted with 75% sensitivity and 75.4% specificity, positive predictive value 36%, negative predictive value 94.2%. CONCLUSIONS: The IGs% as a routinely obtained marker appears to be a promising, independent biomarker and a better predictor of early prognosis in SAP than SIRS and white blood cell.

Skill Learning Modulates RNA Pol II Poising at Immediate Early Genes in the Adult Striatum.

A multilayered complexity of epigenetic and transcriptional regulatory mechanisms underlies neuronal activity-dependent gene transcription. The regulation of RNA Pol II progression along the transcription cycle, from promoter-proximal poising (with RNA Pol II paused at promoter-proximal regions, characterized by a Ser5P+-rich and Ser2P+-poor RPB1 CTD) to active elongation, has emerged as a major step in transcriptional regulation across several organisms, tissues, and developmental stages, including the nervous system. However, it is not known whether this mechanism is modulated by experience. We investigated the impact of learning a motor skill on RNA Pol II phosphorylation dynamics in the adult mouse striatum. We uncovered that learning modulates the in vivo striatal phosphorylation dynamics of the CTD of the RNA Pol II RPB1 subunit, leading to an increased poising index in trained mice. We found that this modulation occurs at immediate early genes (IEGs), with increased poising of RNA Pol II at both Arc and Fos genes but not at constitutively expressed genes. Furthermore, we confirmed that this was learning dependent, and not just regulated by context or motor activity. These experiments demonstrate a novel phenomenon of learning induced transcriptional modulation in adult brain, which may have implications for our understanding of learning, memory allocation, and consolidation.