CD74 is a functional MIF receptor on activated CD4+ T cells.

Next to its classical role in MHC II-mediated antigen presentation, CD74 was identified as a high-affinity receptor for macrophage migration inhibitory factor (MIF), a pleiotropic cytokine and major determinant of various acute and chronic inflammatory conditions, cardiovascular diseases and cancer. Recent evidence suggests that CD74 is expressed in T cells, but the functional relevance of this observation is poorly understood. Here, we characterized the regulation of CD74 expression and that of the MIF chemokine receptors during activation of human CD4+ T cells and studied links to MIF-induced T-cell migration, function, and COVID-19 disease stage. MIF receptor profiling of resting primary human CD4+ T cells via flow cytometry revealed high surface expression of CXCR4, while CD74, CXCR2 and ACKR3/CXCR7 were not measurably expressed. However, CD4+ T cells constitutively expressed CD74 intracellularly, which upon T-cell activation was significantly upregulated, post-translationally modified by chondroitin sulfate and could be detected on the cell surface, as determined by flow cytometry, Western blot, immunohistochemistry, and re-analysis of available RNA-sequencing and proteomic data sets. Applying 3D-matrix-based live cell-imaging and receptor pathway-specific inhibitors, we determined a causal involvement of CD74 and CXCR4 in MIF-induced CD4+ T-cell migration. Mechanistically, proximity ligation assay visualized CD74/CXCR4 heterocomplexes on activated CD4+ T cells, which were significantly diminished after MIF treatment, pointing towards a MIF-mediated internalization process. Lastly, in a cohort of 30 COVID-19 patients, CD74 surface expression was found to be significantly upregulated on CD4+ and CD8+ T cells in patients with severe compared to patients with only mild disease course. Together, our study characterizes the MIF receptor network in the course of T-cell activation and reveals CD74 as a novel functional MIF receptor and MHC II-independent activation marker of primary human CD4+ T cells.

Twelve-month efficacy of second-generation cryoballoon ablation for atrial fibrillation performed at community hospitals: results of the German register on cryoballoon ablation in local hospitals (regional).

BACKGROUND: The 12-month follow-up (F/U) efficacy of CBA PVI performed at community hospitals for treatment of symptomatic paroxysmal and persistent atrial fibrillation (AF) is unknown. This study determined the 12-month efficacy of pulmonary vein isolation (PVI) using cryoballoon ablation (CBA) performed at community hospitals with limited annual case numbers. METHODS: This registry study included 983 consecutive patients (pts) from 19 hospitals, each with an annual procedural volume of < 100 PVI procedures/year. Pts underwent CBA PVI for paroxysmal AF (n = 520), persistent AF (n = 423), or redo PVI (n = 40). The primary endpoint was frequency of documented recurrent AF, the occurrence of atrial flutter or tachycardia following a 90-day period after the index ablation and up to 12 months. The frequency of repeat ablation was determined. RESULTS: Isolation of all PVs was documented in 98% of pts at the end of the procedure. Twelve-month F/U data could be obtained in 916 pts. A 24-h ECG registration was performed in 641 pts (70.0%); in 107 pts (16.7%) of them, recurrent AF was documented. The primary endpoint was met in 193 F/U pts (21.1%). It occurred in 80/486 F/U pts with paroxysmal AF (16.4%), and in 107/390 F/U pts with persistent AF (27.4%). Redo PVI was performed in 71 pts (7.8%), and atrial flutter ablation was performed in 12 pts (1.4%). CONCLUSIONS: CBA PVI for paroxysmal or persistent AF can be performed at community hospitals with adequate rates of 12-month symptom freedom and arrhythmia recurrence. The study was registered at the German register of clinical studies (DRKS00016504).

Safety and acute efficacy of cryoballoon ablation for atrial fibrillation at community hospitals.

AIMS: Pulmonary vein isolation (PVI) using cryoballoon ablation (CBA) is an established procedure for treating symptomatic paroxysmal and persistent atrial fibrillation (AF). The safety and efficacy of PVI performed at community hospitals are unknown. We aimed to determine the safety and acute efficacy of PVI using CBA performed at community hospitals with limited annual case numbers. METHODS AND RESULTS: This registry study included 1004 consecutive patients who had PVI performed for symptomatic paroxysmal (n = 563) or persistent AF (n = 441) from January 2019 to September 2020 at 20 hospitals. Each hospital performed fewer than 100 CBA-PVI procedures/year according to local standards. Procedural data, efficacy, and complication rates were determined. The mean number of CBA procedures performed/year at each centre was 59 ± 25. The average procedure time was 90.1 ± 31.6 min and the average fluoroscopy time was 19.2 ± 11.4 min. Isolation of all pulmonary veins was documented in 97.9% of patients. The most frequent reason for not achieving complete isolation was development of phrenic nerve palsy. No hospital deaths were observed. Two patients (0.2%) suffered a clinical stroke. Pericardial effusion occurred in six patients (0.6%), two of whom (0.2%) required pericardial drainage. Vascular complications occurred in 24 patients (2.4%), two of whom (0.2%) required vascular surgery. Phrenic nerve palsy occurred in 48 patients (4.8%) and persisted up to hospital discharge in six patients (0.6%). CONCLUSION: Pulmonary vein isolation procedures for paroxysmal or persistent AF using CBA can be performed at community hospitals with high acute efficacy and low complication rates.

Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma.

We report on next-generation transcriptome sequencing results of three human hepatocellular carcinoma tumor/tumor-adjacent pairs. This analysis robustly examined ∼12,000 genes for both expression differences and molecular alterations. We observed 4,513 and 1,182 genes demonstrating 2-fold or greater increase or decrease in expression relative to their normal, respectively. Network analysis of expression data identified the Aurora B signaling, FOXM1 transcription factor network and Wnt signaling pathways pairs being altered in HCC. We validated as differential gene expression findings in a large data set containing of 434 liver normal/tumor sample pairs. In addition to known driver mutations in TP53 and CTNNB1, our mutation analysis identified non-synonymous mutations in genes implicated in metabolic diseases, i.e. diabetes and obesity: IRS1, HMGCS1, ATP8B1, PRMT6 and CLU, suggesting a common molecular etiology for HCC of alternative pathogenic origin.

Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma.

The development and progression of cancer is associated with disruption of biological networks. Historically studies have identified sets of signature genes involved in events ultimately leading to the development of cancer. Identification of such sets does not indicate which biologic processes are oncogenic drivers and makes it difficult to identify key networks to target for interventions. Using a comprehensive, integrated computational approach, the authors identify the sonic hedgehog (SHH) pathway as the gene network that most significantly distinguishes tumour and tumour-adjacent samples in human hepatocellular carcinoma (HCC). The analysis reveals that the SHH pathway is commonly activated in the tumour samples and its activity most significantly differentiates tumour from the non-tumour samples. The authors experimentally validate these in silico findings in the same biologic material using Western blot analysis. This analysis reveals that the expression levels of SHH, phosphorylated cyclin B1, and CDK7 levels are much higher in most tumour tissues as compared to normal tissue. It is also shown that siRNA-mediated silencing of SHH gene expression resulted in a significant reduction of cell proliferation in a liver cancer cell line, SNU449 indicating that SHH plays a major role in promoting cell proliferation in liver cancer. The SHH pathway is a key network underpinning HCC aetiology which may guide the development of interventions for this most common form of human liver cancer.

Obesity in adults is associated with reduced lung function in metabolic syndrome and diabetes: the Strong Heart Study.

OBJECTIVE: The purposes of this study were to investigate whether reduced lung function is associated with metabolic syndrome (MS) and diabetes (DM) in American Indians (AIs) and to determine whether lower pulmonary function presents before the development of DM or MS. RESEARCH DESIGN AND METHODS: The Strong Heart Study (SHS) is a multicenter, prospective study of cardiovascular disease (CVD) and its risk factors among AI adults. The present analysis used lung function assessment by standard spirometry at the SHS second examination (1993-1995) in 2,396 adults free of overt lung disease or CVD, with or without DM or MS. Among MS-free/DM-free participants, the development of MS/DM at the SHS third examination (1996-1999) was investigated. RESULTS: Significantly lower pulmonary function was observed for AIs with MS or DM. Impaired pulmonary function was associated with MS and DM after adjustment for age, sex, abdominal obesity, current smoking status, physical activity index, hypertension, and SHS field center. Both forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1) were negatively associated with insulin resistance or DM severity and with serum markers of inflammation (P < 0.05). FVC and FEV1-to-FVC ratio both predicted DM in unadjusted analyses but not when adjusted for covariates, including waist circumference. In the adjusted model, abdominal obesity predicted both MS and DM. CONCLUSIONS: Reduced lung function is independently associated with MS and with DM, and impaired lung function presents before the development of MS or DM; these associations may result from the effects of obesity and inflammation.

The PathOlogist: an automated tool for pathway-centric analysis.

BACKGROUND: The PathOlogist is a new tool designed to transform large sets of gene expression data into quantitative descriptors of pathway-level behavior. The tool aims to provide a robust alternative to the search for single-gene-to-phenotype associations by accounting for the complexity of molecular interactions. RESULTS: Molecular abundance data is used to calculate two metrics--'activity' and 'consistency'--for each pathway in a set of more than 500 canonical molecular pathways (source: Pathway Interaction Database, http://pid.nci.nih.gov). The tool then allows a detailed exploration of these metrics through integrated visualization of pathway components and structure, hierarchical clustering of pathways and samples, and statistical analyses designed to detect associations between pathway behavior and clinical features. CONCLUSIONS: The PathOlogist provides a straightforward means to identify the functional processes, rather than individual molecules, that are altered in disease. The statistical power and biologic significance of this approach are made easily accessible to laboratory researchers and informatics analysts alike. Here we show as an example, how the PathOlogist can be used to establish pathway signatures that robustly differentiate breast cancer cell lines based on response to treatment.

Detecting cancer gene networks characterized by recurrent genomic alterations in a population.

High resolution, system-wide characterizations have demonstrated the capacity to identify genomic regions that undergo genomic aberrations. Such research efforts often aim at associating these regions with disease etiology and outcome. Identifying the corresponding biologic processes that are responsible for disease and its outcome remains challenging. Using novel analytic methods that utilize the structure of biologic networks, we are able to identify the specific networks that are highly significantly, nonrandomly altered by regions of copy number amplification observed in a systems-wide analysis. We demonstrate this method in breast cancer, where the state of a subset of the pathways identified through these regions is shown to be highly associated with disease survival and recurrence.

The BioPAX community standard for pathway data sharing.

Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.

Needles in the haystack: identifying individuals present in pooled genomic data.

Recent publications have described and applied a novel metric that quantifies the genetic distance of an individual with respect to two population samples, and have suggested that the metric makes it possible to infer the presence of an individual of known genotype in a sample for which only the marginal allele frequencies are known. However, the assumptions, limitations, and utility of this metric remained incompletely characterized. Here we present empirical tests of the method using publicly accessible genotypes, as well as analytical investigations of the method's strengths and limitations. The results reveal that the null distribution is sensitive to the underlying assumptions, making it difficult to accurately calibrate thresholds for classifying an individual as a member of the population samples. As a result, the false-positive rates obtained in practice are considerably higher than previously believed. However, despite the metric's inadequacies for identifying the presence of an individual in a sample, our results suggest potential avenues for future research on tuning this method to problems of ancestry inference or disease prediction. By revealing both the strengths and limitations of the proposed method, we hope to elucidate situations in which this distance metric may be used in an appropriate manner. We also discuss the implications of our findings in forensics applications and in the protection of GWAS participant privacy.

The completion of the Mammalian Gene Collection (MGC).

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

Identification of microbial DNA in human cancer.

BACKGROUND: Microorganisms have been associated with many types of human diseases; however, a significant number of clinically important microbial pathogens remain to be discovered. METHODS: We have developed a genome-wide approach, called Digital Karyotyping Microbe Identification (DK-MICROBE), to identify genomic DNA of bacteria and viruses in human disease tissues. This method involves the generation of an experimental DNA tag library through Digital Karyotyping (DK) followed by analysis of the tag sequences for the presence of microbial DNA content using a compiled microbial DNA virtual tag library. RESULTS: To validate this technology and to identify pathogens that may be associated with human cancer pathogenesis, we used DK-MICROBE to determine the presence of microbial DNA in 58 human tumor samples, including brain, ovarian, and colorectal cancers. We detected DNA from Human herpesvirus 6 (HHV-6) in a DK library of a colorectal cancer liver metastasis and in normal tissue from the same patient. CONCLUSION: DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases.

PID: the Pathway Interaction Database.

The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the US National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools.

Superposition of transcriptional behaviors determines gene state.

We introduce a novel technique to determine the expression state of a gene from quantitative information measuring its expression. Adopting a productive abstraction from current thinking in molecular biology, we consider two expression states for a gene--Up or Down. We determine this state by using a statistical model that assumes the data behaves as a combination of two biological distributions. Given a cohort of hybridizations, our algorithm predicts, for the single reading, the probability of each gene's being in an Up or a Down state in each hybridization. Using a series of publicly available gene expression data sets, we demonstrate that our algorithm outperforms the prevalent algorithm. We also show that our algorithm can be used in conjunction with expression adjustment techniques to produce a more biologically sound gene-state call. The technique we present here enables a routine update, where the continuously evolving expression level adjustments feed into gene-state calculations. The technique can be applied in almost any multi-sample gene expression experiment, and holds equal promise for protein abundance experiments.

A revision of Neomegalotomus (Hemiptera: Alydidae).

We recognize two species in Neomegalotomus, N. parvus (Westwood), the type species; and N. rufipes (Westwood). The two species are redescribed from type specimens, and are keyed. We synonymize the following species with Neomegalotomus parvus: N. simplex (Westwood), N. latifascia (Berg), and N. pallescens (Stål) (all new synonymies). We synonymize N. jamaicensis (Westwood) with N. rufipes (new synonymy). The type specimens of all species hitherto placed in the genus are also redescribed, except those of N. debilis (Walker) and N. vicinus (Westwood). N. parvus occurs from México through Central America into northern Argentina and east into Venezuela and adjacent Caribbean islands. N. rufipes is widespread in the Caribbean south towards Venezuela. The two species overlap in distribution: N. parvus is found on St. Vincent and Tobago, whereas N. rufipes occurs on Grenada, which lies between those two islands.

A Revision of Neomegalotomus (Hemiptera: Alydidae)

We recognize two species in Neomegalotomus, N. parvus (Westwood), the type species; and N. rufipes (Westwood). The two species are redescribed from type specimens, and are keyed. We synonymize the following species with Neomegalotomus parvus: N. simplex (Westwood), N. latifascia (Berg), and N. pallescens (Stål) (all new synonymies). We synonymize N. jamaicensis (Westwood) with N. rufipes (new synonymy). The type specimens of all species hitherto placed in the genus are also redescribed, except those of N. debilis (Walker) and N. vicinus (Westwood). N. parvus occurs from México through Central America into northern Argentina and east into Venezuela and adjacent Caribbean islands. N. rufipes is widespread in the Caribbean south towards Venezuela. The two species overlap in distribution: N. parvus is found on St. Vincent and Tobago, whereas N. rufipes occurs on Grenada, which lies between those two islands.

Duas espécies de Neomegalotomus, N. parvus (Westwood), a espécie tipo, e N. rufipes (Westwood) são reconhecidas. As duas espécies são redescritas a partir de espécies tipo e a chave para identificação é apresentada. As seguintes espécies são sinonimizadas com Neomegalotomus parvus: N. simplex (Westwood), N. latifascia (Berg), e N. pallescens (Stål) (todas novas sinonímias). N. jamaicensis (Westwood) é sinonimizada com N. rufipes (nova sinonímia). As espécies tipo de todas as espécies até agora colocadas no gênero são também redescritas, exceto N. debilis (Walker) e N. vicinus (Westwood). N. parvus ocorre do México através da América Central até o norte da Argentina e em direção à Venezuela e ilhas caribenhas adjacentes ao leste. N. rufipes encontra-se espalhada no sul do Caribe em direção à Venezuela. As duas espécies se sobrepõem em distribuição: N. parvus é encontrado em St. Vincent e Tobago, enquanto N. rufipes ocorre em Grenada, a qual situa-se entre essas duas ilhas.

The correct name of the neotropical soybean bug (Hemiptera: Alydidae).

A species of Neomegalotomus is an occasional pest of soybean [Glycine max (L.) Merrill] in the neotropics, including in Brazil. It was known as Neomegalotomus parvus (Westwood); but the discovery of the type specimen of a species described earlier requires that the name be changed to Neomegalotomus simplex (Westwood), which becomes the correct name for the soybean pest.

Identification of key processes underlying cancer phenotypes using biologic pathway analysis.

Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the specific molecular interaction of genes and their products. However, mapping of disease phenotypes to alterations of these networks of interactions is accomplished indirectly and non-systematically. Here we objectively identify pathways associated with malignancy, staging, and outcome in cancer through application of an analytic approach that systematically evaluates differences in the activity and consistency of interactions within canonical biologic processes. Using large collections of publicly accessible genome-wide gene expression, we identify small, common sets of pathways - Trka Receptor, Apoptosis response to DNA Damage, Ceramide, Telomerase, CD40L and Calcineurin - whose differences robustly distinguish diverse tumor types from corresponding normal samples, predict tumor grade, and distinguish phenotypes such as estrogen receptor status and p53 mutation state. Pathways identified through this analysis perform as well or better than phenotypes used in the original studies in predicting cancer outcome. This approach provides a means to use genome-wide characterizations to map key biological processes to important clinical features in disease.

The correct name of the neotropical soybean bug (Hemiptera: Alydidae)

A species of Neomegalotomus is an occasional pest of soybean [Glycine max (L.) Merrill] in the neotropics, including in Brazil. It was known as Neomegalotomus parvus (Westwood); but the discovery of the type specimen of a species described earlier requires that the name be changed to Neomegalotomus simplex (Westwood), which becomes the correct name for the soybean pest.

Uma espécie de Neomegalotomus é praga ocasional de soja [Glycine max (L.) Merrill] na Região Neotropical, incluindo o Brasil. Essa espécie era conhecida como Neomegalotomus parvus (Westwood); entretanto, a descoberta da espécie tipo de uma outra espécie, descrita anteriormente, requer que o nome seja trocado para Neomegalotomus simplex (Westwood), o que o torna o nome correto para essa praga da soja.

Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma.

Cancers have been described as wounds that do not heal, suggesting that the two share common features. By comparing microarray data from a model of renal regeneration and repair (RRR) with reported gene expression in renal cell carcinoma (RCC), we asked whether those two processes do, in fact, share molecular features and regulatory mechanisms. The majority (77%) of the genes expressed in RRR and RCC were concordantly regulated, whereas only 23% were discordant (i.e., changed in opposite directions). The orchestrated processes of regeneration, involving cell proliferation and immune response, were reflected in the concordant genes. The discordant gene signature revealed processes (e.g., morphogenesis and glycolysis) and pathways (e.g., hypoxia-inducible factor and insulin-like growth factor-I) that reflect the intrinsic pathologic nature of RCC. This is the first study that compares gene expression patterns in RCC and RRR. It does so, in particular, with relation to the hypothesis that RCC resembles the wound healing processes seen in RRR. However, careful attention to the genes that are regulated in the discordant direction provides new insights into the critical differences between renal carcinogenesis and wound healing. The observations reported here provide a conceptual framework for further efforts to understand the biology and to develop more effective diagnostic biomarkers and therapeutic strategies for renal tumors and renal ischemia.