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OBJECTIVES The acute respiratory distress syndrome is common in critically ill patients. Recognition is crucial because acute respiratory distress syndrome is associated with a high mortality rate, and low tidal volume ventilation improves mortality. However, acute respiratory distress syndrome often goes unrecognized. Risk factors for under-recognition and trends over time have not been fully described. DESIGN Retrospective chart review of patients with acute respiratory distress syndrome from a prospective cohort study of critically ill patients. For each patient's ICU stay, we searched the chart for terms that indicated that acute respiratory distress syndrome was diagnosed, in the differential diagnosis, or treated with low tidal volume ventilation. SETTING ICUs at a tertiary hospital at the University of California, San Francisco between 2008 and 2016. PATIENTS Critically ill patients with acute respiratory distress syndrome. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Acute respiratory distress syndrome was recognized in 70% of patients, and recognition increased from 60% in 2008-2009 to 92% in 2016 (p = 0.004). Use of tidal volumes less than 6.5 mL/kg also increased (p < 0.001) from 20% to 92%. Increased acute respiratory distress syndrome severity (p = 0.01) and vasopressor use (p = 0.04) were associated with greater recognition. Clinician diagnosis of acute respiratory distress syndrome and inclusion of acute respiratory distress syndrome in the differential diagnosis were associated with tidal volumes less than 6.5 mL/kg (51% use of tidal volume ≤ 6.5 mL/kg if acute respiratory distress syndrome recognized vs 15% if not recognized; p = 0.002). Diagnosing acute respiratory distress syndrome was associated with lower tidal volume in multivariate analysis. CONCLUSIONS Although acute respiratory distress syndrome recognition and low tidal volume ventilation use have increased over time, they remain less than universal. Clinician recognition of acute respiratory distress syndrome is associated with both systemic and respiratory severity of illness and is also associated with use of low tidal volume ventilation.

Chronic neutrophilia is commonly seen with persistent infections, inflammatory disorders, smoking, solid tumors, and specific medications. However, after reactive causes have been excluded, a workup for primary (clonal) neutrophilic disorders, such as myeloproliferative neoplasms (MPNs) and myelodysplastic/myeloproliferative overlap syndromes, should be pursued. Except for chronic myeloid leukemia, which is defined by the presence of the Philadelphia (Ph) chromosome, and the classic Ph chromosome-negative MPNs (polycythemia vera, essential thrombocythemia, and primary myelofibrosis), clonal neutrophilic neoplasms historically have been challenging to diagnose and classify. The 2016 revised World Health Organization classification of these disorders has been based mainly on clinicopathologic features. However, recent discoveries of the molecular alterations underlying these disorders have served to supplement our knowledge of their morphologic and clinical features, opening new therapeutic avenues. In this review, we discuss the diagnostic approach, prognostic features, and treatments of neutrophilic myeloid neoplasms, with a focus on chronic neutrophilic leukemia, atypical chronic myeloid leukemia, and chronic myelomonocytic leukemia.

Human mesenchymal stem/stromal cells (hMSCs) are a promising therapy for acute respiratory distress syndrome (ARDS) and other inflammatory conditions. While considerable research has focused on paracrine effects and mitochondrial transfer that improve lung fluid balance, hMSCs are well known to have immunomodulatory properties as well. Some of these immunomodulatory properties have been related to previously reported paracrine effectors such as indoleamine-2,3-dioxygenase (IDO), but these effects cannot fully account for cell-contact dependent immunomodulation. Here, we report that CD40 is upregulated on hMSCs under the same conditions previously reported to induce IDO. Further, CD40 transcription is also upregulated on hMSCs by ARDS pulmonary edema fluid but not by hydrostatic pulmonary edema fluid. Transcription of CD40, as well as paracrine effectors TSG6 and PTGS2 remained significantly upregulated for at least 12 hours after withdrawal of cytokine stimulation. Finally, induction of this immune phenotype altered the transdifferentiation of hMSCs, one of their hallmark properties. CD40 may play an important role in the immunomodulatory effects of hMSCs in ARDS and inflammation.

Background: Recent efforts to improve outcomes for high-grade serous ovarian cancer, a leading cause of cancer death in women, have focused on identifying molecular subtypes and prognostic gene signatures, but existing subtypes have poor cross-study robustness. We tested the contribution of cell admixture in published ovarian cancer molecular subtypes and prognostic gene signatures. Methods: Gene signatures of tumor and stroma were developed using paired microdissected tissue from two independent studies. Stromal genes were investigated in two molecular subtype classifications and 61 published gene signatures. Prognostic performance of gene signatures of stromal admixture was evaluated in 2,527 ovarian tumors (16 studies). Computational simulations of increasing stromal cell proportion were performed by mixing gene-expression profiles of paired microdissected ovarian tumor and stroma. Results: Recently described ovarian cancer molecular subtypes are strongly associated with the cell admixture. Tumors were classified as different molecular subtypes in simulations where the percentage of stromal cells increased. Stromal gene expression in bulk tumors was associated with overall survival (hazard ratio, 1.17; 95% confidence interval, 1.11–1.23), and in one data set, increased stroma was associated with anatomic sampling location. Five published prognostic gene signatures were no longer prognostic in a multivariate model that adjusted for stromal content. Conclusions: Cell admixture affects the interpretation and reproduction of ovarian cancer molecular subtypes and gene signatures derived from bulk tissue. Elucidating the role of stroma in the tumor microenvironment and in prognosis is important. Impact: Single-cell analyses may be required to refine the molecular subtypes of high-grade serous ovarian cancer.

Background Genetic studies in autism have pinpointed a heterogeneous group of loci and genes. Further, environment may be an additional factor conferring susceptibility to autism. Transcriptome studies investigate quantitative differences in gene expression between patient-derived tissues and control. These studies may pinpoint genes relevant to pathophysiology yet circumvent the need to understand genetic architecture or gene-by-environment interactions leading to disease. Methods We conducted alternate gene set enrichment analyses using differentially expressed genes from a previously published RNA-seq study of post-mortem autism cerebral cortex. We used three previously published microarray datasets for validation and one of the microarray datasets for additional differential expression analysis. The RNA-seq study used 26 autism and 33 control brains in differential gene expression analysis, and the largest microarray dataset contained 15 autism and 16 control post-mortem brains. Results While performing a gene set enrichment analysis of genes differentially expressed in the RNA-seq study, we discovered that genes associated with mitochondrial function were downregulated in autism cerebral cortex, as compared to control. These genes were correlated with genes related to synaptic function. We validated these findings across the multiple microarray datasets. We also did separate differential expression and gene set enrichment analyses to confirm the importance of the mitochondrial pathway among downregulated genes in post-mortem autism cerebral cortex. Conclusions We found that genes related to mitochondrial function were differentially expressed in autism cerebral cortex and correlated with genes related to synaptic transmission. Our principal findings replicate across all datasets investigated. Further, these findings may potentially replicate in other diseases, such as in schizophrenia. Electronic supplementary material The online version of this article (10.1186/s11689-018-9237-x) contains supplementary material, which is available to authorized users.

Accurate classification is essential for understanding the pathophysiology of a disease and can inform therapeutic choices. For hematopoietic malignancies, a classification scheme based on the phenotypic similarity between tumor cells and normal cells has been successfully used to define tumor subtypes; however, use of normal cell types as a reference by which to classify solid tumors has not been widely emulated, in part due to more limited understanding of epithelial cell differentiation compared with hematopoiesis. To provide a better definition of the subtypes of epithelial cells comprising the breast epithelium, we performed a systematic analysis of a large set of breast epithelial markers in more than 15,000 normal breast cells, which identified 11 differentiation states for normal luminal cells. We then applied information from this analysis to classify human breast tumors based on normal cell types into 4 major subtypes, HR0-HR3, which were differentiated by vitamin D, androgen, and estrogen hormone receptor (HR) expression. Examination of 3,157 human breast tumors revealed that these HR subtypes were distinct from the current classification scheme, which is based on estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Patient outcomes were best when tumors expressed all 3 hormone receptors (subtype HR3) and worst when they expressed none of the receptors (subtype HR0). Together, these data provide an ontological classification scheme associated with patient survival differences and provides actionable insights for treating breast tumors.

Mutations that cause neurological phenotypes are highly informative with regard to mechanisms governing human brain function and disease. We report autosomal recessive mutations in the enzyme glutamate pyruvate transaminase 2 (GPT2) in large kindreds initially ascertained for intellectual and developmental disability (IDD). GPT2 [also known as alanine transaminase 2 (ALT2)] is one of two related transaminases that catalyze the reversible addition of an amino group from glutamate to pyruvate, yielding alanine and α-ketoglutarate. In addition to IDD, all affected individuals show postnatal microcephaly and ∼80% of those followed over time show progressive motor symptoms, a spastic paraplegia. Homozygous nonsense p.Arg404* and missense p.Pro272Leu mutations are shown biochemically to be loss of function. The GPT2 gene demonstrates increasing expression in brain in the early postnatal period, and GPT2 protein localizes to mitochondria. Akin to the human phenotype, Gpt2-null mice exhibit reduced brain growth. Through metabolomics and direct isotope tracing experiments, we find a number of metabolic abnormalities associated with loss of Gpt2. These include defects in amino acid metabolism such as low alanine levels and elevated essential amino acids. Also, we find defects in anaplerosis, the metabolic process involved in replenishing TCA cycle intermediates. Finally, mutant brains demonstrate misregulated metabolites in pathways implicated in neuroprotective mechanisms previously associated with neurodegenerative disorders. Overall, our data reveal an important role for the GPT2 enzyme in mitochondrial metabolism with relevance to developmental as well as potentially to neurodegenerative mechanisms.

Activity-dependent neuroprotective protein (ADNP) is a highly conserved transcription factor comprised of nine-zinc finger domains and a homeobox domain.1 ,2 It is highly expressed prenatally during critical stages of embryonic brain development.3 Knockout (KO) mouse embryos demonstrate severe neurodevelopmental morphological profiles.4 Although the ADNP KO is lethal, heterozygous embryos demonstrate typical embryogenesis yet display a neurodevelopmental delay phenotype including decreased neuronal survival.3 ,5 Exome sequencing in the Simons Simplex Collection autism dataset identified ADNP mutations as a putative autism gene candidate.6 ,7 Helsmoortel et al 8 recently reported 10 individuals with autism spectrum disorder (ASD) and mutations in exon 5 of the ADNP gene, nine of which were confirmed de novo. These patients also exhibited intellectual disability (ID) and dysmorphic features such as a prominent forehead. Mutations in the ADNP gene are estimated to be present in at least 0.17% of ASD cases. The current report further expands the ADNP phenotype to include abnormalities in the developing visual system (such as eye movement abnormalities and cortical visual impairment). We advise appropriate screening of eye movement and visual symptoms by clinicians in patients who have mutations in ADNP . The 6-year-old patient was the first child born to healthy non-consanguineous parents. Pregnancy was notable for placenta previa and early dilation and effacement of the cervix 3 weeks prior to delivery. The patient was born at 40 weeks via C-section secondary to failure to progress and maternal (i.e. maternal hypertension) hypertension weighing 6 pounds 14 ounces. She had a short stay in the neonatal intensive care unit (NICU) for breathe holding and feeding problems. She was also hospitalised at 6 weeks for an acute life-threatening event of multiple cyanotic episodes thought to be due to breath holding. Our patient has been diagnosed with hypotonia and mixed developmental …

The acute respiratory distress syndrome (ARDS) is common in critically ill patients and has a high mortality rate. Mesenchymal stromal cells (MSCs) have demonstrated therapeutic potential in animal models of ARDS, and their benefits occur in part through interactions with alveolar type II (ATII) cells. However, the effects that MSCs have on human ATII cells have not been well studied. Using previously published microarray data, we performed genome‐wide differential gene expression analyses of human ATII cells that were (1) unstimulated, (2) exposed to proinflammatory cytokines (CytoMix), or (3) exposed to proinflammatory cytokines plus MSCs. Findings were validated by qPCR. Alveolar type II cells differentially expressed hundreds of genes when exposed either to proinflammatory cytokines or to proinflammatory cytokines plus MSCs. Stimulation with proinflammatory cytokines increased expression of inflammatory genes and downregulated genes related to surfactant function and alveolar fluid clearance. Some of these changes, including expression of some cytokines and genes related to surfactant, were reversed by exposure to MSCs. In addition, MSCs induced upregulation of other potentially beneficial genes, such as those related to extracellular matrix remodeling. We confirmed several of these gene expression changes by qPCR. Thus, ATII cells downregulate genes associated with surfactant and alveolar fluid clearance when exposed to inflammatory cytokines, and mesenchymal stromal cells partially reverse many of these gene expression changes.

Autism is a highly heterogeneous neurodevelopmental disorder with impaired language, social communication, and restricted and repetitive interests and behavior. Monogenic developmental brain disorders with autism features such as Rett syndrome, Angelman syndrome, Fragile X syndrome, and others provide important tractable models of relevance to severe autism. In addition to observing autism symptoms in the monogenic condition, if the gene responsible is also significantly misregulated in the brains of people with idiopathic autism, then these data provide substantial independent support for the importance of the gene in autism pathophysiology. Given this logic, we set out to test if there were gene expression changes in postmortem brain tissue from patients with idiopathic autism in the genes of interest that encode the Na+/H+ exchanger family of proteins, with particular interest in the forms of exchangers localized to endosomes, namely, NHE6 and NHE9. Mutations in the X-linked endosomal Na+/H+ Exchanger 6 (NHE6, also known as SLC9A6) represent a novel neurogenetic syndrome with variable expressivity.1 In a systematic, large-scale resequencing screen of X-chromosome coding exons in >200 pedigrees consistent with X-linked intellectual disability, NHE6 was among the top six most recurrently mutated genes.2 The ‘Christianson syndrome', based on the initial clinical description, reported an association with autistic symptoms as has been reported subsequently.3, 4 In parallel to the description of autistic symptoms associated with mutations in NHE6, Morrow et al.5 published mutations in the highly related endosomal protein NHE9 in severe autism with epilepsy. Endosomal processes, such as would be suggested by mutations in NHE6 and NHE9, represent an important cellular mechanism for investigations regarding disorders of cognitive development. Interestingly, of the six top genes implicated in the Tarpey et al.2 study, two of the genes, NHE6 and AP1S2, are known to be involved in endosomal mechanisms. We therefore investigated whether the expression of NHE genes, NHE6 and NHE9, were altered in autism cerebral cortex. We did this by renormalizing and analyzing publically available microarray data. Specifically, we first analyzed data from Voineagu et al.,6 which were previously used to compare autism and control cortex (n=29 of each). We renormalized the data as described in Voineagu et al.,6 except for when we wished to analyze a subset of NHE genes that were excluded from the analysis because of low expression. Among their results, Voineagu et al.6 reported that synapse-associated genes were downregulated in autism cortex,6 and we confirmed this result by performing differential gene expression analysis7 between autism and control cortex (for detailed Methods, please see Supplementary Information). We then performed DAVID functional annotation clustering analysis8, 9 on the 197 genes with at least 1.3-fold reduction in autism cortex and P 0.15). We further hypothesized that changes in these genes were reflective of broader changes in gene expression, such as downregulation of synapse genes. To investigate the functional changes associated with NHE1, NHE6 and NHE9 gene expression, we found Pearson correlation coefficients between each of these genes and the average expression of the 21 synapse-related genes. NHE1 was not significantly correlated with the synapse genes (r=0.15, P=0.28), but NHE6 and NHE9 both were strongly correlated with the synapse genes (r=0.86, P=4.2 × 10−18 for NHE6; r=−0.62, P=2.2 × 10−7 for NHE9—see Figure 1). Furthermore, the sub-population of samples with the lowest NHE6 expression was almost entirely autism cases, as was the sub-population of high NHE9 expression. Additionally, NHE6 and NHE9 were negatively correlated (P=0.00015), and when NHE6 expression was high, NHE9 was tightly regulated. A similar decrease in NHE9 variability could be seen with high synapse gene expression (Figure 1). Thus, a sub-population within autism is not only associated with lower synapse gene expression, but also with lower NHE6 expression and increased and potentially misregulated NHE9 expression. We also studied the correlation of NHE6 and NHE9 with the downregulated synapse gene set during normal brain development. We capitalized on the large mRNA-seq data set from human brain made available by the Allen Brain Institute (http://www.developinghumanbrain.org). We find that NHE6 clusters strongly during development with this synapse gene group (see Supplementary Information). NHE9 expression was far lower embryonically, increased postnatally but did not appreciably cluster with this synapse group in typical brain development (Supplementary Figures 1–3). Figure 1 Expression plots of NHE6 versus synapse genes, NHE9 versus synapse genes and NHE6 versus NHE9 in three independent data sets. We compared the average log base 2 expression of 21 synapse genes with that of NHE6 and NHE9 expression in microarray data sets ... We used two independent microarray data sets for autism and control cerebral cortex to validate both the differential gene expression of NHE6 and NHE9 in autism cases and these genes' associations with synapse genes. The validation data sets were from Chow et al.11 (n=15 autism, n=18 control) and Garbett et al.12 (n=6 of each; data set details in Supplementary Table 4). The Chow et al.11 data were downloaded from GEO ({"type":"entrez-geo","attrs":{"text":"GSE28475","term_id":"28475"}}GSE28475), and the Garbett et al.12 data were provided by the authors. In the Garbett et al.12 data, NHE9 was significantly higher in autism than control cortex (P=0.039), and while NHE6 was lower on average in autism cortex, this was not statistically significant (P=0.22), although this may have been due to low sample size (Figure 1). In the Chow et al.11 data, although NHE6 and NHE9 had lower and higher expression in autism cortex compared with control, respectively, these trends were not significant (P=0.38 and 0.17). However, the mean expression of synapse genes was also not significantly different in the Chow et al.11 data set (P=0.46), suggesting that the Voineagu et al.6 and Chow et al.11 data sets represent different populations. Additionally, NHE6 and NHE9 were negatively correlated across data sets, except for in Garbett et al.,12 in which the correlation was not significant (P=0.56) but suggesting as yet unknown mechanisms of interaction. Despite this lack of significance in the independent data sets, these genes' associations with synapse genes remained strong in both additional data sets: NHE6 is positively associated with synapse genes (r=0.59, P=0.00029 for NHE6 in Chow et al.11 study; and r=0.6, P=0.041 for NHE6 in Garbett et al.12 study—see Figure 1) and NHE9 negatively associated (r=−0.72, P=2.0 × 10−6 for NHE9 in Chow et al.11 study; and r=−0.78, P=0.0029 for NHE9 in Garbett et al.12 study—see Figure 1). Finally, we tested for an association of gene expression for NHE6 and NHE9 and well-established autism-related genes such as SHANK2/3, NLGN4X, NRXN1 and PTEN. Notably, NHE6 and NHE9 each showed a strong association with NRXN1 (P=2 × 10−10 for NHE6, and P=2.9 × 10−8 for NHE9; Supplementary Figures 4 and 5). In summary, we find interesting gene expression changes in endosomal NHE6 and NHE9 in postmortem autism brains. These gene expression changes are largely replicated across data sets or the trends of these changes are maintained given limitations in sample size. We also report a strong correlation of endosomal NHE6 and NHE9 gene expression with the synapse genes across all data sets. The strong correlation of endosomal NHEs with synapse genes suggests that changes in synapse genes in autism involves a cellular mechanism that involves endosomal NHE6 and NHE9 in at least some autism brains. In conclusion, these gene expression studies in postmortem brains from patients with idiopathic autism provide additional support, in addition to the association of autism symptoms with the single-gene mutations, that endosomal NHEs are mechanistically involved in the pathophysiology of autism.

We report on a pedigree with a pair of brothers each with minor anomalies, developmental delay, and autistic-symptoms who share an unbalanced translocation (not detectable by karyotype). The unbalanced translocation involves a 7.1 Mb loss of the terminal portion of 10q, and a 4.2 Mb gain of 11q. One of the brothers also developed a cerebellar juvenile pilocytic astrocytoma. The father was found to be a balanced carrier and the couple had a previous miscarriage. We demonstrate that the breakpoint for the triplicated region from chromosome 11 is adjacent to two IgLON genes, namely Neurotrimin (NTM) and Opioid Binding Protein/Cell Adhesion Molecule-like (OPCML). These genes are highly similar neural cell adhesion molecules that have been implicated in synaptogenesis and oncogenesis, respectively. The children also have a 10q deletion and are compared to other children with the 10q deletion syndrome which generally does not involve autism spectrum disorders (ASDs) or cancer. Together these data support a role for NTM and OPCML in developmental delay and potentially in cancer susceptibility.

The potential role of the cell-of-origin in determining the tumor phenotype has been raised, but not adequately examined. We hypothesized that distinct cells-of-origin may play a role in determining ovarian tumor phenotype and outcome. Here we describe a new cell culture medium for in vitro culture of paired normal human ovarian (OV) and fallopian tube (FT) epithelial cells from donors without cancer. While these cells have been cultured individually for short periods of time, to our knowledge this is the first long-term culture of both cell types from the same donors. Through analysis of the gene expression profiles of the cultured OV/FT cells we identified a normal cell-of-origin gene signature that classified primary ovarian cancers into OV-like and FT-like subgroups; this classification correlated with significant differences in clinical outcomes. The identification of a prognostically significant gene expression signature derived solely from normal untransformed cells is consistent with the hypothesis that the normal cell-of-origin may be a source of ovarian tumor heterogeneity and the associated differences in tumor outcome.

Purpose: High-grade serous cancer (HGSC) is the most common cancer of the ovary and is characterized by chromosomal instability. Defects in homologous recombination repair (HRR) are associated with genomic instability in HGSC, and are exploited by therapy targeting DNA repair. Defective HRR causes uniparental deletions and loss of heterozygosity (LOH). Our purpose is to profile LOH in HGSC and correlate our findings to clinical outcome, and compare HGSC and high-grade breast cancers. Experimental Design: We examined LOH and copy number changes using single nucleotide polymorphism array data from three HGSC cohorts and compared results to a cohort of high-grade breast cancers. The LOH profiles in HGSC were matched to chemotherapy resistance and progression-free survival (PFS). Results: LOH-based clustering divided HGSC into two clusters. The major group displayed extensive LOH and was further divided into two subgroups. The second group contained remarkably less LOH. BRCA1 promoter methylation was associated with the major group. LOH clusters were reproducible when validated in two independent HGSC datasets. LOH burden in the major cluster of HGSC was similar to triple-negative, and distinct from other high-grade breast cancers. Our analysis revealed an LOH cluster with lower treatment resistance and a significant correlation between LOH burden and PFS. Conclusions: Separating HGSC by LOH-based clustering produces remarkably stable subgroups in three different cohorts. Patients in the various LOH clusters differed with respect to chemotherapy resistance, and the extent of LOH correlated with PFS. LOH burden may indicate vulnerability to treatment targeting DNA repair, such as PARP1 inhibitors. Clin Cancer Res; 18(20); 5806–15. ©2012 AACR.

Although ovarian cancer is often initially chemotherapy-sensitive, the vast majority of tumors eventually relapse and patients die of increasingly aggressive disease. Cancer stem cells are believed to have properties that allow them to survive therapy and may drive recurrent tumor growth. Cancer stem cells or cancer-initiating cells are a rare cell population and difficult to isolate experimentally. Genes that are expressed by stem cells may characterize a subset of less differentiated tumors and aid in prognostic classification of ovarian cancer. The purpose of this study was the genomic identification and characterization of a subtype of ovarian cancer that has stem cell-like gene expression. Using human and mouse gene signatures of embryonic, adult, or cancer stem cells, we performed an unsupervised bipartition class discovery on expression profiles from 145 serous ovarian tumors to identify a stem-like and more differentiated subgroup. Subtypes were reproducible and were further characterized in four independent, heterogeneous ovarian cancer datasets. We identified a stem-like subtype characterized by a 51-gene signature, which is significantly enriched in tumors with properties of Type II ovarian cancer; high grade, serous tumors, and poor survival. Conversely, the differentiated tumors share properties with Type I, including lower grade and mixed histological subtypes. The stem cell-like signature was prognostic within high-stage serous ovarian cancer, classifying a small subset of high-stage tumors with better prognosis, in the differentiated subtype. In multivariate models that adjusted for common clinical factors (including grade, stage, age), the subtype classification was still a significant predictor of relapse. The prognostic stem-like gene signature yields new insights into prognostic differences in ovarian cancer, provides a genomic context for defining Type I/II subtypes, and potential gene targets which following further validation may be valuable in the clinical management or treatment of ovarian cancer.