Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.

The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/ß-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.

Delivery Mode Affects Stability of Early Infant Gut Microbiota.

Mode of delivery strongly influences the early infant gut microbiome. Children born by cesarean section (C-section) lack Bacteroides species until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome. Here, we re-evaluate this hypothesis by comparing the microbial profiles of 75 infants born vaginally or by planned versus emergent C-section. Multiple children born by C-section have a high abundance of Bacteroides in their first few days of life, but at 2 weeks, both C-section groups lack Bacteroides (primarily according to 16S sequencing), despite their difference in exposure to the birth canal. Finally, a comparison of microbial strain profiles between infants and maternal vaginal or rectal samples finds evidence for mother-to-child transmission of rectal rather than vaginal strains. These results suggest differences in colonization stability as an important factor in infant gut microbiome composition rather than birth canal exposure.

Publisher Correction: The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.

A typo in the 'Reviewer information' section of this Letter was corrected online.

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.

The human genome contains thousands of long non-coding RNAs1, but specific biological functions and biochemical mechanisms have been discovered for only about a dozen2-7. A specific long non-coding RNA-non-coding RNA activated by DNA damage (NORAD)-has recently been shown to be required for maintaining genomic stability8, but its molecular mechanism is unknown. Here we combine RNA antisense purification and quantitative mass spectrometry to identify proteins that directly interact with NORAD in living cells. We show that NORAD interacts with proteins involved in DNA replication and repair in steady-state cells and localizes to the nucleus upon stimulation with replication stress or DNA damage. In particular, NORAD interacts with RBMX, a component of the DNA-damage response, and contains the strongest RBMX-binding site in the transcriptome. We demonstrate that NORAD controls the ability of RBMX to assemble a ribonucleoprotein complex-which we term NORAD-activated ribonucleoprotein complex 1 (NARC1)-that contains the known suppressors of genomic instability topoisomerase I (TOP1), ALYREF and the PRPF19-CDC5L complex. Cells depleted for NORAD or RBMX display an increased frequency of chromosome segregation defects, reduced replication-fork velocity and altered cell-cycle progression-which represent phenotypes that are mechanistically linked to TOP1 and PRPF19-CDC5L function. Expression of NORAD in trans can rescue defects caused by NORAD depletion, but rescue is significantly impaired when the RBMX-binding site in NORAD is deleted. Our results demonstrate that the interaction between NORAD and RBMX is important for NORAD function, and that NORAD is required for the assembly of the previously unknown topoisomerase complex NARC1, which contributes to maintaining genomic stability. In addition, we uncover a previously unknown function for long non-coding RNAs in modulating the ability of an RNA-binding protein to assemble a higher-order ribonucleoprotein complex.

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Bacterial community acquisition in the infant gut impacts immune education and disease susceptibility. We compared bacterial strains across and within families in a prospective birth cohort of 44 infants and their mothers, sampled longitudinally in the first months of each child's life. We identified mother-to-child bacterial transmission events and describe the incidence of family-specific antibiotic resistance genes. We observed two inheritance patterns across multiple species, where often the mother's dominant strain is transmitted to the child, but occasionally her secondary strains colonize the infant gut. In families where the secondary strain of B. uniformis was inherited, a starch utilization gene cluster that was absent in the mother's dominant strain was identified in the child, suggesting the selective advantage of a mother's secondary strain in the infant gut. Our findings reveal mother-to-child bacterial transmission events at high resolution and give insights into early colonization of the infant gut.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs, and disease states are connected by virtue of common gene-expression signatures. Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that we term L1000. We show that L1000 is highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts. We further show that the expanded CMap can be used to discover mechanism of action of small molecules, functionally annotate genetic variants of disease genes, and inform clinical trials. The 1.3 million L1000 profiles described here, as well as tools for their analysis, are available at https://clue.io.

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas. We present an expression-based variant-impact phenotyping (eVIP) method that uses gene expression changes to distinguish impactful from neutral somatic mutations. eVIP identified 69% of mutations analyzed as impactful and 31% as functionally neutral. A subset of the impactful mutations induces xenograft tumor formation in mice and/or confers resistance to cellular EGFR inhibition. Among these impactful variants are rare somatic, clinically actionable variants including EGFR S645C, ARAF S214C and S214F, ERBB2 S418T, and multiple BRAF variants, demonstrating that rare mutations can be functionally important in cancer.

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.

UNLABELLED: Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies. SIGNIFICANCE: Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.

Written distractor words influence brain activity during overt picture naming.

Language production requires multiple stages of processing (e.g., semantic retrieval, lexical selection), each of which may involve distinct brain regions. Distractor words can be combined with picture naming to examine factors that influence language production. Phonologically-related distractors have been found to speed picture naming (facilitation), while slower response times and decreased accuracy (interference) generally occur when a distractor is categorically related to the target image. However, other types of semantically-related distractors have been reported to produce a facilitative effect (e.g., associative, part-whole). The different pattern of results for different types of semantically-related distractors raises the question about how the nature of the semantic relation influences the effect of the distractor. To explore the nature of these semantic effects further, we used functional MRI to examine the influence of four types of written distractors on brain activation during overt picture naming. Distractors began with the same sound, were categorically-related, part of the object to be named, or were unrelated to the picture. Phonologically-related trials elicited greater activation than both semantic conditions (categorically-related and part-whole) in left insula and bilateral parietal cortex, regions that have been attributed to phonological aspects of production and encoding, respectively. Semantic conditions elicited greater activation than phonological trials in left posterior MTG, a region that has been linked to concept retrieval and semantic integration. Overall, the two semantic conditions did not differ substantially in their functional activation which suggests a similarity in the semantic demands and lexical competition across these two conditions.

The structure of the cerebral cortex across adult life: age-related patterns of surface area, thickness, and gyrification.

Older adults exhibit global reductions in cortical surface area, but little is known about the regional patterns of reductions or how these relate to other measures of brain structure. This knowledge is critical to understanding the dynamic relationship between different macrostructural properties of the cortex throughout adult life. Here, cortical arealization, local gyrification index (LGI), and cortical thickness were measured vertex wise across the brain surface in 322 healthy adults (20-85 years), with the aims of 1) characterizing age patterns of the three separate cortical measures and 2) testing the age-independent relationships among cortical surface area, gyrification, and thickness. Surface area showed strong age-related decreases, particularly pronounced in dorsomedial prefrontal, lateral temporal, and fusiform cortices, independently of total white matter volume. LGI decreased with age independently of regional surface area, with strongest effects laterally, extending from the angular gyrus in all directions. As expected, regional surface area and LGI were positively related. However, both measures correlated negatively with thickness, indicating increasing local arealization and gyrification with decreasing cortical thickness. We suggest that this pattern of regional "cortical stretching" reflects the well-established phylogenetic principle of maximizing surface area and gyrification rather than increase thickness to facilitate brain connectivity and functional development.

The influence of context on hemispheric recruitment during metaphor processing.

Although the left hemisphere's prominence in language is well established, less emphasis has been placed on possible roles for the right hemisphere. Behavioral, patient, and neuroimaging research suggests that the right hemisphere may be involved in processing figurative language. Additionally, research has demonstrated that context can modify language processes and facilitate comprehension. Here we investigated how figurativeness and context influenced brain activation, with a specific interest in right hemisphere function. Previous work in our laboratory indicated that novel stimuli engaged right inferior frontal gyrus (IFG) and that both novel and familiar metaphors engaged right IFG and right temporal pole. The graded salience hypothesis proposes that context may lessen integration demands, increase the salience of metaphors, and thereby reduce right hemisphere recruitment for metaphors. In the present study, fMRI was used to investigate brain function, whereas participants read literal and metaphoric sentences that were preceded by either a congruent or an incongruent literal sentence. Consistent with prior research, all sentences engaged traditional left hemisphere regions. Differences between metaphors and literal sentences were observed, but only in the left hemisphere. In contrast, a main effect of congruence was found in the right IFG, the right temporal pole, and the dorsal medial pFC. Partially consistent with the graded salience hypothesis, our results highlight the strong influence of context on language, demonstrate the importance of the right hemisphere in discourse, and suggest that, in a wider discourse context, congruence has a greater influence on right hemisphere recruitment than figurativeness.

The influence of sentence novelty and figurativeness on brain activity.

The predominance of the left hemisphere in language comprehension and production is well established. More recently, the right hemisphere's contribution to language has been examined. Clinical, behavioral, and neuroimaging research support the right hemisphere's involvement in metaphor processing. But, there is disagreement about whether metaphors, in and of themselves, engage the right hemisphere or if other factors that vary between metaphors and literal language elicit right hemisphere engagement. It is important to disambiguate these issues to improve our basic knowledge of figurative language processing, to more precisely define how the right hemisphere supports language, and to facilitate our ability to understand and treat language impairments. Here we investigated the role of the right hemisphere in language comprehension with functional magnetic resonance imaging (fMRI) by manipulating familiarity in both literal and metaphoric sentences. In an event-related design, participants viewed English sentences that appeared every 4.5-9s, and to which they made a pleasantness judgment. All sentences elicited activation in traditional language brain regions including left inferior frontal gyrus, left anterior inferior temporal and left posterior middle temporal gyri. Overall, metaphors and novel stimuli elicited activation in bilateral inferior frontal gyri and left temporal regions. Additionally, metaphors elicited greater activation than literal sentences in right temporal pole. Although our results are partially consistent with the graded salience hypothesis and the coarse coding hypothesis, the right hemisphere's sensitivity to familiar metaphors suggests that right hemisphere recruitment is most influenced by semantic integration demands.