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Fletcher and his colleagues also reported that the acid pocket extended above the squamocolumnar junction and suggested that this may be a factor underlying inflammation, intestinal metaplasia and carcinoma at the gastro-oesophageal junction. 8 In this issue of Gut (page 10.1136/gut.2006.109421 ) the team from Glasgow extend their earlier observations to patients with severe reflux oesophagitis and/or Barrett's oesophagus. 9 Refinements to the earlier methodology included use of concurrent manometry to identify the LOS and closely timed radiology to assess the position of the pH electrode relative to the squamo-columnar junction and LOS. [...]there is emerging interest in patterns of acid reflux in the region 1-2 cm immediately above the LOS, a site where the earliest and most severe mucosal damage typically occurs in reflux disease. pH monitoring has shown over double the rate of detection of acid reflux in this region compared with 5 cm, and up to six times higher within the LOS segment itself. 17 The rate of reflux episodes detected in the most distal oesophagus is also higher in patients with reflux disease than in controls. 18 19 Given the proximity of the acid pocket to the distal border of the LOS, and evidence that it might even extend into the distal LOS segment because of meal-induced opening of the distal segment of the LOS, it is possible that continued high levels of acidity at the cardia might have a greater impact on acid exposure in the very distal oesophagus than more proximally.

Up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis; here, in a systematic and nationwide study of 1,133 children with severe, undiagnosed developmental disorders, and their parents, exome sequencing and array-based detection of chromosomal rearrangements reveals novel genes causing developmental disorders, increasing the proportion of children that can now be diagnosed to 31%. Gene linkage to developmental disorders Until recently, the discovery of the genetic causes of monogenic disorders has been predominantly phenotype-driven. Up to half of all children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. This publication from The Deciphering Developmental Disorders Study presents a UK-wide systematic genetic analysis of 1,133 children with severe, undiagnosed developmental disorders, and their parents. Exome sequencing and array-based detection of chromosomal rearrangements revealed 12 previously unknown developmental disorder genes and increased the proportion of children that could be diagnosed by 10%. Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders 1 , up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach 2 to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.

Congenital Heart Disease (CHD) affects approximately 7-9 children per 1000 live births. Numerous genetic studies have established a role for rare genomic variants at the copy number variation (CNV) and single nucleotide variant level. In particular, the role of de novo mutations (DNM) has been highlighted in syndromic and non-syndromic CHD. To identify novel haploinsufficient CHD disease genes we performed an integrative analysis of CNVs and DNMs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm (TAA). We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed mutation rate testing for DNMs identified in 2,489 parent-offspring trios. Our combined analysis revealed 21 genes which were significantly affected by rare genomic deletions and/or constrained non-synonymous de novo mutations in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in singletons and small cases series, or show new associations with CHD. In addition, a systems level analysis revealed shared contribution of CNV deletions and DNMs in CHD probands, affecting protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes.

The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.In this Review, the authors discuss the latest advances in profiling multiple molecular modalities from single cells, including genomic, transcriptomic, epigenomic and proteomic information. They describe the diverse strategies for separately analysing different modalities, how the data can be computationally integrated, and approaches for obtaining spatially resolved data.

Patients with gastro-oesophageal reflux disease (GORD) who are not responding to proton pump inhibitors (PPIs) given once daily are very common. Various underlying mechanisms have been shown to contribute to the failure of PPI treatment. These include weakly acidic reflux, duodenogastro-oesophageal reflux, residual acid reflux and functional heartburn, as well as others. Diagnostic evaluation of patients with GORD who have failed PPI treatment may include an upper endoscopy, pH testing and oesophageal impedance with pH monitoring. Commonly, doubling the PPI dose or switching to another PPI will be pursued by the treating physician. Failure of such a therapeutic strategy may result in the addition of a transient lower oesophageal sphincter reducer or pain modulator. Anti-reflux surgery may be suitable for a subset of carefully studied patients.

Gastro-oesophageal reflux disease (GERD) is a common gastrointestinal disorder in which retrograde flow of gastric content into the oesophagus causes uncomfortable symptoms and/or complications. It has a multifactorial and partially understood pathophysiology. GERD starts in the stomach, where the refluxate material is produced. Following the trajectory of reflux, the failure of the antireflux barrier, primarily the lower oesophageal sphincter and the crural diaphragm, enables the refluxate to reach the oesophageal lumen, triggering oesophageal or extra-oesophageal symptoms. Reflux clearance mechanisms such as primary and secondary peristalsis and the arrival of bicarbonate-rich saliva are critical to prevent mucosal damage. Alterations of the oesophageal mucosal integrity, such as macroscopic oesophagitis or microscopic changes, determine the perception of symptoms. The intensity of the symptoms is affected by peripheral and central neural and psychological mechanisms. In this Review, we describe an updated understanding of the complex and multifactorial pathophysiology of GERD. It is now recognized that different GERD phenotypes have different degrees of reflux, severity of mucosal integrity damage and type, and severity of symptoms. These variations are probably due to the occurrence of a predominant pathophysiological mechanism in each patient. We also describe the main pathophysiological mechanisms of GERD and their implications for personalized diagnosis and management. In this Review, Argüero and Sifrim describe the core pathophysiological mechanisms involved in gastro-oesophageal reflux disease (GERD). They also discuss the implications for clinical management of GERD. Key points Gastro-oesophageal reflux disease (GERD) is a common gastrointestinal disorder and has a multifactorial pathophysiology; there are two phenotypes of GERD, erosive and non-erosive reflux disease, and their distinct pathophysiology is not completely known. The oesophagogastric junction works as a functional antireflux barrier; transient lower oesophageal sphincter relaxations are the most frequent mechanism for reflux in healthy individuals and in patients with GERD. Hiatal hernia is an important mechanism of GERD. Motility impairment of both the oesophagus and the proximal stomach is involved in GERD pathophysiology. The refluxate is a mix of gastric and biliopancreatic secretions. Acid reflux is associated with heartburn and mucosal damage. Bile reflux provokes more severe oesophagitis or Barrett oesophagus. Non-acid reflux is mainly associated with symptoms but no mucosal damage. Impairment of oesophageal mucosal integrity, innervation and microinflammation has a crucial role in symptom perception. Severity of GERD symptoms is influenced by psychoneuroimmune modulation; psychosocial comorbidities and hypervigilance determine the severity of GERD symptoms as well as response to treatment.

Clinical history, questionnaire data and response to antisecretory therapy are insufficient to make a conclusive diagnosis of GERD in isolation, but are of value in determining need for further investigation. Conclusive evidence for reflux on oesophageal testing include advanced grade erosive oesophagitis (LA grades C and D), long-segment Barrett’s mucosa or peptic strictures on endoscopy or distal oesophageal acid exposure time (AET) >6% on ambulatory pH or pH-impedance monitoring. A normal endoscopy does not exclude GERD, but provides supportive evidence refuting GERD in conjunction with distal AET <4% and <40 reflux episodes on pH-impedance monitoring off proton pump inhibitors. Reflux-symptom association on ambulatory reflux monitoring provides supportive evidence for reflux triggered symptoms, and may predict a better treatment outcome when present. When endoscopy and pH or pH-impedance monitoring are inconclusive, adjunctive evidence from biopsy findings (histopathology scores, dilated intercellular spaces), motor evaluation (hypotensive lower oesophageal sphincter, hiatus hernia and oesophageal body hypomotility on high-resolution manometry) and novel impedance metrics (baseline impedance, postreflux swallow-induced peristaltic wave index) can add confidence for a GERD diagnosis; however, diagnosis cannot be based on these findings alone. An assessment of anatomy, motor function, reflux burden and symptomatic phenotype will therefore help direct management. Future GERD management strategies should focus on defining individual patient phenotypes based on the level of refluxate exposure, mechanism of reflux, efficacy of clearance, underlying anatomy of the oesophagogastric junction and psychometrics defining symptomatic presentations.

The ability of the skin to grow in response to stretching has been exploited in reconstructive surgery 1 . Although the response of epidermal cells to stretching has been studied in vitro 2 , 3 , it remains unclear how mechanical forces affect their behaviour in vivo. Here we develop a mouse model in which the consequences of stretching on skin epidermis can be studied at single-cell resolution. Using a multidisciplinary approach that combines clonal analysis with quantitative modelling and single-cell RNA sequencing, we show that stretching induces skin expansion by creating a transient bias in the renewal activity of epidermal stem cells, while a second subpopulation of basal progenitors remains committed to differentiation. Transcriptional and chromatin profiling identifies how cell states and gene-regulatory networks are modulated by stretching. Using pharmacological inhibitors and mouse mutants, we define the step-by-step mechanisms that control stretch-mediated tissue expansion at single-cell resolution in vivo. Single-cell analysis in a mouse model of skin stretching shows that stretching causes a transient expansion bias in a population of epidermal stem cells, which is associated with chromatin remodelling and changes in transcriptional profiles.