X chromosome inactivation (XCI) is a strategy used by mammals to silence genes along one of the two female X chromosomes and equilibrate expression dosage between XY males and XX females. This epigenetically-inherited silencing is established during early embryonic development and maintained thereafter through cell divisions. Seeding of multiple repressive epigenetic marks along the inactive X chromosome (Xi) makes inactivation extremely robust and difficult to reverse upon single genetic perturbations. Reversal of XCI has, however, been observed when somatic cells are reprogrammed towards pluripotency, and in vitro reprogramming techniques have been used in recent years to dissect Xi gene reactivation mechanisms. These studies pave the way for developing novel therapeutic approaches for X-linked diseases. Here, the author reviews Xi reactivation during pluripotent reprogramming of mouse and human somatic cells, highlight recent advances and species-specific differences, and discuss the relevance for human diseases.

Aim: Whole exome sequencing technology has permitted the discovery of genes that cause Mendelian disorders and was used in clinical laboratories. However, identifying the disease causing variant(s) for a specific disorder from thousands of variants is challenging. In this study, we describe the Cincinnati Clinical Exome Pipeline Analysis Suite (CCEPAS) that utilizes a four-level framework into one analysis procedure that rapidly identify the most likely causative gene variants to establish a clinical diagnosis.

Methods: We developed and validated CCEPAS using 100 clinical exome cases. We applied this pipeline to clinical cases by first translating phenotypic information into candidate gene lists using Pheno2Gene. This list of candidate genes was given to the VarEval algorithm to guide variant filtering and prioritization. Finally, a short list of filtered variants was produced for clinical interpretation.

Results: We demonstrated the development and implementation of CCEPAS to aid in the variant prioritization and filtering to produce a short list of candidate variants for clinical diagnosis. Its unique Pheno2Gene tool utilized an extensive list of resources and provided an accurate, sensitive and specific way to obtain gene lists from clinical feature keywords. In addition, VarEval narrowed down the variants from ~150,000 to the top 20 (trios) and top 50 (singleton) for further variant curation and candidate determination.

Conclusion: Significantly, employment of CCEPAS rapidly provided causative variants in the top 20 and top 50 variants for single and trio cases, respectively, thus, ending the diagnostic odyssey in more than 30% of our clinical exome cases.

The dosage compensation in placental mammals is achieved by silencing of one copy of the X chromosomes in a female cell by a process called X chromosome inactivation (XCI). XCI ensures equal gene dosage for X-linked genes between the two genders. Although the choice of X chromosome to be silenced is random, once the silencing of the X chromosome has been established, this process is highly regulated and maintained throughout subsequent cell divisions. A long non-coding RNA, Xist, and its interacting proteins execute this multistep process, but several of these regulatory proteins remain unidentified. Recent technological advances based on the genetic and proteomics screening have identified several new regulatory factors as well as dissected the molecular details of XCI regulation. Moreover, identification of regulators of XCI offers an opportunity to explore reactivation of the inactive X chromosome (Xi) as a potential therapeutic strategy to treat X-linked diseases, like Rett syndrome. Here, we summarize recent reports that identified new regulatory proteins and RNA species playing a crucial role in Xist localization and spreading, recruitment of silencing machinery to the Xi, Xist interaction with chromatin, and structural organization of the Xi in the nuclei.

Aim: Idiopathic cardiomyopathy is often genetic in origin, typically autosomal dominant, and restrictive cardiomyopathy (RCM) is the rarest form. Clinically, RCM prognosis is poor with most patients requiring heart transplant due to impaired diastolic function leading to heart failure. In some cases, desminopathy is also observed, whereby desmin protein aggregates in the myocardium. Many genes are known to be involved in cardiomyopathy, and we sought to find the pathogenic mutation of a four-generation family with RCM and desminopathy.

Methods: We employed whole exome sequence analysis of four RCM patients from the family, to identify the underlying pathogenic mutation(s).

Results: Analysis of the exome data led to identification of two putative pathogenic variants. One, a nonsense mutation in ADD3, encoding adducin 3, was found in the proband and his affected daughter, but not other family members. The other was a missense mutation (G1546S) in the gene encoding filamin C (FLNC), found in all of the affected individuals. Both of these proteins interact with proteins involved in sarcomere function, and are expressed in both heart and skeletal muscle. FLNC has recently been implicated as a cardiomyopathy gene, but ADD3 has not at this point.

Conclusion: We present bioinformatic analyses that suggest that the FLNC variant is the major pathogenic variant affecting this family, but cannot rule out some contribution of the ADD3 mutation in at least two patients.

Many important medical conditions may be the result of an inherited mutation in one of a number of different genes. Technical advances have reduced the cost of whole genome sequencing and whole exome sequencing to a level where it is now feasible to analyse multiple genes in one test. Every human carries several hundred potentially pathogenic coding variants, so a major challenge is to understand which of these is relevant to the patient’s disease. This requires considerable computing power, the use of international unaffected “normal” population and disease cohort databases, clinical scientist input as well as a medical context provided by accurate phenotyping and understanding of Bayesian probability. The guidelines of the American College of Medical Genetics provide a useful framework for the evaluation and reporting of sequence variants. In England, the 100,000 Genomes Project was established within the National Health Service to introduce these technologies into mainstream healthcare. From January 2019, genomic laboratory hubs will deliver a genomics service. In this paper, we review what has been learnt from the project to date and consider how other health care systems could use similar approaches.

Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease, generally the first clinical manifestation of atopy and the start of atopic march. Effective treatment of AD could potentially interrupt the progression of atopic march. MicroRNAs (miRNAs), a recently described class of gene expression regulators in inflammatory conditions, affect expression of numerous proteins. The role of miRNAs has been investigated in several atopic conditions, including asthma, eosinophilic esophagitis, allergic rhinitis as well as atopic dermatitis. They have been shown to be involved in the morphogenesis of skin. The therapeutic effects of inhibition or overexpression of miRNAs have been demonstrated in murine models. Considering their role as master switches of complex cellular processes, they could be potential therapeutic targets for inflammatory skin conditions including atopic dermatitis. MiRNAs can be detected in different cell-free body fluids, such as serum, plasma, urine and saliva, raising the obvious question whether they can be used as biomarkers of disease. This review article summarizes what is known so far abut miRNAs and atopic dermatitis.

Aim: Whole exome sequencing technology has permitted the discovery of genes that cause Mendelian disorders and was used in clinical laboratories. However, identifying the disease causing variant(s) for a specific disorder from thousands of variants is challenging. In this study, we describe the Cincinnati Clinical Exome Pipeline Analysis Suite (CCEPAS) that utilizes a four-level framework into one analysis procedure that rapidly identify the most likely causative gene variants to establish a clinical diagnosis.

Methods: We developed and validated CCEPAS using 100 clinical exome cases. We applied this pipeline to clinical cases by first translating phenotypic information into candidate gene lists using Pheno2Gene. This list of candidate genes was given to the VarEval algorithm to guide variant filtering and prioritization. Finally, a short list of filtered variants was produced for clinical interpretation.

Results: We demonstrated the development and implementation of CCEPAS to aid in the variant prioritization and filtering to produce a short list of candidate variants for clinical diagnosis. Its unique Pheno2Gene tool utilized an extensive list of resources and provided an accurate, sensitive and specific way to obtain gene lists from clinical feature keywords. In addition, VarEval narrowed down the variants from ~150,000 to the top 20 (trios) and top 50 (singleton) for further variant curation and candidate determination.

Conclusion: Significantly, employment of CCEPAS rapidly provided causative variants in the top 20 and top 50 variants for single and trio cases, respectively, thus, ending the diagnostic odyssey in more than 30% of our clinical exome cases.

Many important medical conditions may be the result of an inherited mutation in one of a number of different genes. Technical advances have reduced the cost of whole genome sequencing and whole exome sequencing to a level where it is now feasible to analyse multiple genes in one test. Every human carries several hundred potentially pathogenic coding variants, so a major challenge is to understand which of these is relevant to the patient’s disease. This requires considerable computing power, the use of international unaffected “normal” population and disease cohort databases, clinical scientist input as well as a medical context provided by accurate phenotyping and understanding of Bayesian probability. The guidelines of the American College of Medical Genetics provide a useful framework for the evaluation and reporting of sequence variants. In England, the 100,000 Genomes Project was established within the National Health Service to introduce these technologies into mainstream healthcare. From January 2019, genomic laboratory hubs will deliver a genomics service. In this paper, we review what has been learnt from the project to date and consider how other health care systems could use similar approaches.

Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease, generally the first clinical manifestation of atopy and the start of atopic march. Effective treatment of AD could potentially interrupt the progression of atopic march. MicroRNAs (miRNAs), a recently described class of gene expression regulators in inflammatory conditions, affect expression of numerous proteins. The role of miRNAs has been investigated in several atopic conditions, including asthma, eosinophilic esophagitis, allergic rhinitis as well as atopic dermatitis. They have been shown to be involved in the morphogenesis of skin. The therapeutic effects of inhibition or overexpression of miRNAs have been demonstrated in murine models. Considering their role as master switches of complex cellular processes, they could be potential therapeutic targets for inflammatory skin conditions including atopic dermatitis. MiRNAs can be detected in different cell-free body fluids, such as serum, plasma, urine and saliva, raising the obvious question whether they can be used as biomarkers of disease. This review article summarizes what is known so far abut miRNAs and atopic dermatitis.

X chromosome inactivation (XCI) is a strategy used by mammals to silence genes along one of the two female X chromosomes and equilibrate expression dosage between XY males and XX females. This epigenetically-inherited silencing is established during early embryonic development and maintained thereafter through cell divisions. Seeding of multiple repressive epigenetic marks along the inactive X chromosome (Xi) makes inactivation extremely robust and difficult to reverse upon single genetic perturbations. Reversal of XCI has, however, been observed when somatic cells are reprogrammed towards pluripotency, and in vitro reprogramming techniques have been used in recent years to dissect Xi gene reactivation mechanisms. These studies pave the way for developing novel therapeutic approaches for X-linked diseases. Here, the author reviews Xi reactivation during pluripotent reprogramming of mouse and human somatic cells, highlight recent advances and species-specific differences, and discuss the relevance for human diseases.

The dosage compensation in placental mammals is achieved by silencing of one copy of the X chromosomes in a female cell by a process called X chromosome inactivation (XCI). XCI ensures equal gene dosage for X-linked genes between the two genders. Although the choice of X chromosome to be silenced is random, once the silencing of the X chromosome has been established, this process is highly regulated and maintained throughout subsequent cell divisions. A long non-coding RNA, Xist, and its interacting proteins execute this multistep process, but several of these regulatory proteins remain unidentified. Recent technological advances based on the genetic and proteomics screening have identified several new regulatory factors as well as dissected the molecular details of XCI regulation. Moreover, identification of regulators of XCI offers an opportunity to explore reactivation of the inactive X chromosome (Xi) as a potential therapeutic strategy to treat X-linked diseases, like Rett syndrome. Here, we summarize recent reports that identified new regulatory proteins and RNA species playing a crucial role in Xist localization and spreading, recruitment of silencing machinery to the Xi, Xist interaction with chromatin, and structural organization of the Xi in the nuclei.

Prostate cancer is the second most frequently diagnosed non-skin male malignancy worldwide, with over 1.1 million new diagnoses each year. Population screening based on serum prostate-specific antigen (PSA) has shifted the disease burden toward earlier stage, localized disease. However, clinical outcomes for localized prostate cancer are highly heterogeneous, despite the use of clinical prognostic factors (PSA, Gleason grade, and TNM stage). Recent advances in massively-parallel DNA sequencing and computational biology have permitted detailed genomic analyses of all major human cancer types, including prostate cancer. However, the long natural history of prostate cancer has largely precluded rapid translation of this knowledge into clinical practice. Herein, we provide a “state of the field” overview of prostate cancer genomics, with particular focus on localized, non-indolent disease. We discuss recurrent somatic aberrations, across multiple mutational classes, which characterize this disease state, and suggest strategies through which an improved understanding of these molecular aberrations may be utilized in the curative setting. Finally, we summarize the major outstanding questions in prostate cancer genomics, and discuss hypotheses and potential strategies to begin to address these questions.

This article discusses the benefits of personalized genomic medicine, some of the challenges of adoption into the clinic, and provides examples of UK and European projects that are developing the practice of personalized genomic medicine. It highlights the work of the UK Pharmacogenetics and Stratified Medicine Network in providing information, developing multidisciplinary collaborations, and organizing events, to support the advancement of personalized genomic medicine.

Aim: Triple negative breast cancer (TNBC) is the most severe subtype of breast cancer with poor prognosis even when treated at a localized stage. The treatment of metastatic TNBC is still challenging daily clinical practice, mainly because of the lack of targeted therapies. In the last years, a molecular sub-classification of TNBC has opened the way to personalized medicine for this type of severe cancer.

Methods: In this study, we assessed the added value of combining molecular analyses with individual xenografts to personalize the treatment of resort for five women with metastatic TNBC. While a patient was receiving one or two lines of chemotherapy, the corresponding xenograft model was tested with different drugs or drug combinations, mainly based on transcriptomic analyses of the tumor and on theoretical activated canonical pathways.

Results: On the basis of transcriptomic analyses and chemosensitivity data obtained from TNBC individual xenografts, we personalized the resort treatment for the five women in our study. In all cases, despite the fact that this resort treatment was a third-line or a fourth-line treatment, the time to progression was longer than that observed with previous lines of chemotherapy. When we explored the 19 chemotherapy regimens given to these women and their corresponding xenograft models, there was a strong correlation between ΔSUV_max (maximum standard uptake value) on positron emission tomography-computed tomography and the corresponding coefficients of inhibition obtained in mice.

Conclusion: The combination of gene expression profiling and individual xenografts is a promising method and could be proposed as a personalized therapeutic resort for women with metastatic TNBCs.

Aim: Asthma is a chronic inflammatory syndrome that is characterized by heterogeneous disease pathogeneses that produce distinct subtypes. There is a great need to develop biomarkers to distinguish these subtypes and help guide specific therapy and better predict outcomes, particularly in severe asthma where a number of targeted therapeutics are now available. We sought to determine whether expression of asthma-specific microRNAs (miRNAs) could distinguish phenotypic differences in a diverse cohort of asthmatic subjects that spanned a range of disease severity.

Methods: RNA was isolated from peripheral blood from human subjects. Expression of 39 miRNAs was then screened. Sample cycle threshold values were normalized. Normally distributed data were analyzed and hierarchical cluster was performed.

Results: Peripheral blood was obtained from 62 adults. We identified four clusters of asthmatics defined by 5 distinct miRNA expression patterns. Cluster 1 was associated with mild asthma, low inhaled corticosteroid use, and low eosinophil levels. Cluster 3 and 4 consisted primarily of severe asthmatics with poor asthma control, and Cluster 3 was specifically associated with high IgE, high blood eosinophil levels, and racial disparity (higher proportion of Black subjects). Cluster 2 was comprised predominantly of mild-moderate asthmatics that had higher blood eosinophils than Cluster 1.

Conclusion: These results indicate the miRNA expression profiling can be useful to identify distinct asthma phenotypes, and have potential to better understand disease pathogenesis and help guide therapy.

Renal cell carcinoma (RCC) represents a heterogeneous group of malignancies derived from the kidney, of which clear cell RCC (ccRCC) accounts for nearly 75% of cases. Despite major advances in effective therapies, metastatic ccRCC is still associated with a 10%-20% 5-year survival and remains quite lethal. Great effort has been placed into understanding the genetics and genomics of ccRCC and their prognostic and therapeutic implications. Large-scale cancer genomics sequencing studies have identified several driver genes beyond VHL, particularly PBRM1 (40%), SETD2 (15%), and BAP1 (10%), drastically changing the concept of single-gene pathology underlying sporadic ccRCC. In this mini-review, we explore the pathways by which the loss of VHL, PBRM1, SETD2, and/or BAP1 induce ccRCC through discussion of gene function, disease models, prognostic indications, and therapeutic advances.

The large number of different syndromes and seizure types together with an interindividual variable response to antiepileptic drugs (AEDs) make the treatment of epilepsy challenging. Fortunately, the last few years have been characterized by a huge interest in epilepsy genetics and two methods, genome-wide analyses and next-generation sequencing, have definitely given the possibility to write a new chapter in the book of treatment of epilepsy, the chapter on precision medicine. Epilepsy offers a good opportunity for the personalization of therapy if we consider that at least one third of epileptic patients do not achieve complete seizure control with the currently available pharmacological treatments, treatment is still often empirical and precise therapy, based on the pathogenesis and the mechanism of each AED is not generally possible because this mechanism often remains incompletely known. In addition, new drugs are often not targeted but developed using in vivo seizure models, to be potentially used by the largest number of patients. This method leads to a therapy aimed at treating the symptoms and the seizures rather than the single pathogenic mechanism of each seizure type or syndrome. In this narrative review, we summarize the established evidence regarding pharmacogenomics in epilepsy and discuss the basis of precision medicine.

Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease, generally the first clinical manifestation of atopy and the start of atopic march. Effective treatment of AD could potentially interrupt the progression of atopic march. MicroRNAs (miRNAs), a recently described class of gene expression regulators in inflammatory conditions, affect expression of numerous proteins. The role of miRNAs has been investigated in several atopic conditions, including asthma, eosinophilic esophagitis, allergic rhinitis as well as atopic dermatitis. They have been shown to be involved in the morphogenesis of skin. The therapeutic effects of inhibition or overexpression of miRNAs have been demonstrated in murine models. Considering their role as master switches of complex cellular processes, they could be potential therapeutic targets for inflammatory skin conditions including atopic dermatitis. MiRNAs can be detected in different cell-free body fluids, such as serum, plasma, urine and saliva, raising the obvious question whether they can be used as biomarkers of disease. This review article summarizes what is known so far abut miRNAs and atopic dermatitis.

X chromosome inactivation (XCI) is a strategy used by mammals to silence genes along one of the two female X chromosomes and equilibrate expression dosage between XY males and XX females. This epigenetically-inherited silencing is established during early embryonic development and maintained thereafter through cell divisions. Seeding of multiple repressive epigenetic marks along the inactive X chromosome (Xi) makes inactivation extremely robust and difficult to reverse upon single genetic perturbations. Reversal of XCI has, however, been observed when somatic cells are reprogrammed towards pluripotency, and in vitro reprogramming techniques have been used in recent years to dissect Xi gene reactivation mechanisms. These studies pave the way for developing novel therapeutic approaches for X-linked diseases. Here, the author reviews Xi reactivation during pluripotent reprogramming of mouse and human somatic cells, highlight recent advances and species-specific differences, and discuss the relevance for human diseases.

The dosage compensation in placental mammals is achieved by silencing of one copy of the X chromosomes in a female cell by a process called X chromosome inactivation (XCI). XCI ensures equal gene dosage for X-linked genes between the two genders. Although the choice of X chromosome to be silenced is random, once the silencing of the X chromosome has been established, this process is highly regulated and maintained throughout subsequent cell divisions. A long non-coding RNA, Xist, and its interacting proteins execute this multistep process, but several of these regulatory proteins remain unidentified. Recent technological advances based on the genetic and proteomics screening have identified several new regulatory factors as well as dissected the molecular details of XCI regulation. Moreover, identification of regulators of XCI offers an opportunity to explore reactivation of the inactive X chromosome (Xi) as a potential therapeutic strategy to treat X-linked diseases, like Rett syndrome. Here, we summarize recent reports that identified new regulatory proteins and RNA species playing a crucial role in Xist localization and spreading, recruitment of silencing machinery to the Xi, Xist interaction with chromatin, and structural organization of the Xi in the nuclei.

Parathyroid carcinoma is a rare but clinically-aggressive tumor. While most cases are sporadic, parathyroid cancer is overrepresented in hyperparathyroidism-jaw tumor syndrome, or rarely other heritable syndromes. Evidence suggests that sporadic parathyroid carcinomas rarely, if ever, evolve through an identifiable benign tumor intermediate. A few genes have been directly implicated in the pathogenesis of sporadic parathyroid cancer; somatic (and less common germline) mutations in the CDC73 tumor suppressor gene are the most frequent finding and the only firmly established molecular drivers of parathyroid cancer. Alterations in other important human cancer genes, including CCND1/cyclin D1, PIK3CA, MTOR and PRUNE2 have also been described in parathyroid cancer, however their abilities to drive malignant parathyroid tumorigenesis remains to be demonstrated experimentally.

There is a general failure of reductionist and mechanistic approaches to rejuvenation biomedical technologies which aim at providing treatments against aging (defined as “time-dependent dysfunction”). Importantly, it is becoming increasingly recognised that genomic research findings in animals may not adequately be translated into effective human anti-aging therapies. There exist translational impediments, which although individually formidable, can theoretically be overcome. However, the combined effects of these obstacles render this reductionist avenue of quest unattainable, at least for the foreseeable future. Some of the clinical problems of physical and genomic-based therapies against aging include side effects, interactions, inter-subject variability, compliance, patient self-reporting of data, motivation, administrative issues, infrastructure, etc. A systematic review spanning over the past 5 years, describes these problems and identifies novel approaches. New and emerging disciplines and concepts such as molecular pathological epidemiology, social genomics and other “systems-thinking” methods provide a more comprehensive view of the entire subject of aging, and study its indivisible bonds with the environment, society and culture. The so-called “fountain of youth” cannot be found in a physical item.