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.

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.

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.

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.

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.

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.

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.

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.

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.

Liposarcoma (LPS) is among the most common soft tissue sarcoma affecting adults. LPS is divided into three biologic subtypes characterized by specific genetic alterations. The most common LPS subtypes, well-differentiated and dedifferentiated LPS, are nearly uniformly characterized by ring chromosomes and giant markers with chromosomal amplification of 12q13-15 and resulting amplification of oncogenes MDM2, CDK4, and HMGA2. Myxoid/round cell LPS commonly exhibits a distinctive (12; 16) translocation resulting in the FUS-DDIT3 fusion gene. Finally, pleomorphic LPS harbors diverse complex genomic changes and chromosomal rearrangements and frequent mutations in TP53, RB1, and NF1 leading to dysregulation of tumor suppressor pathways. In this review, we summarize the currently available knowledge on the genomics and genetics of LPS subtypes as well as recent advances in the multimodality management of LPS.

Cutaneous melanoma is caused by the uncontrolled growth of epidermal melanocytes. Melanoma continues to be a rare form of skin cancer but causes the majority of skin cancer related deaths. For many years the scientific community has focused on the investigation of the pathogenesis leading to melanoma, with the aim of better understanding its complexity and the potential advancement of therapeutic strategies. In this paper, the genomic features characterising the development of cutaneous melanoma are reviewed. Next-generation sequencing technologies and bioinformatics tools are currently state-of-the-art approaches in basic, applied and clinical cancer research. In this review, most of the available tools for revealing the mutational landscape are outlined.

The clinical behavior of prostate cancer is highly heterogeneous, with most patients diagnosed with localized disease that successfully responds to surgery or radiotherapy or that can be followed by active surveillance. However, a fraction of men will relapse after initial treatment and eventually progress to an aggressive resistant form with metastasis spreading and high mortality, a state referred to as castration resistant prostate cancer (CRPC). The technological advances in next generation sequencing have enabled the deep genomic and epigenomic characterization of both the hormone naïve and CRPC states, leading to the definition of molecular subclasses of prostate cancer that could inform the clinicians on therapeutic strategies. These studies also shed light on the mechanisms driving resistance to therapy. CRPCs adapt to androgen receptor (AR) signaling impairment - which follows first-line therapies as androgen deprivation or AR targeting - by restoring the nuclear receptor signaling by means of multiple mechanisms. Alternatively, tumor cells might become resistant to targeted therapies by exploiting lineage plasticity and activating alternative pathways. This review will discuss the main mechanisms leading to the emergence of resistance to therapy in prostate cancer patients in the context of genomic and molecular features of CRPC and on their causal role in the development of resistance.

With the prevalence of end stage renal disease steadily increasing, chronic kidney disease (CKD) represents an impending public healthcare challenge. Classical diagnostic biomarkers of CKD, including creatinine, have low sensitivity and specificity. Thus, novel diagnostic and prognostic biomarkers for patients at high risk of early-stage progression are urgently needed. Personalized medicine approaches generally stratify patients according to their biological or genomic make-up. Targeted clinical trials require more precise identification of these subgroups. The use of new biomarkers obtained via high-throughput technologies is expected in future, accompanied by vast improvements in computational power applied in genomics, proteomics, and metabolomics studies using biological fluids and renal biopsy tissue. Genomic biomarkers may not only provide additional information regarding the etiology and mechanisms underlying CKD progression, but may also enable early diagnosis and the selection of appropriate drugs, thereby personalizing therapy. This review discusses commonly used research methods in genomic medicine and summarizes currently available genomic biomarkers in inherited and acquired CKD.

Genomic medicine, that is to say, using genomic information about a patient in order to set the diagnostic path and to tailor therapy to his/her specific characteristics, is one of the cornerstones of modern precision medicine and forms an integral part of several fields, oncology first of all. Lung cancer is the leading cause of cancer mortality, causing more than 1.6 million deaths worldwide per year and non-small-cell lung cancer (NSCLC) accounts for approximately 85% of lung cancers. In a small subset of NSCLC (5%-8%), we can detect a genomic rearrangement on chromosome 2, between the Echinoderm microtubule-associated protein-like 4 (EML4) gene and the anaplastic lymphoma kinase (ALK) gene, resulting in the chimeric protein EML4-ALK, that acts as an oncogene and that can be specifically targeted by an ALK-tyrosine kinase inhibitor (TKI) therapy. However, a major clinical challenge is represented by the fact that, after a first line ALK-TKI treatment, patients eventually develop acquired resistance to these agents, opening new scenarios for the right second-line drug choice.

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.