Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities.

Sci Rep. 2018 Mar 09;8(1):4202

Authors: Ahmad R, Sahidin I, Taher M, Low C, Noor NM, Sillapachaiyaporn C, Chuchawankul S, Sarachana T, Tencomnao T, Iskandar F, Rajab NF, Baharum SN

Abstract
Polygonumins A, a new compound, was isolated from the stem of Polygonum minus. Based on NMR results, the compound's structure is identical to that of vanicoside A, comprising four phenylpropanoid ester units and a sucrose unit. The structure differences were located at C-3″″'. The cytotoxic activity of polygonumins A was evaluated on several cancer cell lines by a cell viability assay using tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The compound showed the highest antiproliferative (p < 0.05) activities against K562 (Human Leukaemia Cell Line), MCF7 (Human breast adenocarcinoma cell line), and HCT116 (Colorectal cancer cells) cells. Cytotoxic studies against V79-4 cells were carried out and showed that polygonumins A was toxic at 50 µg/ml, suggesting that this compound may be used as an anticancer drug without affecting normal cells. Polygonumins A also showed promising activity as an HIV-1 protease inhibitor with 56% relative inhibition. Molecular docking results indicated that the compound possesses high binding affinity towards the HIV protease over the low binding free energy range of -10.5 to -11.3 kcal/mol. P. minus is used in Malaysian traditional medicine for the treatment of tumour cells. This is the first report on the use of P. minus as an HIV-1 protease inhibitor.

PMID: 29523802 [PubMed - in process]

Ion mobility-derived collision cross section database: Application to mycotoxin analysis.

Anal Chim Acta. 2018 Jul 19;1014:50-57

Authors: Righetti L, Bergmann A, Galaverna G, Rolfsson O, Paglia G, Dall'Asta C

Abstract
The recent hyphenation of ion mobility spectrometry (IMS) with high resolution mass spectrometry (HRMS) has risen as a powerful technique for both targeted and non-targeted screening, reducing background noise and allowing separation of isomeric and isobaric compounds. Nevertheless, such an approach remains largely unexplored in food safety applications, such as mycotoxin analysis. To implement ion mobility in routinely MS-based mycotoxin workflows, searchable databases with collusion cross section (CCS) values and accurate mass-values are required. This paper provides for the first time a traveling-wave IMS (TWIMS)-derived CCS database for mycotoxins, including more than 100 CCS values. The measurements showed high reproducibility (RSD < 2%) across different instrumental conditions as well as several complex cereal matrices, showing a mean inter-matrix precision of RSD <0.9%. As a proof of concept, the database was applied to the analysis of several spiked as well as naturally incurred cereal-based samples. In addition, the effect of adducts on the drift time was studied in a series of mycotoxins in order to understand potential deviations from expected drift time behaviors. Overall, our study confirmed that CCS values represent a physicochemical property that can be used alongside the traditional molecular identifiers of precursor ion accurate mass, fragment ions, isotopic pattern, and retention time.

PMID: 29523251 [PubMed - in process]

Adverse Drug Events Associated with Low-Dose (10 mg) Versus High-Dose (25 mg) Empagliflozin in Patients Treated for Type 2 Diabetes Mellitus: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

Diabetes Ther. 2018 Mar 09;:

Authors: Dai X, Luo ZC, Zhai L, Zhao WP, Huang F

Abstract
INTRODUCTION: Empagliflozin is a new, emerging oral hypoglycemic agent (OHA) which has shown significant benefits in type 2 diabetes mellitus (T2DM) patients with cardiovascular disease. In this analysis, our aim was to systematically compare the adverse drug events (ADEs) associated with a low (10 mg) versus a high (25 mg) dose of empagliflozin as (1) monotherapy, (2) as an add-on to other OHAs, and (3) as an add-on specifically to metformin, in patients who were treated for T2DM.
METHODS: This was a systematic review and meta-analysis of randomized controlled trials that compared empagliflozin 10 mg versus 25 mg in patients who were treated for T2DM and which reported adverse drug reactions as their clinical endpoints. Statistical analysis was carried out using the latest version of the RevMan software (ver. 5.3) whereby odds ratios (OR) and 95% confidence intervals (CI) were generated.
RESULTS: Eight trials with a total number of 8514 patients treated for T2DM were included in this meta-analysis and systematic review, of whom 4261 patients received 10 mg empagliflozin and 4253 patients received 25 mg empagliflozin. Our results showed that there were no significant differences between the patients with T2DM receiving 10 empagliflozin and those receiving 25 mg empagliflozin in terms of drug-related adverse effects (OR 1.06, 95% CI 0.93-1.21; P = 0.40, I2 = 0%), adverse events leading to drug discontinuation (OR 0.99, 95% CI 0.86-1.14; P = 0.87, I2 = 0%), and serious adverse events (OR 1.06, 95% CI 0.95-1.18; P = 0.31, I2 = 0%) when empagliflozin was provided as monotherapy or as an add-on to other anti-diabetic medications. The same results were obtained when empagliflozin was used as an add-on to metformin or as monotherapy. The duration of the follow-up periods did not affect the results. However, the incidence of genital and urinary tract infections (UTIs) was significantly higher in female patients than in male patients with 10 or 25 mg empagliflozin.
CONCLUSIONS: The incidence of ADEs was not significantly different in T2DM patients receiving 10 versus 25 mg empagliflozin as monotherapy or as add-on to metformin or other anti-diabetic drugs during a shorter or longer follow-up period. However, genital and UTIs were more common in female patients with T2DM irrespective of empagliflozin dosage.

PMID: 29524188 [PubMed - as supplied by publisher]

11 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

pharmacogenomics

These pubmed results were generated on 2018/03/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

39 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/03/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

In Silico Chemogenomics Drug Repositioning Strategies for Neglected Tropical Diseases.

Curr Med Chem. 2018 Mar 08;:

Authors: Andrade CH, Neves BJ, Melo-Filho CC, Rodrigues J, Silva DC, Braga RC, Cravo PVL

Abstract
Only ~1% of all drug candidates against Neglected Tropical Diseases (NTDs) have reached clinical trials in the last decades, underscoring the need for new, safe and effective treatments. In such context, drug repositioning, which allows finding novel indications for approved drugs whose pharmacokinetic and safety profiles are already known, is emerging as a promising strategy for tackling NTDs. Chemogenomics is a direct descendent of the typical drug discovery process that involves the systematic screening of chemical compounds against drug targets in high-throughput screening (HTS) efforts, for the identification of lead compounds. However, different to the one-drug-one-target paradigm, chemogenomics attempts to identify all potential ligands for all possible targets and diseases. In this review, we summarize current methodological development efforts in drug repositioning that use state-of-the-art computational ligand- and structure-based chemogenomics approaches. Furthermore, we highlighted the recent progress in computational drug repositioning for some NTDs, based on curation and modeling of genomic, biological, and chemical data. Additionally, we also present in-house and other successful examples and suggest possible solutions to existing pitfalls.

PMID: 29521204 [PubMed - as supplied by publisher]

The Rare Extragonadal Omental Teratoma: A Case Report.

J Minim Invasive Gynecol. 2017 Sep - Oct;24(6):1046-1048

Authors: Rampinelli F, Donarini P, Visenzi C, Ficarelli S, Gambino A, Ciravolo G

Abstract
Teratomas of extragonadal origin are extremely rare, and the most common extragonadal site to find teratomas is the omentum. Teratomas are typically found in women of reproductive age, but they are also seen in young girls and postmenopausal women. Generally, teratomas arise from germ cells that may induce different cells to originate from the 3 primitive embryonic layers. Three main theories have been proposed to explain their location. The present report summarizes these theories as well as describes a case of a mature cystic teratoma of the omentum that was managed by laparoscopic resection.

PMID: 28662988 [PubMed - indexed for MEDLINE]

Rare cancers: Challenges & issues.

Indian J Med Res. 2017 Jan;145(1):17-27

Authors: Pillai RK, Jayasree K

Abstract
Rare cancers account for about 22 per cent of all cancers diagnosed worldwide, disproportionately affecting some demographic groups, with an occurrence of less than 6 per 100,000 individuals annually. Many rare cancers in adults, adolescents and children are not curable, and patients and care providers have little option to take therapeutic decisions. The epidemiology of rare cancers is a challenging area of study but is inadequately addressed. Despite efforts mainly in some European nations, a few improvements have been observed in the management of rare cancers. Reasons for this obvious stagnation are multifactorial and are mainly inherent to logistical difficulties in carrying out clinical trials in very small patient populations, hesitation of the pharmaceutical industry to spend in small markets and complexity in creating adequate information for the development of cost-effective drugs. Rare cancers also face specific challenges that include late and incorrect diagnosis, lack of clinical expertise and lack of research interest and development of new therapies. The utilization of nationally representative study findings for the patients' evaluation may possibly offer chances to find out pathogenesis and prevalence, and this will eventually lead to control and prevention. Currently, advancing targeted therapies offer a great opportunity for the better management of rare cancers. Conducting clinical trials with small patient population, innovative clinical trial approach, prevailing controlling obstacles for international cooperation and financial support for research are the present challenges for rare cancers. The International Rare Cancers Initiative functions as a main platform for achieving new international clinical trials in rare tumours. This review delineates the current challenges and issues in the interpretation, management and research scenarios of rare cancers.

PMID: 28574010 [PubMed - indexed for MEDLINE]

Twenty-First Century Diseases: Commonly Rare and Rarely Common?

Antioxid Redox Signal. 2017 Sep 20;27(9):511-516

Authors: Daunert S, Sittampalam GS, Goldschmidt-Clermont PJ

Abstract
Alzheimer's drugs are failing at a rate of 99.6%, and success rate for drugs designed to help patients with this form of dementia is 47 times less than for drugs designed to help patients with cancers ( www.scientificamerican.com/article/why-alzheimer-s-drugs-keep-failing/2014 ). How can it be so difficult to produce a valuable drug for Alzheimer's disease? Each human has a unique genetic and epigenetic makeup, thus endowing individuals with a highly unique complement of genes, polymorphisms, mutations, RNAs, proteins, lipids, and complex sugars, resulting in distinct genome, proteome, metabolome, and also microbiome identity. This editorial is taking into account the uniqueness of each individual and surrounding environment, and stresses the point that a more accurate definition of a "common" disorder could be simply the amalgamation of a myriad of "rare" diseases. These rare diseases are being grouped together because they share a rather constant complement of common features and, indeed, generally respond to empirically developed treatments, leading to a positive outcome consistently. We make the case that it is highly unlikely that such treatments, despite their statistical success measured with large cohorts using standardized clinical research, will be effective on all patients until we increase the depth and fidelity of our understanding of the individual "rare" diseases that are grouped together in the "buckets" of common illnesses. Antioxid. Redox Signal. 27, 511-516.

PMID: 28482684 [PubMed - indexed for MEDLINE]

A clinical study of 21 patients with hemophagocytic syndrome in 295 cases diagnosed with nasal type, extranodal nature killer/T cell lymphoma.

Cancer Biol Ther. 2017 Apr 03;18(4):252-256

Authors: Li N, Zhang L, Liu J, Zhang J, Weng HW, Zhuo HY, Zou LQ

Abstract
Nasal type, extranodal nature killer (NK)/T cell lymphoma-associated hemophagocytic syndrome (NK/T-LAHS) is a rare and fatal disorder with extremely poor prognosis. To investigate its clinical characteristics and risk factors, we retrospectively analyzed 295 patients with nasal type, extranodal nature killer/T cell lymphoma, of which 21 were diagnosed with hemophagocytic syndrome, with a cumulative incidence of 7.1%. The most frequently clinical characteristics were fever, lymphadenopathy, hepatosplenomegaly, pancytopenia, hyperferritinemia, liver dysfunction, hypertriglyceridemia, hypofibrinogenemia and evaluated lactate dehydrogenase (LDH) level. After a median follow-up of 27 months, the 2-year survival for the 295 patients was 74.6%. Significant difference for 2-year survival was found between patients with and without hemophagocytic syndrome (4.8% vs. 80.0%, P<0.001). After developing hemophagocytic syndrome, all patients survived no more than 3 months, with a median survival of 35 days. Risk factors for NK/T-LAHS were bone marrow (BM) involvement (P = 0.019; relative risk, 13.649; 95% confidence interval (CI): 1.538-121.103), hepatosplenomegaly (P = 0.003; relative risk, 9.616; 95%CI: 2.154-42.918), and elevated LDH level (>314U/L) (P = 0.038; relative risk, 6.293; 95%CI: 1.108-35.735). We conducted a risk model for all 295 patients based on the 3 adverse factors as follows: low risk (233 cases, 79.0%), no factor; intermediate risk (43 cases, 14.6%), one factor; high risk (19 cases, 6.4%), 2 or 3 factors. The probabilities for developing LAHS were 0.9% for low-, 14.0% for intermediate-, and 68.4% for high-risk group. Significant differences in the 3 risk groups were observed (P<0.001).

PMID: 28278074 [PubMed - indexed for MEDLINE]

High-dose vitamin D in Addison's disease regulates T-cells and monocytes: A pilot trial.

Nutrition. 2017 Dec 02;49:66-73

Authors: Penna-Martinez M, Filmann N, Bogdanou D, Shoghi F, Huenecke S, Schubert R, Herrmann E, Koehl U, Husebye ES, Badenhoop K

Abstract
OBJECTIVES: On the basis of the immunomodulatory actions of vitamin D (VD), we investigated the effects of high-dose VD therapy over a 3 mo period on the immune response in patients with Addison's disease (AD).
METHODS: This randomized, controlled, crossover trial included 13 patients with AD who received either cholecalciferol (4000 IU/d) for 3 mo followed by 3 mo placebo oil or the sequential alternative placebo followed by verum. Glucocorticoid replacement doses remained stable. The primary outcome measures were changes in 25-hydroxyvitamin D3 (25(OH)D3) levels and immune cells including T helper cells (Th; CD3+CD4+), late-activated Th cells (CD3+CD4+HLA-DR+), regulatory T cells (CD3+CD4+CD25brightCD127dim/neg), cytotoxic T cells (Tc; CD3+CD8+), late-activated Tc cells (CD3+CD8+HLA-DR+), and monocytes. The explorative analysis included the correlation of changes with VD-related gene polymorphisms and 21-hydroxylase antibody titers.
RESULTS: Ten of 13 patients (77%) were VD deficient. Median 25(OH)D3 concentrations increased significantly to 41.5 ng/ml (median changes: 19.95 ng/ml; P = 0.0005) after 3 mo of cholecalciferol treatment. Within the T-cells, only the late-activated Th (median changes: 1.6%; P = 0.02) and late-activated Tc cells (median changes: 4.05%; P = 0.03) decreased, whereas monocytes (median changes: 1.05%; P = 0.008) increased after VD therapy. T-cell changes were associated with two polymorphisms (CYP27B1-rs108770012 and VDR-rs10735810), but no changes in the 21-hydroxylase antibody titers were observed.
CONCLUSIONS: Three months of treatment with cholecalciferol achieved sufficient 25(OH)D3 levels and can regulate late-activated T-cells and monocytes in patients with AD. Explorative analysis revealed potential genetic contributions. This pilot trial provides novel insights about immunomodulation in AD.

PMID: 29522979 [PubMed - as supplied by publisher]

Microarray analysis in pregnancies with isolated echogenic bowel.

Early Hum Dev. 2018 Mar 06;119:25-28

Authors: Singer A, Maya I, Koifman A, Nasser Samra N, Baris HN, Falik-Zaccai T, Ben Shachar S, Sagi-Dain L

Abstract
INTRODUCTION: Fetal echogenic bowel is a frequent sonographic finding, demonstrated in about 1% of pregnancies. The advised evaluation of fetal echogenic bowel includes maternal serology, genetic testing for cystic fibrosis, detailed sonographic anatomic survey, and invasive prenatal testing for fetal chromosomal aberrations. The objective of our study was to evaluate the risk for clinically significant chromosomal microarray analysis (CMA) findings in pregnancies with isolated echogenic bowel.
METHODS: Data from all CMA analyses performed due to isolated echogenic bowel reported to the Israeli Ministry of Health between January 2013 and September 2016 were retrospectively obtained. Risk estimation was performed comparing the rate of abnormal microarray findings to the control population, based on a systematic review of 9272 pregnancies and a large local cohort of 5541 fetuses with normal ultrasound, undergoing CMA testing due to maternal request.
RESULTS: Of 103 CMA analyses performed due to isolated echogenic bowel, two (1.94%) pathogenic findings were detected (47,XYY and 16p11.2 duplication). This risk was not significantly elevated compared to the control groups. In addition, three variants of unknown significance were demonstrated.
CONCLUSIONS: To our best knowledge, our study is the first report describing the rate of clinically significant copy number variants in pregnancies with isolated echogenic bowel. According to our results, it seems that pregnancies with isolated echogenic bowel do not have an increased risk for abnormal CMA compared to fetuses with no evidence of sonographic anomalies. Our findings suggest that the consideration to perform CMA analysis in such pregnancies should not differ from any pregnancy with normal ultrasound.

PMID: 29522884 [PubMed - as supplied by publisher]

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis.

PLoS One. 2018;13(3):e0194060

Authors: Carmody LA, Caverly LJ, Foster BK, Rogers MAM, Kalikin LM, Simon RH, VanDevanter DR, LiPuma JJ

Abstract
Bacteria that infect the airways of persons with cystic fibrosis (CF) include a group of well-described opportunistic pathogens as well as numerous, mainly obligate or facultative anaerobic species typically not reported by standard sputum culture. We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 sputum specimens collected from 111 CF patients over 10 years. We describe fluctuations in the relative abundances of typical CF pathogens, as well as anaerobic species, in relation to changes in patients' clinical state and lung disease stage. Both bacterial community diversity and the relative abundance of anaerobes increased during exacerbation of symptoms (prior to antibiotic treatment), although this trend was not observed uniformly across disease stages. Community diversity and the relative abundance of anaerobic species decreased during antibiotic treatment. These results support current hypotheses regarding the role of anaerobes in CF pulmonary exacerbations and lung disease progression.

PMID: 29522532 [PubMed - in process]

Biological Activity of Trans-Membrane Anion Carriers.

Curr Med Chem. 2018 Mar 08;:

Authors: Tosolini M, Pengo P, Tecilla P

Abstract
Natural and synthetic anionophores promote the trans-membrane transport of anions such as chloride and bicarbonate. This process may alter the cellular homeostasis with possible effects on internal ions concentration and pH levels triggering several and diverse biological effects. In this article an overview of the recent results on the study of anion-transporters, mainly acting with a carrier-type mechanism, is given with emphasis on the structure/activity relationship and on their biological activity as antibiotic and anticancer agents and in the development of new drugs for treating conditions derived by dysregulation of natural anion channels.

PMID: 29521206 [PubMed - as supplied by publisher]

Clinical characterization and diagnosis of cystic fibrosis through exome sequencing in Chinese infants with Bartter-syndrome-like hypokalemia alkalosis.

Front Med. 2018 Mar 09;:

Authors: Qiu L, Yang F, He Y, Yuan H, Zhou J

Abstract
Cystic fibrosis (CF) is a fatal autosomal-recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. CF is characterized by recurrent pulmonary infection with obstructive pulmonary disease. CF is common in the Caucasian population but is rare in the Chinese population. The symptoms of early-stage CF are often untypical and may sometimes manifest as Bartter syndrome (BS)-like hypokalemic alkalosis. Therefore, the ability of doctors to differentiate CF from BS-like hypokalemic alkalosis in Chinese infants is a great challenge in the timely and accurate diagnosis of CF. In China, sporadic CF has not been diagnosed in children younger than three years of age to date. Three infants, who were initially admitted to our hospital over the period of June 2013 to September 2014 with BS-like hypokalemic alkalosis, were diagnosed with CF through exome sequencing and sweat chloride measurement. The compound heterozygous mutations of the CFTR gene were detected in two infants, and a homozygous missense mutation was found in one infant. Among the six identified mutations, two are novel point mutations (c.1526G > C and c.3062C > T) that are possibly pathogenic. The three infants are the youngest Chinese patients to have been diagnosed with sporadic CF at a very early stage. Follow-up examination showed that all of the cases remained symptom-free after early intervention, indicating the potential benefit of very early diagnosis and timely intervention in children with CF. Our results demonstrate the necessity of distinguishing CF from BS in Chinese infants with hypokalemic alkalosis and the significant diagnostic value of powerful exome sequencing for rare genetic diseases. Furthermore, our findings expand the CFTR mutation spectrum associated with CF.

PMID: 29520692 [PubMed - as supplied by publisher]

A 24-Year-Old Woman With Precipitous Respiratory Failure After Lung Transplantation.

Chest. 2018 Mar;153(3):e53-e56

Authors: Warren WA, Franco-Palacios D, King CS, Shlobin OA, Nathan SD, Katugaha SB, Mani H, Brown AW

Abstract
CASE PRESENTATION: A 24-year-old woman with ΔF508/Y1092X cystic fibrosis (CF) complicated by severe obstructive lung disease (FEV1 of 30% predicted) was admitted for IV antibiotics for planned sinus surgery resulting from severe chronic sinusitis causing frequent exacerbations and declining lung function. She had persistent airway infection with multidrug-resistant Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus, and growth of a fungus presumed to be an airway colonizer, identified as Stephanoascus ciferrii 1 year before presentation. Two days after surgery, she developed acute respiratory failure requiring mechanical ventilation. On day 4 of mechanical ventilation, venovenous-extracorporeal membrane oxygenation (VV-ECMO) was initiated for refractory respiratory failure. The following day, she was listed for bilateral lung transplant and was transplanted 4 days later. Following transplantation, she was decannulated from ECMO; however, over the next 12 hours, oxygenation deteriorated requiring reinstitution of VV-ECMO for presumed severe primary graft dysfunction. Despite treatment with broad spectrum antimicrobial coverage with piperacillin/tazobactam, ciprofloxacin, linezolid, micafungin, voriconazole, and ganciclovir, she failed to improve and developed complex bilateral pleural effusions.

PMID: 29519311 [PubMed - in process]

Antibacterial and Antifungal Activities of Poloxamer Micelles Containing Ceragenin CSA-131 on Ciliated Tissues.

Molecules. 2018 Mar 07;23(3):

Authors: Hashemi MM, Holden BS, Taylor MF, Wilson J, Coburn J, Hilton B, Nance T, Gubler S, Genberg C, Deng S, Savage PB

Abstract
Ceragenins were designed as non-peptide mimics of endogenous antimicrobial peptides, and they display broad-spectrum antibacterial and antifungal activities, including the ability to eradicate established biofilms. These features of ceragenins make them attractive potential therapeutics for persistent infections in the lung, including those associated with cystic fibrosis. A characteristic of an optimal therapeutic for use in the lungs and trachea is the exertion of potent antimicrobial activities without damaging the cilia that play a critical role in these tissues. In previous work, potent antimicrobial activities of ceragenin CSA-131 have been reported; however, we found in ex vivo studies that this ceragenin, at concentrations necessary to eradicate established biofilms, also causes loss of cilia function. By formulating CSA-131 in poloxamer micelles, cilia damage was eliminated and antimicrobial activity was unaffected. The ability of CSA-131, formulated with a poloxamer, to reduce the populations of fungal pathogens in tracheal and lung tissue was also observed in ex vivo studies. These findings suggest that CSA-131, formulated in micelles, may act as a potential therapeutic for polymicrobial and biofilm-related infections in the lung and trachea.

PMID: 29518893 [PubMed - in process]

Exome-wide somatic mutation characterization of small bowel adenocarcinoma.

PLoS Genet. 2018 Mar 09;14(3):e1007200

Authors: Hänninen UA, Katainen R, Tanskanen T, Plaketti RM, Laine R, Hamberg J, Ristimäki A, Pukkala E, Taipale M, Mecklin JP, Forsström LM, Pitkänen E, Palin K, Välimäki N, Mäkinen N, Aaltonen LA

Abstract
Small bowel adenocarcinoma (SBA) is an aggressive disease with limited treatment options. Despite previous studies, its molecular genetic background has remained somewhat elusive. To comprehensively characterize the mutational landscape of this tumor type, and to identify possible targets of treatment, we conducted the first large exome sequencing study on a population-based set of SBA samples from all three small bowel segments. Archival tissue from 106 primary tumors with appropriate clinical information were available for exome sequencing from a patient series consisting of a majority of confirmed SBA cases diagnosed in Finland between the years 2003-2011. Paired-end exome sequencing was performed using Illumina HiSeq 4000, and OncodriveFML was used to identify driver genes from the exome data. We also defined frequently affected cancer signalling pathways and performed the first extensive allelic imbalance (AI) analysis in SBA. Exome data analysis revealed significantly mutated genes previously linked to SBA (TP53, KRAS, APC, SMAD4, and BRAF), recently reported potential driver genes (SOX9, ATM, and ARID2), as well as novel candidate driver genes, such as ACVR2A, ACVR1B, BRCA2, and SMARCA4. We also identified clear mutation hotspot patterns in ERBB2 and BRAF. No BRAF V600E mutations were observed. Additionally, we present a comprehensive mutation signature analysis of SBA, highlighting established signatures 1A, 6, and 17, as well as U2 which is a previously unvalidated signature. Finally, comparison of the three small bowel segments revealed differences in tumor characteristics. This comprehensive work unveils the mutational landscape and most frequently affected genes and pathways in SBA, providing potential therapeutic targets, and novel and more thorough insights into the genetic background of this tumor type.

PMID: 29522538 [PubMed - as supplied by publisher]

Morphogenetic defects underlie Superior Coloboma, a newly identified closure disorder of the dorsal eye.

PLoS Genet. 2018 Mar 09;14(3):e1007246

Authors: Hocking JC, Famulski JK, Yoon KH, Widen SA, Bernstein CS, Koch S, Weiss O, FORGE Canada Consortium, Agarwala S, Inbal A, Lehmann OJ, Waskiewicz AJ

Abstract
The eye primordium arises as a lateral outgrowth of the forebrain, with a transient fissure on the inferior side of the optic cup providing an entry point for developing blood vessels. Incomplete closure of the inferior ocular fissure results in coloboma, a disease characterized by gaps in the inferior eye and recognized as a significant cause of pediatric blindness. Here, we identify eight patients with defects in tissues of the superior eye, a congenital disorder that we term superior coloboma. The embryonic origin of superior coloboma could not be explained by conventional models of eye development, leading us to reanalyze morphogenesis of the dorsal eye. Our studies revealed the presence of the superior ocular sulcus (SOS), a transient division of the dorsal eye conserved across fish, chick, and mouse. Exome sequencing of superior coloboma patients identified rare variants in a Bone Morphogenetic Protein (Bmp) receptor (BMPR1A) and T-box transcription factor (TBX2). Consistent with this, we find sulcus closure defects in zebrafish lacking Bmp signaling or Tbx2b. In addition, loss of dorsal ocular Bmp is rescued by concomitant suppression of the ventral-specific Hedgehog pathway, arguing that sulcus closure is dependent on dorsal-ventral eye patterning cues. The superior ocular sulcus acts as a conduit for blood vessels, with altered sulcus closure resulting in inappropriate connections between the hyaloid and superficial vascular systems. Together, our findings explain the existence of superior coloboma, a congenital ocular anomaly resulting from aberrant morphogenesis of a developmental structure.

PMID: 29522511 [PubMed - as supplied by publisher]

RSRC1 mutation affects intellect and behaviour through aberrant splicing and transcription, downregulating IGFBP3.

Brain. 2018 Mar 07;:

Authors: Perez Y, Menascu S, Cohen I, Kadir R, Basha O, Shorer Z, Romi H, Meiri G, Rabinski T, Ofir R, Yeger-Lotem E, Birk OS

Abstract
RSRC1, whose polymorphism is associated with altered brain function in schizophrenia, is a member of the serine and arginine rich-related protein family. Through homozygosity mapping and whole exome sequencing we show that RSRC1 mutation causes an autosomal recessive syndrome of intellectual disability, aberrant behaviour, hypotonia and mild facial dysmorphism with normal brain MRI. Further, we show that RSRC1 is ubiquitously expressed, and that the RSRC1 mutation triggers nonsense-mediated mRNA decay of the RSRC1 transcript in patients' fibroblasts. Short hairpin RNA (shRNA)-mediated lentiviral silencing and overexpression of RSRC1 in SH-SY5Y cells demonstrated that RSRC1 has a role in alternative splicing and transcription regulation. Transcriptome profiling of RSRC1-silenced cells unravelled specific differentially expressed genes previously associated with intellectual disability, hypotonia and schizophrenia, relevant to the disease phenotype. Protein-protein interaction network modelling suggested possible intermediate interactions by which RSRC1 affects gene-specific differential expression. Patient-derived induced pluripotent stem cells, differentiated into neural progenitor cells, showed expression dynamics similar to the RSRC1-silenced SH-SY5Y model. Notably, patient neural progenitor cells had 9.6-fold downregulated expression of IGFBP3, whose brain expression is affected by MECP2, aberrant in Rett syndrome. Interestingly, Igfbp3-null mice have behavioural impairment, abnormal synaptic function and monoaminergic neurotransmission, likely correlating with the disease phenotype.

PMID: 29522154 [PubMed - as supplied by publisher]