A Genomic Approach to Delineating the Occurrence of Scoliosis in Arthrogryposis Multiplex Congenita.

Arthrogryposis multiplex congenita (AMC) describes a group of conditions characterized by the presence of non-progressive congenital contractures in multiple body areas. Scoliosis, defined as a coronal plane spine curvature of ≥10 degrees as measured radiographically, has been reported to occur in approximately 20% of children with AMC. To identify genes that are associated with both scoliosis as a clinical outcome and AMC, we first queried the DECIPHER database for copy number variations (CNVs). Upon query, we identified only two patients with both AMC and scoliosis (AMC-SC). The first patient contained CNVs in three genes (FBN2, MGF10, and PITX1), while the second case had a CNV in ZC4H2. Looking into small variants, using a combination of Human Phenotype Ontogeny and literature searching, 908 genes linked with scoliosis and 444 genes linked with AMC were identified. From these lists, 227 genes were associated with AMC-SC. Ingenuity Pathway Analysis (IPA) was performed on the final gene list to gain insight into the functional interactions of genes and various categories. To summarize, this group of genes encompasses a diverse group of cellular functions including transcription regulation, transmembrane receptor, growth factor, and ion channels. These results provide a focal point for further research using genomics and animal models to facilitate the identification of prognostic factors and therapeutic targets for AMC.

The Clinical and Genotypic Spectrum of Scoliosis in Multiple Pterygium Syndrome: A Case Series on 12 Children.

BACKGROUND: Multiple pterygium syndrome (MPS) is a genetically heterogeneous rare form of arthrogryposis multiplex congenita characterized by joint contractures and webbing or pterygia, as well as distinctive facial features related to diminished fetal movement. It is divided into prenatally lethal (LMPS, MIM253290) and nonlethal (Escobar variant MPS, MIM 265000) types. Developmental spine deformities are common, may present early and progress rapidly, requiring regular fo llow-up and orthopedic management. METHODS: Retrospective chart review and prospective data collection were conducted at three hospital centers. Molecular diagnosis was confirmed with whole exome or whole genome sequencing. RESULTS: This case series describes the clinical features and scoliosis treatment on 12 patients from 11 unrelated families. A molecular diagnosis was confirmed in seven; two with MYH3 variants and five with CHRNG. Scoliosis was present in all but our youngest patient. The remaining 11 patients spanned the spectrum between mild (curve ≤ 25°) and malignant scoliosis (≥50° curve before 4 years of age); the two patients with MYH3 mutations presented with malignant scoliosis. Bracing and serial spine casting appear to be beneficial for a few years; non-fusion spinal instrumentation may be needed to modulate more severe curves during growth and spontaneous spine fusions may occur in those cases. CONCLUSIONS: Molecular diagnosis and careful monitoring of the spine is needed in children with MPS.

A comparative study of ChIP-seq sequencing library preparation methods.

BACKGROUND: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. RESULTS: In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. CONCLUSIONS: We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.

A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition.

Leukemia stem cells (LSCs) play a pivotal role in the resistance of chronic myeloid leukemia (CML) to tyrosine kinase inhibitors (TKIs) and its progression to blast crisis (BC), in part, through the alternative splicing of self-renewal and survival genes. To elucidate splice-isoform regulators of human BC LSC maintenance, we performed whole-transcriptome RNA sequencing, splice-isoform-specific quantitative RT-PCR (qRT-PCR), nanoproteomics, stromal coculture, and BC LSC xenotransplantation analyses. Cumulatively, these studies show that the alternative splicing of multiple prosurvival BCL2 family genes promotes malignant transformation of myeloid progenitors into BC LSCS that are quiescent in the marrow niche and that contribute to therapeutic resistance. Notably, sabutoclax, a pan-BCL2 inhibitor, renders marrow-niche-resident BC LSCs sensitive to TKIs at doses that spare normal progenitors. These findings underscore the importance of alternative BCL2 family splice-isoform expression in BC LSC maintenance and suggest that the combinatorial inhibition of prosurvival BCL2 family proteins and BCR-ABL may eliminate dormant LSCs and obviate resistance.

Development of a nonsurgical diagnostic tool for endometriosis based on the detection of endometrial leukocyte subsets and serum CA-125 levels.

OBJECTIVE: To determine whether the proportion of several leukocyte subsets is modulated in the endometrium of patients with endometriosis and, if yes, whether it can be used for diagnostic purposes. DESIGN: Case-control study. SETTING: Eight clinical institutions of the Montreal area. PATIENT(S): Women who underwent laparoscopy or laparotomy between 1997 and 2001, who had regular menstrual cycles and were not under hormone treatment for the previous 3 months were selected. This study included 368 women, 173 with surgically confirmed endometriosis and 195 controls with no surgical evidence of endometriosis. MAIN OUTCOME MEASURE(S): Cytometry analysis was used to measure the proportion of several leukocyte subsets among CD45(+) endometrial cells. RESULT(S): The proportion of CD3(+), CD16(+), CD3(-)HLADR(-), CD3(-)CD45RA(-), CD3(+)CD16(-), CD3(+)CD56(-), CD56(-)CD16(+), and CD16b(+) leukocytes was significantly altered in the endometrium of cases compared with controls. A multiple logistic regression model was adjusted with these endometrial leukocytes, serum CA-125 levels, risk factors, and confounders. The diagnostic performance of this predictive model was defined by a specificity of 95% and a sensitivity of 61%. Furthermore, the positive and negative predictive values were 91% and 75%, respectively. CONCLUSION(S): This predictive model represents a novel diagnostic tool to identify women with a high likelihood of suffering from endometriosis.

Blood leukocyte subsets are modulated in patients with endometriosis.

OBJECTIVE: To determine whether blood leukocyte populations could be modulated in endometriosis. DESIGN: Case-control study. SETTING: Eight clinical institutions of the Montreal area. PATIENT(S): Women with regular menstrual cycles who underwent laparoscopy or laparotomy between 1997 and 2001 and who were not under hormonal treatment for at least 3 months were selected. This study includes 175 cases and 131 controls. MAIN OUTCOME MEASURE(S): The proportion of blood leukocytes expressing markers for T, B lymphocytes, monocytes, or natural killer (NK) cells were compared by flow cytometric analysis between cases and controls. RESULT(S): Age and parity were identified as important confounders. Given that smoking, history of acute infection, and previous use of oral contraceptives strongly correlate with the level of some blood leukocyte populations, these parameters were taken into account in addition with age and parity when the level of blood leukocyte subsets were evaluated in cases and controls. Blood monocytes expressing CD14 and CD44 molecules were increased in patients with endometriosis. Alternatively, B lymphocytes were shown to be significantly decreased in cases compared with controls. CONCLUSION(S): Although these results suggest that endometriosis is associated with some systemic manifestations, the exact role of these modulations remains unclear.