Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types

Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.

The human Y and inactive X chromosomes similarly modulate autosomal gene expression

Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.

The human Y and inactive X chromosomes similarly modulate autosomal gene expression

Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.

Male vitamin D status and male factor infertility

OBJECTIVE

To determine the association between vitamin D levels in the male partner and fertility outcomes in couples with mild male factor infertility.

DESIGN

Secondary analysis of a randomized, controlled trial.

SETTING

Nine fertility centers in the United States.

PATIENT(S)

Men (n = 154) with sperm concentration between 5 and 15 million/mL, motility ≤40%, or normal morphology ≤4% were eligible. Female partners were ovulatory, ≤40 years old, and had documented tubal patency.

INTERVENTION(S)

Men provided semen and blood at baseline for semen analysis and 25-hydroxyvitamin D (25(OH)D) levels. They were randomly assigned to receive a vitamin formulation including vitamin D 2,000 IU daily or placebo for up to 6 months. Couples attempted to conceive naturally during the first 3 months and with clomiphene citrate with intrauterine insemination of the female partner in months 4 through 6.

MAIN OUTCOME MEASURE(S)

Primary: sperm concentration, motility, morphology, and DNA fragmentation at baseline. Secondary: cumulative pregnancy, miscarriage, and live birth rates.

RESULT(S)

Semen parameters and sperm DNA fragmentation were not statistically significantly different between men with vitamin D deficiency and men with 25(OH)D levels ≥20 ng/mL. In addition, clinical pregnancy and live birth rates were similar. Male 25(OH)D level <20 ng/mL was associated with a higher rate of pregnancy loss (adjusted odds ratio 9.0; 95% confidence interval 1.3 to 61.3).

CONCLUSION(S)

Vitamin D deficiency in the male partner did not significantly impact semen parameters or treatment outcomes. Further study is warranted to better characterize the rate of miscarriage in couples with male vitamin D deficiency.

Circle of Willis anomalies in Turner syndrome: Absent A1 segment of the anterior cerebral artery

PURPOSE

Turner syndrome (TS) is the most common sex chromosome disorder in women and is associated with a higher than expected death rate secondary to cerebrovascular disease, including stroke. This study evaluates the cerebral vascular anatomy of individuals with TS.

METHODS

Twenty-one women with TS had brain magnetic resonance angiography (MRA). These MRAs were evaluated in a blinded manner with a control group of 25 men and 25 women who had MRA imaging for multiple indications including migraine headaches, psychiatric disorders, and seizures.

RESULTS

Twenty-nine percent of women with TS were missing an A1 segment of the anterior cerebral artery (ACA) compared to 0% in the control group (p < .001). There were no other significant differences in the circle of Willis (COW) in women with TS compared with the control group. A complete COW was found in 3 of 21 (14%) of women with TS and 12 of 47 (26%) controls (p = .36).

CONCLUSION

Women with TS have a significantly different intracranial vascular anatomy, specifically the absence of the A1 segment of the ACA when compared to male and female controls. More research in brain imaging in women with TS and stroke and other cerebrovascular diseases is needed to determine the clinical significance of this anomaly.

Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening

CONTEXT

Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities.

OBJECTIVES

This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS.

DESIGN, SETTING, PATIENTS

Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health. Female control subjects (n = 37) and male subjects (n = 27) also underwent WES. Copy number variation was evaluated using EXCAVATOR2 and B allele frequency was calculated from informative single nucleotide polymorphisms. Simulated WES data were generated for detection of low-level mosaicism and complex structural chromosome abnormalities.

RESULTS

We detected monosomy for chromosome X in all 27 TS samples, including 1 mosaic for 45,X/46,XX and another with previously unreported material on chromosome Y. Sensitivity and specificity were both 100% for the diagnosis of TS with no false-positive or false-negative results. Using simulated WES data, we detected isochromosome Xq and low-level mosaicism as low as 5%.

CONCLUSION

We present an accurate method of diagnosing TS using WES, including cases with low-level mosaicism, isochromosome Xq, and cryptic Y-chromosome material. Given the potential use of next-generation sequencing for NBS in many different diseases and syndromes, we propose WES can be used as a screening test for TS in newborns.

Is FMR1 CGG repeat length a predictor of in vitro fertilization stimulation response or outcome?

OBJECTIVE

To study a broad range of FMR1 CGG repeat lengths and assisted reproduction technology (ART) outcomes.

DESIGN

Retrospective cohort study.

SETTING

Private ART practice.

PATIENT(S)

Fresh autologous ART stimulation cycles.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Oocyte yield, live birth.

RESULT(S)

We screened 14,088 fresh autologous ART cycles from 2012 to 2015, of which 4,690 cycles in 3,290 patients met the inclusion criteria. The FMR1 repeat length was statistically significantly but weakly associated with oocyte yield and other markers of ovarian response. The receiver operating characteristic curve analysis suggested extremely limited predictive ability. Moreover, the FMR1 repeat length was not statistically significantly associated with outcomes in multivariable models, including other markers of ovarian reserve. The FMR1 repeat length was not associated with embryo quality or live birth. Only patient age had a strong ability to predict live birth.

CONCLUSION(S)

The FMR1 repeat length is associated with ART response, but only weakly. It provides no incremental predictive ability beyond the conventionally used predictors, including patient age, antimüllerian hormone concentration, antral follicle count, and follicle-stimulating hormone level. These data suggest a possible role of the FMR1 repeat length within the normal range in ovarian response but demonstrate no clinically relevant indication for testing FMR1 as a predictor of ART outcomes.

Pregnancy in autosomal recessive polycystic kidney disease

PURPOSE

Autosomal recessive polycystic kidney disease (ARPKD) is the most common childhood-onset ciliopathy. As treatments improve, more women are reaching reproductive age, but little is known about ARPKD and pregnancy.

METHODS

In our ongoing study on ARPKD and other ciliopathies, 12 females over 18 years of age were identified and systematically evaluated. Six had children; four carried pregnancies and delivered, one used assisted reproductive technology and had a surrogate carry the pregnancy, and one adopted. We report the outcomes of four pregnancies with live birth deliveries and two women who chose alternate family building options.

RESULTS

Patient one was diagnosed at 6 months, and at age 21 had a pregnancy complicated by transient worsening of renal function (creatinine increase from 1.15 to 1.78 mg/dL). Patient two was diagnosed with ARPKD at age seven and had an uncomplicated pregnancy at age 23. Patient three was diagnosed incidentally with ARPKD at age 23, 3 months after completion of an uncomplicated pregnancy. Patient four who had an uncomplicated pregnancy at age 33 was diagnosed with ARPKD at age 46.

CONCLUSIONS

Women with ARPKD face reproductive decisions largely bereft of information about the pregnancies of other ARPKD patients. We report four cases of pregnancy and ARPKD to expand current knowledge and encourage further research.

Positive outcome after looped peripherally inserted central catheter malposition. A case study

Tip malposition of peripherally inserted central catheters (PICCs) is a frequently encountered problem. Invasive and noninvasive techniques for resolution of malpositions described in the literature are reviewed. A positive outcome using non-invasive techniques after a looped malposition in the axillary vein is discussed.

Assessing HCFA's Health Care Quality Improvement Program

BACKGROUND

In 1992 the Health Care Financing Administration introduced the Health Care Quality Improvement Program (HCQIP), through which quality improvement projects are conducted in partnership with quality improvement organizations (QIOs), hospitals, health plans, or physicians. An evaluation of HCQIP began in May 1996 in response to the QIOs' request for an independent assessment of their activities.

METHODOLOGY

The methodology and objectives of the evaluation were determined by an independent panel. The QIOs' full cohort of 970 HQIP projects could not be reviewed in the 10-month time frame available, but two topics were chosen: the management of warfarin or aspirin in patients with atrial fibrillation and the management of community-acquired pneumonia.

FINDINGS

Analyses were limited to the 49 of the 68 projects that had progressed to the "improvement plan implemented" stage. However, only 39 of these 49 projects had information on outcomes, organization changes, and/or changes in process of care--and only 20 of the 49 had moved beyond the "improvement plan implemented" phase. Feedback of data led hospitals collaborating on improvement projects to revise or create processes of care.

DISCUSSION

Although the assessment is the most comprehensive of its type to date, it should be viewed as a pilot study of some of the methods that could be incorporated in a more extensive and rigorous future evaluation of the impact of the HCQIP projects. Specific recommendations include random sampling of HCQIP projects across all clinical areas, conducting both prospective and retrospective assessments, developing uniform process and outcome program impact measures, and developing sustainable, ongoing automated data abstraction and analysis systems.

Designing and using measures of quality based on physician office records

This article presents our principles for developing performance measures to assess the quality of ambulatory care. The measures were developed as part of a project for developing and evaluating methods to promote ambulatory care quality (DEMPAQ). We describe our design for the performance measures, present examples of the DEMPAQ review criteria, and show the formats we used to feed back information to physicians. We conclude by presenting the results of our appraisal of the performance measures showing how evaluation can aid in the interpretation of measurement findings.

Body image measurement in overweight females

This article details two studies of the reliability and validity of three instruments to measure body image and suggestions for their use in interventions for weight control programs. Weight control programs often fail because there is no attempt to modify clients' negative body images; hence clients may regain weight to match incorrect images. Short, easily administered instruments, such as the Nash Body Image Scale, the Body Image Photo Technique, and the Body Shape Questionnaire used in these studies, are needed to evaluate clients' progress in weight control programs. Subjects were 120 women who were either satisfied or dissatisfied with their body image and weight. All subjects completed body image measures at the outset of the study and 43 subjects completed measures again to determine trait stability of body image at 1 year. Cronbach's alpha estimates provided evidence of reliability, with internal consistency coefficients ranging from .83 to .96. Validity of the measures was supported by significant correlations with scores on the Physical subscale of the Tennessee Self-Concept Scale (r = .60 to .63) as well as by significant differences on the three measures between normal-weight and overweight groups (Nash: F = 28.03, p = .001; Photo: F = 11.58, p = .001). Body image was found to be stable over the 1-year period on the Nash Body Image Scale and the Body Image Photo Technique. These instruments can provide valuable information and potential intervention content for practitioners and researchers alike. The three body image instruments discussed were found to have sufficient reliability and validity to warrant their use in practice and research.

A microELISA Raji cell assay to detect immune complexes

The Raji cell assay to detect immune complexes has been modified to a microtiter ELISA system. Raji cells were fixed to microplate wells, then reacted with serum samples or aggregated human IgG. Horseradish peroxidase-conjugated anti-human IgG was used to detect bound complexes. There was a linear relationship between aggregated IgG added and optical density reading, with less than 2 micrograms/ml of aggregated IgG readily detected. When applied to human serum this technique gave results comparable to those obtained with the standard Raji cell assay. The Raji micro-ELISA is simpler to perform than the standard assay, is equally reliable, and avoids the hazards of radioactivity.