A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.

Evaluation of Pathway to Diagnosis of Pediatric Brain Tumors in Tamil Nadu, India.

PURPOSE: Delayed diagnosis and poor awareness are significant barriers to the early intervention of pediatric brain tumors. This multicenter observational study aimed to evaluate the baseline routes and time to diagnosis for pediatric brain tumors in Tamil Nadu (TN), with the goal of promoting early diagnosis and timely referrals in the future. METHODS: A standard proforma was used to retrospectively collect information on demographics, diagnosis, referral pathways, and symptoms of incident pediatric brain tumor cases between January 2018 and October 2020 across eight tertiary hospitals in TN. Dates of symptom onset, first presentation of health care, and diagnosis were used to calculate total diagnostic interval (TDI), patient interval (PI), and diagnostic interval (DI). RESULTS: A total of 144 cases (mean age, 6.64 years; range, 0-15.1 years) were included in the analysis. Among those, 94% (135/144) were from city/district areas, 40% (55/144) were self-referred, and 90% (129/144) had one to three health care professional visits before diagnosis. Median TDI, PI, and DI were 3.5 (IQR, 1-9.3), 0.6 (IQR, 0.1-4.6), and 0.6 (IQR, 0-3.3) weeks, respectively. Low-grade gliomas had the longest median TDI (6.6 weeks), followed by medulloblastomas (4.6 weeks) and high-grade gliomas (3.3 weeks). Average number of symptoms recorded was 1.7 at symptom onset and 1.9 at diagnosis. CONCLUSION: Although there are some similarities with data from the United Kingdom, many low-grade and optic pathway tumors were unaccounted for in our study. DIs were relatively short, which suggests that infrastructure may not be a problem in this cohort. Increased training and establishment of proper cancer registries, combined with proper referral pathways, could enhance early diagnosis for these children.

A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.

Association of Elevated Serum Aldosterone Concentrations in Pregnancy with Hypertension.

Emerging evidence indicates a previously unrecognized, clinically relevant spectrum of abnormal aldosterone secretion associated with hypertension severity. It is not known whether excess aldosterone secretion contributes to hypertension during pregnancy. We quantified aldosterone concentrations and angiotensin peptides in serum (using liquid chromatography with tandem mass spectrometry) in a cohort of 128 pregnant women recruited from a high-risk obstetrics clinic and followed prospectively for the development of gestational hypertension, pre-eclampsia, superimposed pre-eclampsia, chronic hypertension, or remaining normotensive. The cohort was grouped by quartile of aldosterone concentration in serum measured in the first trimester, and blood pressure, angiotensin peptides, and hypertension outcomes compared across the four quartiles. Blood pressures and body mass index were greatest in the top and bottom quartiles, with the top quartile having the highest blood pressure throughout pregnancy. Further stratification of the top quartile based on increasing (13 patients) or decreasing (19 patients) renin activity over gestation revealed that the latter group was characterized by the highest prevalence of chronic hypertension, use of anti-hypertensive agents, pre-term birth, and intrauterine growth restriction. Serum aldosterone concentrations greater than 704 pmol/L, the 75th percentile defined within the cohort, were evident across all categories of hypertension in pregnancy, including normotensive. These findings suggest that aldosterone excess may underlie the development of hypertension in pregnancy in a significant subpopulation of individuals.

Activation of the Renin-Angiotensin-Aldosterone System Is Attenuated in Hypertensive Compared with Normotensive Pregnancy.

Hypertension during pregnancy increases the risk of adverse maternal and fetal outcomes, but the mechanisms of pregnancy hypertension are not precisely understood. Elevated plasma renin activity and aldosterone concentrations play an important role in the normal physiologic adaptation to pregnancy. These effectors are reduced in patients with pregnancy hypertension, creating an opportunity to define the features of the renin-angiotensin-aldosterone system (RAAS) that are characteristic of this disorder. In the current study, we used a novel LC-MS/MS-based methodology to develop comprehensive profiles of RAAS peptides and effectors over gestation in a cohort of 74 pregnant women followed prospectively for the development of gestational hypertension and pre-eclampsia (HYP, 27 patients) versus those remaining normotensive (NT, 47 patients). In NT pregnancy, the plasma renin activity surrogate, (PRA-S, calculated from the sum of Angiotensin I + Angiotensin II) and aldosterone concentrations significantly increased from the first to the third trimester, accompanied by a modest increase in the concentrations of angiotensin peptide metabolites. In contrast, in HYP pregnancies, PRA-S and angiotensin peptides were largely unchanged over gestation, and third-trimester aldosterone concentrations were significantly lower compared with those in NT pregnancies. The results indicated that the predominant features of pregnancies that develop HYP are stalled or waning activation of the RAAS in the second half of pregnancy (accompanied by unchanging levels of angiotensin peptides) and the attenuated secretion of aldosterone.

Care-by-parent model as a tool for reduction of neonatal opioid withdrawal syndrome in neonates exposed to buprenorphine maintenance therapy in-utero.

Objective: To determine if a structured care-by-parent (CBP) protocol is associated with a reduction in diagnosis of treatment-requiring Neonatal Opioid Withdrawal Syndrome (NOWS).Study design: We performed a pilot retrospective, case control study of pregnant women enrolled in a comprehensive prenatal care program for opioid-dependent patients during which they received buprenorphine for Medication Assisted Treatment (MAT) for Opioid Use Disorder (OUD). Patients who participated in the CBP program actively roomed-in with their infants even after maternal hospital discharge while infants continued to be monitored for development of treatment-requiring NOWS. The primary outcome was the rate of treatment-requiring NOWS in the CBP grouping.Results: Thirty-two (32) cases that were enrolled in the CBP model were compared with 32 matched controls that were not enrolled in this model. There was a significant reduction in the rate of treatment-requiring NOWS among cases compared to the controls (OR = 0.10; p = .001). Neonates undergoing CBP had a decreased length of stay and lower Finnegan scores compared to those who did not undergo CBPConclusion: Among infants born to mothers with OUD in pregnancy, CBP significantly reduces the rate of treatment-requiring NOWS.

Mono-(2-Ethylhexyl) Phthalate Promotes Pro-Labor Gene Expression in the Human Placenta.

Women exposed to phthalates during pregnancy are at increased risk for delivering preterm, but the mechanism behind this relationship is unknown. Placental corticotropin-releasing hormone (CRH) and cyclooxygenase-2 (COX-2) are key mediators of parturition and are regulated by the non-canonical NF-kB (RelB/p52) signaling pathway. In this study, we demonstrate that one of the major phthalate metabolites, mono-(2-ethylhexyl)-phthalate (MEHP), increased CRH and COX-2 mRNA and protein abundance in a dose-dependent manner in primary cultures of cytotrophoblast. This was coupled with an increase in nuclear import of RelB/p52 and its association with the CRH and COX-2 promoters. Silencing of NF-kB inducing kinase, a central signaling component of the non-canonical NF-kB pathway, blocked MEHP-induced upregulation of CRH and COX-2. These results suggest a potential mechanism mediated by RelB/p52 by which phthalates could prematurely induce pro-labor gene activity and lead to preterm birth.

Laparoscopic management of an abdominal pregnancy.

Background. Ectopic pregnancy is one of the leading causes of significant maternal morbidity and mortality. Abdominal surgeries increase the risk of postoperative adhesions. We here present a case of omental ectopic pregnancy in a patient with a prior history of cesarean section. Case. A 20-year-old female presented with a two-day history of crampy lower abdominal pain. Patient was hemodynamically stable with a beta HCG of 1057 mI/mL. Transvaginal ultrasound did not show an intrauterine pregnancy but revealed an ill-defined mass in the midline pelvis extending to the right of the midline. Diagnostic laparoscopy revealed large clots in the pelvis with normal uterus and adnexa. Intra-abdominal survey revealed an omental adhesion close to the right adnexa with a hematoma. Partial omentectomy was completed and the portion of the omentum with the hematoma was sent to pathology for confirmation. Final pathology confirmed the presence of chorionic villi consistent with products of conception. Conclusion. Omental ectopic pregnancy is a rare diagnosis and often missed. We recommend careful intra-abdominal survey for an ectopic pregnancy in the presence of hemoperitoneum with normal uterus and adnexa. This can be safely achieved using laparoscopy in early gestational ages when the patient is hemodynamically stable.

Pallister-Killian syndrome.

PATIENT: Male, 0 FINAL DIAGNOSIS: Pallister-Killian syndrome Symptoms: Decidious tooth • flattened nasal bridge • frontal bossing • grooved palate • low-set ears • mid-facial hypoplasia • nuchal fold thickening • right inquinal testis • shortened upper extremities • undescended left intraabdominal testis • widely spaced nipples MEDICATION: - Clinical Procedure: - Specialty: Pediatrics and Neonatology. OBJECTIVE: Congenital defects/diseases. BACKGROUND: Pallister-Killian syndrome (PKS) is a rare, sporadic, polydysmorphic condition that often has highly distinctive features. The clinical features are highly variable, ranging from mild to severe intellectual disability and birth defects. We here report the first case of PKS diagnosed at our institution in a patient in the second trimester of pregnancy. CASE REPORT: A pregnant 43-year-old woman presented for genetic counseling secondary to advanced maternal age and an increased risk for Down syndrome. Ultrasound showed increased fetal nuchal fold thickness, short limbs, polyhydramnios, and a small stomach. The ultrasound evaluation was compromised due to the patient's body habitus. The patient subsequently underwent amniocentesis and the karyotype revealed the presence of an isochromosome in the short arm of chromosome 12 consistent with the diagnosis of Pallister-Killian syndrome. Postnatally, the infant showed frontal bossing, a flattened nasal bridge, mid-facial hypoplasia, low-set ears, a right upper deciduous tooth, grooved palate, nuchal fold thickening, widely spaced nipples, left ulnar polydactyly, simian creases, flexion contractures of the right middle finger, shortened upper extremities, undescended left intraabdominal testis, and right inguinal testis. CONCLUSIONS: The occurrence of PKS is sporadic in nature, but prenatal diagnosis is possible.