Combined Gap-Polymerase Chain Reaction and Targeted Next-Generation Sequencing Improve α- and ß-Thalassemia Carrier Screening in Pregnant Women in Vietnam.

Vietnam has a high thalassemia burden. We collected blood samples from 5880 pregnant Vietnamese women during prenatal health checks to assess thalassemia carrier frequency using combined gap-polymerase chain reaction (gap-PCR) and targeted next-generation sequencing (NGS). Thalassemia carriers were identified with prevalence of 13.13% (772), including 7.82% (460) carriers of α-thalassemia (α-thal), 5.31% (312) carriers of ß-thalassemia (ß-thal), and 0.63% (37) concurrent α-/ß-thal carriers. Deletional mutations (368) accounted for 80.0% of α-thal carriers, of which, --SEA (Southeast Asian) (n = 254; 55.0%) was most prevalent, followed by the -α3.7 (rightward) (n = 66; 14.0%) and -α4.2 (leftward) (n = 45; 9.8%) deletions. Hb Westmead (HBA2: c.369C>G) (n = 53) and Hb Constant Spring (Hb CS or HBA2: c.427T>C) (in 28) are the two most common nondeletional α-globin variants, accounting for 11.5 and 6.0% of α-thal carriers. We detected 11 different ß-thal genotypes. Hb E (HBB: c.79G>A) (in 211) accounted for 67.6% of ß-thal carriers. The most common ß-thal genotypes were associated with mutations at codon 17 (A>T) (HBB: c.52A>T), codons 41/42 (-TTCT) (HBB: c.126_129delCTTT), and codon 71/72 (+A) (HBB: c.217_218insA) (prevalence 0.70%, 0.68%, and 0.2%, respectively). Based on mutation frequencies calculated in this study, estimates of 5021 babies in Vietnam are affected with clinically severe thalassemia annually. Our data suggest a higher thalassemia carrier frequency in Vietnam than previously reported. We established that combining NGS with gap-PCR creates an effective large-scale thalassemia screening method that can detect a broad range of mutations.

Profiling the HER3/PI3K pathway in breast tumors using proximity-directed assays identifies correlations between protein complexes and phosphoproteins.

BACKGROUND: The identification of patients for targeted antineoplastic therapies requires accurate measurement of therapeutic targets and associated signaling complexes. HER3 signaling through heterodimerization is an important growth-promoting mechanism in several tumor types and may be a principal resistance mechanism by which EGFR and HER2 expressing tumors elude targeted therapies. Current methods that can study these interactions are inadequate for formalin-fixed, paraffin-embedded (FFPE) tumor samples. METHODOLOGY AND PRINCIPAL FINDINGS: Herein, we describe a panel of proximity-directed assays capable of measuring protein-interactions and phosphorylation in FFPE samples in the HER3/PI3K/Akt pathway and examine the capability of these assays to inform on the functional state of the pathway. We used FFPE breast cancer cell line and tumor models for this study. In breast cancer cell lines we observe both ligand-dependent and independent activation of the pathway and strong correlations between measured activation of key analytes. When selected cell lines are treated with HER2 inhibitors, we not only observe the expected molecular effects based on mechanism of action knowledge, but also novel effects of HER2 inhibition on key targets in the HER receptor pathway. Significantly, in a xenograft model of delayed tumor fixation, HER3 phosphorylation is unstable, while alternate measures of pathway activation, such as formation of the HER3PI3K complex is preserved. Measurements in breast tumor samples showed correlations between HER3 phosphorylation and receptor interactions, obviating the need to use phosphorylation as a surrogate for HER3 activation. SIGNIFICANCE: This assay system is capable of quantitatively measuring therapeutically relevant responses and enables molecular profiling of receptor networks in both preclinical and tumor models.

ARC-111 inhibits hypoxia-mediated hypoxia-inducible factor-1alpha accumulation.

ARC-111, a small-molecule topoisomerase I inhibitor, is a potent cytotoxic drug against multiple human cancer cell lines under normoxic conditions (Li et al., Cancer Res 2003; 63:8400-8407). In this study, we explore the potential of ARC-111 as a hypoxia-inducible factor-1alpha inhibitor under hypoxic conditions. The transcription factor, hypoxia-inducible factor-1alpha, is an essential regulator of tumorigenesis and an attractive molecular target for cancer therapy. We demonstrate that ARC-111 specifically inhibits hypoxia-induced accumulation of hypoxia-inducible factor-1alpha, but not other short half-life proteins in multiple human cancer cell lines. ARC-111 inhibits hypoxia-inducible factor-1alpha protein synthesis specifically and does not inhibit protein synthesis globally. We demonstrate that inhibition of hypoxia-inducible factor-1alpha accumulation by ARC-111 is independent of proteasomal degradation. In addition, we demonstrate using topoisomerase I-resistant cell lines that topoisomerase I is required for ARC-111-mediated hypoxia-inducible factor-1alpha inhibition. Experiments performed with nocodazole indicate that ARC-111 inhibits hypoxia-inducible factor-1alpha accumulation in a cell-cycle-independent manner. Analysis of AKT and mammalian target of rapamycin phosphorylation reveals that ARC-111 does not exhibit inhibitory effect on the phosphatidylinositol-3-kinase AKT mammalian target of rapamycin signaling pathway. It has been previously shown that topotecan, a topoisomerase I inhibitor, can also modulate hypoxia-induced hypoxia-inducible factor-1alpha accumulation (Rapisarda et al., Cancer Res 2003; 64:1475-1482). In addition to inhibiting hypoxia-induced accumulation of hypoxia-inducible factor-1alpha, ARC-111 exhibits antiproliferative effects against multiple human cancer cell lines. We demonstrate that topoisomerase I is required for the antiproliferative effects of ARC-111. Antiproliferative effects of ARC-111, however, are oxygen-independent, which is distinguishable from inhibition of hypoxia-inducible factor-1alpha accumulation by ARC-111, which is only observed under hypoxia. The results indicate that inhibiting hypoxia-inducible factor-1alpha accumulation and exhibiting antiproliferation of ARC-111 are through distinct mechanisms of action, which reinforce the potential anticancer effect of ARC-111 on hypoxic tumors.

Biochemical and biophysical properties of purified phospholipid vesicles containing bovine heart cytochrome c oxidase.

Liposomes containing bovine heart cytochrome c oxidase (COV) prepared by the cholate dialysis technique were purified from those devoid of the enzyme using discontinuous sucrose density ultra centrifugation to eliminate interference in proton-pumping assays. This technique was also used to purify liposomes containing cytochrome c oxidase depleted in subunit III (COV-III), a COX enzyme preparation with altered subunit structure, to assess if the technique could be applied to COX enzymes in which structural and functional changes have occurred. Upon discontinuous sucrose density ultra gradient ultracentrifugation, either COV or COV-III were separated into two bands. Liposomes devoid of enzyme sedimented into the 12% sucrose layer, whereas enzyme-containing liposomes (pCOV or pCOV-III) were found in the 13% sucrose layer. The yield of both pCOV or pCOV-III was greater than 60% (based on heme aa(3) content), suggesting a similar distribution of cytochrome c oxidase (COX) and subunit III-depleted enzyme (COX-III) in the purified liposomes. The number of COX or COX-III molecules per phospholipid vesicle in purified fractions was estimated to be two. Removal of subunit III (M(r)=29,918) from COX resulted in a 30% decrease in electron transfer activity (either in COV-III or pCOV-III) when compared with COV and pCOV, respectively. Both pCOV and pCOV-III exhibited low endogenous proton permeability, as assessed by possessing high respiratory control ratios (14 and greater) and by having similar valinomycin concentration dependencies for stimulation of electron transfer activity in the presence of saturating amounts of CCCP. COV-III and pCOV-III exhibited a 39-44% decrease in proton-pumping activity when compared with COV and pCOV. These results showed that the separation of COX containing liposomes from those lacking enzyme by sucrose density gradient centrifugation can be used to characterize the biophysical properties of these liposomes.