Integrative analyses of RNA-seq and ChIP-seq Reveal MITF as a Target Gene of TFPI-2 in MDA231 Cells.

Breast cancer is the most prevalent cancer in female patients worldwide. Tissue factor pathway inhibitor 2 (TFPI-2) is identified as an important tumor suppressor in various cancers. Recent studies have shown that TFPI-2 translocates into the nucleus, where it modulates the transcription of the matrix metalloproteinase-2 (MMP-2) gene. However, its biological role and molecular mechanisms in the progression of breast cancer remain unclear. In this study, we identified 5125 differentially expressed genes (DEGs) from RNA sequencing (RNA-seq) in TFPI-2-overexpressing MDA231 cells compared with control cells. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis shown that cell cycle, cell differentiation, proteoglycans in cancer, and pathways associated with cancer were highly enriched in downregulated DEGs. Integration of the RNA-seq and ChIP-sequencing (ChIP-seq) data identified 73 genes directly controlled by TFPI-2 in MDA231 cells. Among them, melanocyte inducing transcription factor (MITF) gene expression was repressed by TFPI-2, which was further verified by a luciferase reporter assay and ChIP-quantitative PCR. Our study provides evidence of a novel role of TFPI-2 in human breast cancer involving targeting of the MITF.

Hb New York, preliminary results concerning the hematologic characteristics and the effects on thalassemia.

BACKGROUND: The hematological phenotype and genotype analysis of hemoglobin New York (Hb New York) combined with α or ß thalassemia has been rarely reported, and whether there is any effect of Hb New York on thalassemia has not been well explored. METHODS AND RESULTS: In this study, peripheral blood samples from 346 Hb New York carriers were collected for blood cell parameter analysis. When comparing Hb New York heterozygotes, Hb New York combined with α0 thalassemia or α+ thalassemia, we found that the differences in hemoglobin (HGB), MCV and MCH values were statistically significant (P < 0.05). The HGB, MCV and MCH values of α thalassemia patients were not different from Hb New York combined with α thalassemia group (P > 0.05). When Hb New York heterozygotes were compared to Hb New York combined with ß0 thalassemia or ß+ thalassemia, the differences in MCV and MCH values were statistically significant (P < 0.05). However, the differences in MCV and MCH values were not statistically significant between Hb New York combined with ß thalassemia and ß thalassemia (P > 0.05). CONCLUSIONS: Our study shows that the hematological characteristics of Hb New York combined with thalassemia are similar to the corresponding thalassemia, and Hb New York does not aggravate the clinical manifestations of thalassemia.

Phenanthroline-based microporous organic materials for removal of Cu(II) from aqueous solution and reutilization of spent adsorbent as catalysts.

Microporous organic polymers (MOPs) possessing large specific surface area with high stability are suitable adsorbent to remove contaminants from water, such as organic pollutant and heavy metal contaminants. Herein, a phenanthroline-based microporous organic polymer (Phen-MOP) has been synthesized through the coupling between benzene and 1,10-phenanthroline. The adsorption kinetics and thermodynamics were investigated. This Phen-MOP exhibited good adsorption efficiency for removal of Cu(II) from water with high structural stability and reusability. The maximum removal efficiency could reach to 98.47% at a Cu(II) concentration of 20 mg/L, pH = 7, 25 °C. It was found by investigating the adsorption isotherms that the maximum adsorption capacity Qm was 128.53 mg/g. Interestingly, after the adsorption of Cu(II), the resulting Phen-MOP-Cu can serve as an efficient heterogeneous catalyst for the Ullmann-type reaction. The structure and composition of the Phen-MOP-Cu were characterized by Fourier transform infrared (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), Brunauer-Emmett-Teller (BET), scanning electron microscope (SEM), energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS). The results indicated that this catalyst possessed immense specific surface area, large pore volume and high stability. The catalyst was easily recyclable and did not significantly lose catalytic activity after being reused six times.

[Genetic diagnosis of a case of Smith-Magenis syndrome due to a rare small-scale deletion].

OBJECTIVE: To report on a case of Smith-Magenis syndrome (SMS) due to a rare small-scale deletion. METHODS: Muscle samples from the the third fetus was collected after the in Medical history and clinical data of the patient were collected. The child and his parents were subjected to chromosome karyotyping analysis, multiplex ligation-dependent probe amplification (MLPA) and copy number variation sequencing (CNV-seq). RESULTS: The child was found to have a normal karyotype. MLPA and CNV-seq detection showed that he has harbored a 1.22 Mb deletion and a 0.3 Mb duplication in the 17p11.2 region. Neither of his parents was found to have similar deletion or duplication. CONCLUSION: The child was diagnosed with SMS due to a rare 1.22 Mb deletion in the 17p11.2 region, which is among the smallest deletions associated with this syndrome.

Compound heterozygosity for Southeast Asian hereditary persistence of fetal hemoglobin and ß0-thalassemia results in thalassemia intermedia: Pedigree analysis and genetic research in a family from South China. A case report.

RATIONALE: Compound heterozygotes for deletional ß-thalassemia can be difficult to diagnose due to its diverse clinical presentations and no routine screenings. This can lead to disease progression and delay in treatment. PATIENT CONCERNS: We reported pedigree analysis and genetic research in a family with rare ß-thalassemia. DIAGNOSIS: Pedigree analysis and genetic research demonstrated that the patient was a compound heterozygote for ß-thalassemia CD17/Southeast Asian hereditary persistence of fetal hemoglobin deletion, inherited from the parents. Magnetic resonance imaging T2* examination revealed severe iron deposition in the liver. Echocardiography revealed endocardial cushion defect. INTERVENTIONS: The patient was treated with Deferasirox after receiving the final molecular genetic diagnosis. The initial once-daily dose of Deferasirox was 20 mg/kg/d. OUTCOMES: The patient discontinued the medication three months after the first visit. Two years later, the patient visited the Department of Hepatobiliary and Pancreatic Diseases. He was recommended to undergo splenectomy after surgical repair of the congenital heart disease. However, the patient refused surgical treatment because of the economic burden. LESSONS: We report that fetal hemoglobin is a sensitive indicator for screening large deletions of the ß-globin gene, which can be effectively confirmed by the multiplex ligation-dependent probe amplification assay. In non-transfusion-dependent thalassemia patients, iron status assessment should be regularly performed, and iron chelation treatment should be initiated early. This case will provide insights for the diagnosis of rare genotypes of ß-thalassemia and has important implications for genetic counseling.

Genotype analysis of 55,281 cases of thalassemia in northern Guangxi.

OBJECTIVE: To understand the genotype and distribution of thalassemia in northern Guangxi. METHODS: The study subjects were 55,281 individuals who came to the Affiliated Hospital of Guilin Medical University for genetic diagnosis of thalassemia from January 2012 to August 2023. All of their household registration was in the precincts of Guibei District and its affiliated counties. Red blood cell parameters and hemoglobin analysis were used for thalassemia screening. Gap-PCR, PCR-reverse dot blot hybridization (PCR-RDB), and multicolor melting curve analysis (MMCA) were used to identify common thalassemia genes. Multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, and third-generation single-molecule real-time (SMRT) sequencing were employed to identify rare thalassemia genes. RESULTS: Among the 55,281 samples, 16,442 (29.74%) were diagnosed with thalassemia. The detection rates of α, ß, and α combined ß-thalassemia were 18.57%, 9.99% and 1.18%, respectively. Among ethnical groups, allele mutation frequency of thalassemia was the highest in Zhuang (44.97%), followed by Yao (40.11%), Dong (31.33%), Han (29.85%), Miao (24.31%), and Hui (20.6%). A total of 11,659 alleles (21.09%) of 8 types of α-thalassemia were identified in 55,281 samples, primarily --SEA (53.9%), followed by -α3.7 (21.3%), including rare alleles: --THAI (0.45%) and HKαα (0.38%). A total of 6367 (11.52%) and 14 types of ß-thalassemia alleles were identified, mainly CD41-42 (50.12%), followed by CD17 (22.22%), including rare alleles: ßCD37 (0.16%) and Gγ+ (Aγδß)0/ßN (0.05%). A total of 31 genotypes were detected in 10,264 cases of α-thalassemia, and the main types were --SEA/αα (53.23%), -α3.7/αα (19.15%), and -α4.2/αα (7.21%). A total of 34 genotypes were detected in 5525 cases of ß-thalassemia, and the main types were ßCD41-42/ßN (50.53%), ßCD17/ßN (21.77%), and ßIVS-II-654/ßN (12.16%). A total of 78 gene types were detected in 653 cases of α- and ß-thalassemia, and the main types were --SEA/αα, ßCD41-42/ßN (18.68%) and -α3.7/αα, ßCD41-42/ßN (13.02%). There were 580 cases (5.65%) of HbH disease (α0/α+), and 4 cases of Hemoglobin Bart's Hydrops Foetus syndrome (--SEA/--SEA). In addition, there were 92 cases (1.67%) of intermedia or severe types of ß-thalassemia (ß0/ß0, ß0/ß+, ß+/ß+), including 23 cases of combined α-thalassemia. Among the samples screened negative for thalassemia, 3.7% of them were found to carry thalassemia genes, and 91.35% of the genotypes were αWSα/αα, -α3.7/αα, and -α4.2/αα. In addition, 40.26% of αWSα/αα, 22.89% of -α3.7/αα, and 18.51% of -α4.2/αα had no hematological phenotype. CONCLUSION: The population in northern Guangxi exhibited rich ethnic diversity, with high allelic carrying rates among the Zhuang, Yao and Dong ethnic groups. Thalassemia gene mutations are diverse, encompassing a variety of gene types, with α thalassemia predominating, notably the --SEA/αα gene type. The prevalence of intermedia or severe types of thalassemia is not low, but there are still some carriers of thalassemia in people who are initially tested negative.

The timely diagnosis of 49, XXXXY with the combined detection of MLPA, karyotype, and QF-PCR in a newborn with multiple congenital malformations: a case report.

Background: 49, XXXXY is a rare sex chromosomal aneuploidy syndrome. The patients usually are diagnosed several months or years after birth. Herein a neonate with respiratory distress and multiple malformations was diagnosed with 49, XXXXY syndrome by an economical method of multiplex ligation-dependent probe amplification (MLPA) followed karyotype analysis. Case Description: An infant was born via spontaneous vaginal delivery at 41+3 weeks' gestation and hospitalized due to neonatal asphyxia. He was the first child to a 24-year-old gravida1, para1 (G1P1) mother. The newborn was characterized low birth weight (2.4 Kg, below the 3rd percentile), and an Apgar score of 6 at 1 minute, 8 at 5 minutes, and 9 at 10 minutes. The physical examinations of the patient revealed ocular hypertelorism, epicanthal folds, low nasal bridge, high-arched palate, cleft palate, micrognathia, low-set ears, microcephaly, hypotonia, and micropenis. Echocardiography revealed atrial septal defects (ASD). The brainstem auditory evoked potential (BAEP) reflected auditory function impairment. Genetic testing methods, including MLPA, karyotyping, and quantitative fluorescent polymerase chain reaction (QF-PCR), were performed for definitive diagnosis, which confirmed 49, XXXXY syndrome. Conclusions: The presentation of the 49, XXXXY newborn was atypical, they may only include low birth weight, multiple malformations and a characteristic facial appearance which were consistent with the characteristics of autosomal and sex chromosome aneuploidies. At this time, the economical and rapid method of MLPA to screen the number of chromosome, and then choose the appropriate means to make the final diagnosis and improve the quality of life of patients with timely therapy.

Accurate genotype diagnosis of Hong Kongαα thalassemia based on third-generation sequencing.

Background: The Hong Kongαα (HKαα) allele is a complex structural rearrangement of the α-globin gene containing -α3.7 and αααanti 4.2 crossover junctions. Clinically, individuals carrying the HKαα allele are often misdiagnosed or missed using conventional thalassemia gene detection technology. This study aims to identify and validate different HKαα thalassemia subtypes using third-generation sequencing (TGS) technology. Methods: Between January 2015 and June 2021, 32 patients suspected of having HKαα thalassemia were included in this study. Genomic DNA was extracted, and gap-polymerase chain reaction (PCR), two-round nested PCR, multiplex ligation-dependent probe amplification (MLPA), and TGS were used for thalassemia gene detection. Results: The results of HKαα/αα and HKαα/-α3.7 were similar to -α3.7/αα using the gap-PCR method. Two-round nested PCR could be used to verify the HKαα gene, but could not distinguish the subtypes of HKαα thalassemia. The MLPA assay was used to detect the change in the copy number of the α-globin gene, but it could not determine whether -α3.7 and αααanti 4.2 were in cis or in trans. Long-read TGS technology could accurately detect the HKαα allele and distinguish the genotypes of HKαα/αα, HKαα/-α3.7, HKαα/-α4.2, and HKαα/--SEA without pedigree analysis. The contiguous sequence of the HKαα allele was detected using the TGS approach. This study also demonstrated that individuals with HKαα/αα and ßN/ßN genotypes tended to have normal hematological phenotypes. Conclusions: Long-read TGS is a reliable and efficient approach for accurate detection of HKαα thalassemia, which can be widely used in clinical practice. Accurate molecular diagnosis of HKαα thalassemia will benefit clinical genetic counseling and prenatal diagnosis.