Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC. VIDEO ABSTRACT.

Clinical characteristics of membranous nephropathy after allogeneic hematopoietic stem cell transplantation: A real-world multicenter study.

Membranous nephropathy (MN) is a rare complication that can occur after allogeneic hematopoietic stem cell transplantation (allo-HSCT). MN patients may develop nephrotic syndrome or even kidney failure, which greatly affects their quality of life and prognosis. However, current knowledge regarding MN after allo-HSCT is limited. Thus, a multicenter nested case‒control study was conducted. Patients who had been diagnosed with MN after allo-HSCT were retrospectively identified at 8 HSCT centers. A total of 51 patients with MN after allo-HSCT were included. The median age of MN patients after allo-HSCT was 38 years, and the median duration from HSCT to MN was 18 months. The use of HLA-matched donors (P = 0.0102) and peripheral blood as the graft source (P = 0.0060) were identified as independent predisposing risk factors for the onset of MN after allo-HSCT. Compared to those in the control group, the incidence of extensive chronic graft-versus-host disease was greater in the MN patients (P = 0.0002). A total of 31 patients developed nephrotic syndrome. Patients receiving combination treatments of corticosteroids and immunosuppressants appeared to have better outcomes. In conclusion, MN is a rare but occasionally severe complication following HSCT and may require active treatment.

High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population.

INTRODUCTION: The α-globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0 -thalassemia (α0 -thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α-thal diagnosis. METHODS: In this study, we used the single-molecule real-time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next-generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and ß thalassemia were utilized. RESULTS: According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α-thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two "pure" heterozygotes: one was compound heterozygote with anti-3.7 triplication, and the other was homozygote. CONCLUSION: Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one-step properties.

Application of real-time PCR-based multicolor melting curve with automatic analysis system in pregestational and prenatal thalassemia diagnoses.

BACKGROUND: To evaluate the value of the real-time PCR-based multicolor melting curve analysis (MMCA) with an automatic analysis system used in a mass thalassemia screening and prenatal diagnosis program. METHODS: A total of 18,912 peripheral blood samples from 9456 couples and 1150 prenatal samples were detected by MMCA assay. All prenatal samples were also tested by a conventional method. Samples with unknown melting peaks, unusual peak height ratios between a wild allele and a mutant allele, or a discordant phenotype-genotype match were further studied by using multiplex ligation-dependent probe amplification (MLPA) or Sanger sequencing. All MMCA results were automatically analyzed and manually checked. The consistency between MMCA assay and conventional methods among prenatal samples was investigated. RESULTS: Except for initiation codon (T > G) (HBB:c.2T > G), all genotypes of thalassemia inside the scope of conventional methods were detected by MMCA assay. Additionally, 27 carriers with 10 rare HBB variants, 13 with α fusion gene, 1 with a rare deletion in α globin gene, and 1 with rare HBA variant were detected by using MMCA assay. CONCLUSION: MMCA can be an alternative approach used in routine thalassemia carrier screening and prenatal diagnosis for its high throughput, sufficient stability, low cost, and easy operation.

Impact of a novel prognostic model on allogeneic hematopoietic stem cell transplantation outcomes in patients with CMML.

Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic stem cell malignancy, and allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the only curable treatment. The outcomes after transplant are influenced by both disease characteristics and patient comorbidities. To develop a novel prognostic model to predict the post-transplant survival of CMML patients, we identified risk factors by applying univariable and multivariable Cox proportional hazards regression to a derivation cohort. In multivariable analysis, advanced age (hazard ratio [HR] 3.583), leukocyte count (HR 3.499), anemia (HR 3.439), bone marrow blast cell count (HR 2.095), and no chronic graft versus host disease (cGVHD; HR 4.799) were independently associated with worse survival. A novel prognostic model termed ABLAG (Age, Blast, Leukocyte, Anemia, cGVHD) was developed and the points were assigned according to the regression equation. The patients were categorized into low risk (0-1), intermediate risk (2, 3), and high risk (4-6) three groups and the 3-year overall survival (OS) were 93.3% (95%CI, 61%-99%), 78.9% (95%CI, 60%-90%), and 51.6% (95%CI, 32%-68%; p < .001), respectively. In internal and external validation cohort, the area under the receiver operating characteristic (ROC) curves of the ABLAG model were 0.829 (95% CI, 0.776-0.902) and 0.749 (95% CI, 0.684-0.854). Compared with existing models designed for the nontransplant setting, calibration plots, and decision curve analysis showed that the ABLAG model revealed a high consistency between predicted and observed outcomes and patients could benefit from this model. In conclusion, combining disease and patient characteristic, the ABLAG model provides better survival stratification for CMML patients receiving allo-HSCT.

Hb Lepore-Hong Kong: First Report of a Novel δ/ß-Globin Gene Fusion in a Chinese Family.

We describe a new δ/ß fusion gene causing ß-thalassemia (ß-thal) trait and its formation mechanism. The proband was a 39-year-old woman who presented with persistent microcytic microcytosis without iron deficiency. Molecular diagnoses revealed a 뫧 configuration within a 54 bp region between the Cap site (+22) and codon 8, causing a deletion (NG_000007.3: g.63154_70565del). This results in a variant that has been named Hb Lepore-Hong Kong and shows a decreased ß-globin mRNA in carriers compared to that of normal subjects. It is assumed that combination of this variant with ß-thal may cause severe ß-thal syndrome.

The Trend in Timing of Prenatal Diagnosis for Thalassemia at a Chinese Tertiary Obstetric Center.

Thalassemia is a great health burden in mainland China. Carrier screening and prenatal diagnosis (PND) are essential for its prevention. The aim of this study was to describe the trend in the timing of PND for thalassemia in at-risk families in mainland China. All women who were at-risk for thalassemia and received PND at a mainland Chinese tertiary obstetric center between 2011 and 2019 were included. Information required for the survey was obtained from the database of the institute. In total, 4045 women underwent PND for thalassemia, including 1720 for ß-thalassemia (ß-thal) and 2325 for α-thalassemia (α-thal). The median gestational age for the PND procedure was 13 weeks. The number of PNDs performed increased year by year over this period. For both ß-thal and α-thal, the proportion of women undergoing early PND also increased along with the time span. A total of 428 cases was diagnosed prenatally to be affected with ß-thal major (ß-TM) and 769 were affected with Hb Bart's disease. Most of the ß-TM pregnancies and all of the Hb Bart's disease pregnancies were terminated. With the implementation of effective screening measures, births of affected infants have been dramatically avoided, and early PND has become the main approach, thus allowing the possibility of obtaining results at an earlier stage of pregnancy.

Hb Westmead (HBA2: c.369C>G): Hematological Characteristics in Heterozygotes with and without α0-Thalassemia.

Hb Westmead (α122(H5)His>Gln) (HBA2: c.369C>G) is a common α-globin variant causing α-thalassemia (α-thal) in Mainland China. In this study, we report the hematological characteristics in Hb Westmead carriers in a Chinese population. There were 546 individuals carrying Hb Westmead based on their molecular diagnosis: 514 Hb Westmead heterozygotes and 32 compound heterozygotes for Hb Westmead and α0-thal. Compared to common deletional α+-thal, Hb Westmead was associated with higher mean corpuscular hemoglobin (Hb) (MCH) values. Compound heterozygotes for Hb Westmead and α0-thal showed significantly higher Hb, mean corpuscular volume (MCV) and MCH values than subjects with deletional Hb H disease. When compared to α0-thal carriers, compound heterozygotes for Hb Westmead and α0-thal showed similar Hb values, but significantly lower MCV and MCH values. Our results indicate that Hb Westmead is a silent nondeletional α+-thal, with a deficiency of α-globin chain milder than deletional α+-thal, and compound heterozygotes for Hb Westmead/α0-thal have a phenotype similar to simple α0-thal.

Hematological Characteristics of Hb Constant Spring (HBA2: c.427T>C) Carriers in Mainland China.

Hb Constant Spring (Hb CS) (HBA2: c.427T>C) is a common α-globin variant causing α-thalassemia (α-thal) phenotypes in mainland China. In this study, we evaluated the efficiency of erythrocyte parameters and capillary electrophoresis (CE) in the determination of Hb CS in blood samples from Hb CS carriers. Based on molecular diagnosis, there were 462 patients carrying Hb CS: 411 Hb CS heterozygotes, seven carried Hb H-Hb CS disease, 18 compound heterozygotes for Hb CS/α+-thal, and 26 double heterozygotes for Hb CS and ß-thalassemia (ß-thal). Forty-three cases had no Hb CS peak visible on CE, including all 26 cases of double heterozygotes for Hb CS and ß-thal, and 17 cases of heterozygotes carrying only Hb CS. Hb CS heterozygotes, those without a Hb CS peak, presented with lower hemoglobin (Hb), mean corpuscular volume (MCV) and mean corpuscular Hb (MCH) values than those with a Hb CS peak. The MCV <80.0 fL yielded a detection rate of 87.8% for screening individuals carrying Hb CS. Therefore, we emphasize that if one partner of a couple has tested positive for α0-thal, the other should be subjected to detailed screening for this nondeletional allele using molecular analysis, regardless of his/her red cell indices and electrophoretic chromatogram.

Artemisia pollen allergy in China: Component-resolved diagnosis reveals allergic asthma patients have significant multiple allergen sensitization.

BACKGROUND: Artemisia pollen allergy is a major cause of asthma in Northern China. Possible associations between IgE responses to Artemisia allergen components and clinical phenotypes have not yet been evaluated. This study was to establish sensitization patterns of four Artemisia allergens and possible associations with demographic characteristics and clinical phenotypes in three areas of China. METHODS: Two hundred and forty patients allergic to Artemisia pollen were examined, 178 from Shanxi and 30 from Shandong Provinces in Northern China, and 32 from Yunnan Province in Southwestern China. Allergic asthma, rhinitis, conjunctivitis, and eczema symptoms were diagnosed. All patients' sera were tested by ImmunoCAP with mugwort pollen extract and the natural components nArt v 1, nArt ar 2, nArt v 3, and nArt an 7. RESULTS: The frequency of sensitization and the IgE levels of the four components in Artemisia allergic patients from Southwestern China were significantly lower than in those from the North. Art v 1 and Art an 7 were the most frequently recognized allergens (84% and 87%, respectively), followed by Art v 3 (66%) and Art ar 2 (48%). Patients from Northern China were more likely to have allergic asthma (50%) than patients from Southwestern China (3%), and being sensitized to more than two allergens increased the risk of allergic asthma, in which co-sensitization to three major allergens Art v 1, Art v 3, and Art an 7 is prominent. CONCLUSIONS: Component-resolved diagnosis of Chinese Artemisia pollen-allergic patients helps assess the potential risk of mugwort-associated allergic asthma.

Unstable Hemoglobin Variants: The Need for Clinical Vigilance in Infants with Congenital Jaundice.

Unstable hemoglobin (Hb) variants are a rare etiology of congenital jaundice caused by hemolytic anemia. For infant patients with jaundice this disorder is often under diagnosed or the last consideration. We report a 14-month-old boy, who presented with a long-standing jaundice. His diagnosis of Hb Sabine [ß91(F7)Leu→Pro; HBB: c.275T > C] was not revealed until gene sequencing of the ß-globin gene was performed.

Regulatory Single Nucleotide Polymorphism rs368698783 (G>A): a Genetic Modifier of Hb F Production Only under Erythropoietic Stress Characteristic for ß-Globin Chain Deficiency?

A regulatory single nucleotide polymorphism (rSNP), the Aγ (+25 G>A) (rs368698783) (NG_000007.3: g47783G>A) located in the HBG1 proximal promoter, is a significant predictor of clinical severity by elevating Hb F levels in ß-thalassemia (ß-thal). In this study, the presence of the Aγ (+25 G>A) and Aγ (+25 A>A) genotypes was investigated in four subgroups from a total of 611 subjects, including 88 α-thalassemia (α-thal) carriers (group A), 162 ß-thal carriers of point mutations (group B), 57 carriers of ß-thal deletions (group C) and 152 non thalassemic individuals (group D). The result is that the genotypes G>A and A>A exhibit significantly high levels of Hb F compared with the genotype G>G in both groups B and C, while no significant difference was observed in both groups A and D. We assume that the effect of Aγ (+25 G>A) polymorphism on Hb F production is only under erythropoietic stress characteristic for ß-globin chain deficiency.

Coinheritance of Hb City of Hope (HBB: c.208G>A) and ß-Thalassemia: Compromising the Molecular Diagnosis of the Codons 71/72 (+A) (HBB: c.216_217insA) Mutation by Reverse Dot-Blot Hybridization.

More than 900 abnormal hemoglobin (Hb) ß chain variants have now been characterized. The majority are due to point mutations resulting in a single amino acid substitution within the globin gene involved, with nearly twice as many ß chain variants identified compared to α chain variants. Although most of these variants are clinically and hematologically silent, they can interact with different thalassemia mutations, which could sometimes render laboratory diagnostics in a routine setting difficult. In this study, we present a case of coinheritance of Hb City of Hope [ß69(E13)Gly→Ser; HBB: c.208G>A] and ß-thalassemia (ß-thal), that compromises the molecular diagnosis of ß-thal trait.

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis.

Results of Coexistence of ß-Thalassemia Minor in Hb H Disease Patients.

The aim of this study was to determine the hematological characteristics in a large group of Hb H (ß4) patients with or without a coexisting ß-thalassemia (ß-thal), identified by a thalassemia screening program in mainland China. A total of 361 patients with Hb H disease were found, including 343 with deletional types and 18 with nondeletional types. ß-Thalassemia was found in 28 (7.8%) out of the 361 Hb H cases, and all of the 28 cases had the deletional type of Hb H disease. Lower hemoglobin (Hb) levels were detected in cases with the nondeletional type compared to those in cases with the deletional type. ß-Thalassemia significantly increases the Hb levels in Hb H cases. The Hb H and Hb Bart's (γ4) fractions were visible in 270 (85.7%) and 122 (38.7%) out of 315 deletional type cases, respectively, while no Hb H or Hb Bart's fractions were detectable in 28 deletional type cases with ß-thal. Therefore, the diagnosis of Hb H disease in a ß-thal carrier is challenging. Molecular analysis of α- and ß-globin genes is imperative in all cases with a ß-thal trait.

Analysis of the Genotypes in a Chinese Population with Increased Hb A2 and Low Hematological Indices.

Increased Hb A2 is considered the most reliable hematological finding for the identification of ß-thalassemia (ß-thal) carriers. The aim of this study was to determine the underlying genetic factors associated with a high Hb A2 level in a Chinese population. Subjects were recruited from couples preparing for pregnancy who participated in the thalassemia screening program during a 2-year period. DNA analyses were used for diagnosis of ß-thal and other genetic factors. A total of 5985 adults who screened positive for ß-thal were recruited. Of these, 5933 (99.1%) were detected to have a ß-thal mutation. In the remaining 52 (0.9%) individuals without mutations involving the ß-globin gene cluster, 16 were found to have Krüppel-like factor 1 (KLF1) gene variants, and two had an α-globin gene triplication. There were still 34 individuals with unknown genetic factors for their raised Hb A2 values. The results of this study indicate that genetic factors other than ß-thal can rarely contribute to the elevation of Hb A2. These subjects usually have borderline microcytic red cell indices and Hb A2 values.

KFL1 Gene Variants in α-Thalassemia Individuals with Increased Fetal Hemoglobin in a Chinese Population.

Krüppel-like factor 1 (KLF1) is a pleiotropic erythroid transcription factor that is a regulator of definitive erythropoiesis. The aim of this study was to detect KLF1 gene variants in α-thalassemia (α-thal) carriers with an increased Hb F level in a Chinese population, and determine the changes of hematological parameters as a result of interactions between KLF1 gene mutations and α-thal. Subjects with α-thal and Hb F levels of ≥1.0% were selected for further investigation. Direct sequencing was used to detect KLF1 gene mutations. Hematological parameters of subjects with α-thal and concomitant KLF1 gene mutations and those with α-thal alone were compared. The KLF1 gene variants were detected in 46 of 275 (16.7%) individuals with α-thal and Hb F levels of ≥1.0%. The detection rate of KLF1 gene mutations rose correspondingly when the Hb F level increased. For α0-thal carriers, significantly lower mean corpuscular volume (MCV) and mean corpuscular hemoglobin (Hb) (MCH) values were observed in KLF1 gene mutation-positive carriers than that in KLF1 gene mutation-free carriers; conversely, significantly higher Hb A2 and Hb F levels were observed in the former condition rather than in the latter condition. The results of this study indicate that KLF1 gene variants are common in Chinese subjects with α-thal and increased Hb F levels, and KLF1 gene mutations decreased the red blood cell (RBC) indices in α-thal carriers as that in normal adults.

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues.

Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. We evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating six 2D LC-MS/MS data sets for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assess the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we derived a quantification confidence score based on the quality of each peptide-spectrum match to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS data sets collected over a 7-month period. This study provides the first quality assessment on long-term stability and technical considerations for study design of a large-scale clinical proteomics project.

First Report of the Rare IVS-II-705 (T>G) ß-Thalassemia Mutation in a Chinese Family.

We have found an example of the mutation at the intronic region of the second intervening sequence of the ß-globin gene, IVS-II-705 (T>G) (HBB: c.316-146T>G), in a Chinese family. The two subjects heterozygous for this mutation presented with typical ß-thalassemia (ß-thal) trait.

Combination of Hb Heze [ß144(HC1)Lys→Arg; HBB: c.434A>G] and ß0-Thalassemia in a Chinese Patient with ß-Thalassemia Intermedia.

We first report a novel ß chain variant, Hb Heze [ß144(HC1)Lys→Arg; HBB: c.434A>G], in a Chinese family. Heterozygous inheritance of the mutation results in a mild ß-thalassemia (ß-thal) phenotype, whereas compound heterozygosity of Hb Heze with ß0-thal appears as the cause of ß-thal intermedia (ß-TI) in our case.