The genetic framework of primary ciliary dyskinesia assessed by soft computing analysis

BACKGROUND

International guidelines disagree on how best to diagnose primary ciliary dyskinesia (PCD), not least because many tests rely on pattern recognition. We hypothesized that quantitative distribution of ciliary ultrastructural and motion abnormalities would detect most frequent PCD-causing groups of genes by soft computing analysis.

METHODS

Archived data on transmission electron microscopy and high-speed video analysis from 212 PCD patients were re-examined to quantitate distribution of ultrastructural (10 parameters) and functional ciliary features (4 beat pattern and 2 frequency parameters). The correlation between ultrastructural and motion features was evaluated by blinded clustering analysis of the first two principal components, obtained from ultrastructural variables for each patient. Soft computing was applied to ultrastructure to predict ciliary beat frequency (CBF) and motion patterns by a regression model. Another model classified the patients into the five most frequent PCD-causing gene groups, from their ultrastructure, CBF and beat patterns.

RESULTS

The patients were subdivided into six clusters with similar values to homologous ultrastructural phenotype, motion patterns, and CBF, except for clusters 1 and 4, attributable to normal ultrastructure. The regression model confirmed the ability to predict functional ciliary features from ultrastructural parameters. The genetic classification model identified most of the different groups of genes, starting from all quantitative parameters.

CONCLUSIONS

Applying soft computing methodologies to PCD diagnostic tests optimizes their value by moving from pattern recognition to quantification. The approach may also be useful to evaluate atypical PCD, and novel genetic abnormalities of unclear disease-producing potential in the future.

Isolated aberrant right subclavian artery: an underlying clue for genetic anomalies

OBJECTIVE

Aberrant right subclavian artery (ARSA) is known to be associated with specific chromosomal abnormalities. However, there is no agreement regarding clinical decisions related to isolated ARSA. This study evaluated the association between ARSA and genetic abnormalities to provide evidence for prenatal consultation and the postpartum management of isolated ARSA.

METHODS

This single-center cross-sectional study involved fetuses diagnosed with ARSA between January 2014 and May 2021. A range of data was recorded for each patient, including screening ultrasound, fetal echocardiograms, genetic results, postnatal information, and follow-up records.

RESULTS

ARSA was detected in 151 fetuses, of which 136 were considered isolated cases. The remaining 9.9% (15/151) of cases had cardiac and/or extracardiac abnormalities or soft markers. Data from karyotype analysis and chromosomal microarray analysis (CMA) were available for 56 and 33 (out of 56) fetuses, respectively. Genetic abnormalities were detected in 10.7% of fetuses (6/56). Of these, 4.4% (2/45) and 36.4% (4/11) were associated with isolated and non-isolated ARSA, respectively, with a significant difference between these two groups regarding the frequency of genetic abnormality (p = 0.011). The analysis detected Klinefelter Syndrome (47, XXY) and 16p11.2 microdeletion in two isolated cases. One case each of trisomy 21 and 22q11.2 deletion, and another case of 47, XXY, were detected in fetuses with cardiac anomalies. Partial 5q deletion was found in a fetus with extracardiac malformations. In total, 141 of the fetuses survived after birth; termination of pregnancy was performed for 10 fetuses; only two fetuses had mild symptoms of dysphagia.

CONCLUSION

ARSA may be an underlying ultrasonic clue for genetic anomalies even in isolated ARSA. Fetuses with isolated ARSA cannot be ruled out for invasive antenatal diagnosis.

Updates in pathobiological aspects of anaplastic large cell lymphoma

Anaplastic large cell lymphomas (ALCL) encompass several distinct subtypes of mature T-cell neoplasms that are unified by the expression of CD30 and anaplastic cytomorphology. Identification of the cytogenetic abnormality t(2;5)(p23;q35) led to the subclassification of ALCLs into ALK+ ALCL and ALK- ALCL. According to the most recent World Health Organization (WHO) Classification of Haematolymphoid Tumours as well as the International Consensus Classification (ICC) of Mature Lymphoid Neoplasms, ALCLs encompass ALK+ ALCL, ALK- ALCL, and breast implant-associated ALCL (BI-ALCL). Approximately 80% of systemic ALCLs harbor rearrangement of ALK, with NPM1 being the most common partner gene, although many other fusion partner genes have been identified to date. ALK- ALCLs represent a heterogeneous group of lymphomas with distinct clinical, immunophenotypic, and genetic features. A subset harbor recurrent rearrangement of genes, including TYK2, DUSP22, and TP63, with a proportion for which genetic aberrations have yet to be characterized. Although primary cutaneous ALCL (pc-ALCL) is currently classified as a subtype of primary cutaneous T-cell lymphoma, due to the large anaplastic and pleomorphic morphology together with CD30 expression in the malignant cells, this review also discusses the pathobiological features of this disease entity. Genomic and proteomic studies have contributed significant knowledge elucidating novel signaling pathways that are implicated in ALCL pathogenesis and represent candidate targets of therapeutic interventions. This review aims to offer perspectives on recent insights regarding the pathobiological and genetic features of ALCL.

Simultaneous Occurrence of Multiple Neoplasms in Children with Cancer Predisposition Syndromes: Collaborating with Abnormal Genes

The identification of cancer predisposition syndromes (CPSs) plays a crucial role in understanding the etiology of pediatric cancers. CPSs are genetic mutations that increase the risk of developing cancer at an earlier age compared to the risk for the general population. This article aims to provide a comprehensive analysis of three unique cases involving pediatric patients with CPS who were diagnosed with multiple simultaneous or metachronous cancers. The first case involves a child with embryonal rhabdomyosarcoma, nephroblastoma, glioma, and subsequent medulloblastoma. Genetic analysis identified two pathogenic variants in the BRCA2 gene. The second case involves a child with alveolar rhabdomyosarcoma, juvenile xanthogranuloma, gliomas, and subsequent JMML/MDS/MPS. A pathogenic variant in the NF1 gene was identified. The third case involves a child with pleuropulmonary blastoma and pediatric cystic nephroma/nephroblastoma, in whom a pathogenic variant in the DICER1 gene was identified. Multiple simultaneous and metachronous cancers in pediatric patients with CPSs are a rare but significant phenomenon. Comprehensive analysis and genetic testing play significant roles in understanding the underlying mechanisms and guiding treatment strategies for these unique cases. Early detection and targeted interventions are important for improving outcomes in these individuals.

Biomarkers for patients with Wilms tumor: a review

Wilms tumor, originating from aberrant fetal nephrogenesis, is the most common renal malignancy in childhood. The overall survival of children is approximately 90%. Although existing risk-stratification systems are helpful in identifying patients with poor prognosis, the recurrence rate of Wilms tumors remains as high as 15%. To resolve this clinical problem, diverse studies on the occurrence and progression of the disease have been conducted, and the results are encouraging. A series of molecular biomarkers have been identified with further studies on the mechanism of tumorigenesis. Some of these show prognostic value and have been introduced into clinical practice. Identification of these biomarkers can supplement the existing risk-stratification systems. In the future, more biomarkers will be discovered, and more studies are required to validate their roles in improving the detection rate of occurrence or recurrence of Wilms tumor and to enhance clinical outcomes.

Experience in prenatal ultrasound diagnosis of fetal microtia and associated abnormalities

Objective

Prenatal ultrasound features, associated anomalies and genetic abnormalities of microtia cases were analyzed to explore the feasibility and value of prenatal ultrasound for the diagnosis of microtia.

Methods

The ultrasonographic features, associated anomalies, chromosome examination results and follow-up results of 81 fetuses with congenital microtia were analyzed retrospectively.

Results

Among the 81 fetuses with microtia diagnosed after birth, 2 cases were missed diagnosis on prenatal ultrasound, and 1 case was diagnosed as unilateral microtia by prenatal ultrasound but was found to be bilateral microtia after birth. Microtia was accompanied by an accessory auricle in 4 cases (4.94%) and low-set ears in 7 cases (8.64%). 22 cases (27.16%) were complicated with other structural anomalies, including 11 cases (13.58%) of cardiac anomalies, 7 cases (8.64%) of ultrasonographic soft marker anomalies, 6 cases (7.41%) of facial anomalies, 6 cases (7.41%) of nervous system anomalies, 3 cases (3.70%) of urogenital system anomalies, 3 cases (3.70%) of digestive tract anomalies and 2 cases (2.47%) of limb anomalies. Chromosome karyotype analysis and gene detection were performed in 44 cases. Trisomy 18, trisomy 13, trisomy 21, pericentric inversion of chromosome 9, partial loss of heterozygosity on chromosome 14, 22q11 microdeletion and a normal karyotype were found in 2 cases, 2 cases, 3 cases, 1 case, 1 case, 1 case, and 34 cases, respectively.

Conclusion

In summary, microtia is often accompanied by congenital defects of other organs and structures, especially the heart and face, and prenatal ultrasound diagnosis of microtia and associated anomalies is of important clinical significance.

The Etiological Profile of Global Developmental Delay at a Tertiary Care Hospital in India: An Observational Study

Background Global developmental delay (GDD) is common and has a significant impact on affected children, families, and society. Understanding its etiology is crucial for management and prevention strategies. However, data on the etiological profile of GDD in developing countries are limited. This study aimed to identify the etiological profile of GDD at a tertiary care hospital in India. Methodology This observational study included children aged three months to five years with a developmental quotient below 70%. Data on demographics, clinical features, relevant investigations, and diagnoses were collected. Etiologies were categorized into prenatal, perinatal, postnatal, and unknown causes. Informed consent was obtained from the parents. Results A total of 52 children, with a median age of 15.5 months, were included in the study, with 69.2% being males. Prenatal causes accounted for half of the cases, with genetic abnormalities (32.7%) and chromosomal abnormalities (7.7%) being prominent. Perinatal causes were the next most common (34.6%), including hypoxic-ischemic encephalopathy (26.7%). Postnatal causes were rare (3.8%). The overall etiological yield was 88.4%, with some cases remaining unidentified. Conclusions Prenatal causes, including genetic and chromosomal abnormalities, are common in GDD. The utilization of genetic testing enhances etiological yield. Hypoxic-ischemic encephalopathy remains a significant factor and highlights the importance of perinatal care in preventing developmental delays. Large multicentric studies are needed for a comprehensive database of etiological profiles.

Factors Influencing the Duration of Termination of Pregnancy for Fetal Anomaly with Mifepristone in Combination with Misoprostol

This study's aim was to determine relevant factors that influence the time interval between first induction and fetal expulsion in late termination of pregnancy (TOP) and TOP after previous feticide for severe fetal malformation with a mifepristone-misoprostol regime. This retrospective study included 913 TOPs from a single tertiary care referral center. In 197 out of 913 TOPs, a previous feticide had been performed due to advanced gestational age (after 22 + 0 weeks of gestation). Induction was accomplished using 600 mg mifepristone followed by 400 μg misoprostol. The interval between first induction with misoprostol and fetal expulsion was examined. Univariate and multivariate logistic regression analysis were used to predict an induction interval of 12 h or less. The median gestational age at induction of labor was 18.9 weeks of pregnancy. In 487 (53.3%) cases women delivered within 12 h; in 344 (37.7%) cases the induction interval was between 12 h and 36 h. In 82 (9%) cases induction took longer than 36 h. Factors that were significantly associated with a delivery duration of <12 h were a lower gestational age at induction (OR 0.87; 95% CI 0.84-0.89; p < 0.001) and a history of at least one previous vaginal delivery (OR 1.57; 95% CI 1.20-2.05; p < 0.001). Factors that had no impact included previous cesarean section, performing feticide before induction and maternal age. Maternal BMI showed a non-significant trend.

Increased interstage morbidity and mortality following stage 1 palliation in patients with genetic abnormalities

BACKGROUND

Hypoplastic left heart syndrome and single ventricle variants with aortic hypoplasia are commonly classified as severe forms of CHD. We hypothesised patients with these severe defects and reported genetic abnormalities have increased morbidity and mortality during the interstage period.

METHODS AND RESULTS

This was a retrospective review of the National Pediatric Cardiology Quality Improvement Collaborative Phase I registry. Three patient groups were identified: major syndromes, other genetic abnormalities, and no reported genetic abnormality. Tukey post hoc test was applied for pairwise group comparisons of length of stay, death, and combined outcome of death, not a candidate for stage 2 palliation, and heart transplant. Participating centres received a survey to establish genetic testing and reporting practices. Of the 2182 patients, 110 (5%) had major genetic syndromes, 126 (6%) had other genetic abnormalities, and 1946 (89%) had no genetic abnormality. Those with major genetic syndromes weighed less at birth and stage 1 palliation. Patients with no reported genetic abnormalities reached full oral feeds sooner and discharged earlier. The combined outcome of death, not a candidate for stage 2 palliation, and heart transplant was more common in those with major syndromes. Survey response was low (n = 23, 38%) with only 14 (61%) routinely performing and reporting genetic testing.

CONCLUSIONS

Patients with genetic abnormalities experienced greater morbidity and mortality during the interstage period than those with no reported genetic abnormalities. Genetic testing and reporting practices vary significantly between participating centres.

Mitochondria and Their Relationship with Common Genetic Abnormalities in Hematologic Malignancies

Hematologic malignancies are known to be associated with numerous cytogenetic and molecular genetic changes. In addition to morphology, immunophenotype, cytochemistry and clinical characteristics, these genetic alterations are typically required to diagnose myeloid, lymphoid, and plasma cell neoplasms. According to the current World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues, numerous genetic changes are highlighted, often defining a distinct subtype of a disease, or providing prognostic information. This review highlights how these molecular changes can alter mitochondrial bioenergetics, cell death pathways, mitochondrial dynamics and potentially be related to mitochondrial genetic changes. A better understanding of these processes emphasizes potential novel therapies.

The Presence of Mycotoxins in Human Amniotic Fluid

Mycotoxin exposure assessments through biomonitoring studies, based on the analysis of amniotic fluid, provides useful information about potential exposure of mothers and fetuses to ubiquitous toxic metabolites that are routinely found in food and the environment. In this study, amniotic fluid samples (n = 86) were collected via abdominal amniocentesis at 15–22 weeks of gestation from pregnant women with a high risk of chromosomal anomalies or genetic fetal defects detected during 1st trimester prenatal screening. These samples were analyzed for the presence of the most typical Aspergillus, Penicillium and Fusarium mycotoxins, with a focus on aflatoxins, ochratoxins and trichothecenes, using the LC-FLD/DAD method. The results showed that the toxin was present in over 75% of all the tested samples and in 73% of amniotic fluid samples from fetuses with genetic defects. The most frequently identified toxins were nivalenol (33.7%) ranging from <LOQ to 4037.6 ng/mL, and aflatoxins (31.4%), including aflatoxin G1, ranging from <LOQ to 0.4 ng/mL. Ochratoxin A and deoxynivalenol were identified in 26.7% and 27.9% of samples, respectively. Bearing in mind the above, the detection of mycotoxin levels in amniotic fluid is useful for the estimation of overall risk characterization with an attempt to link the occurrence of fetal abnormalities with exposure to mycotoxins in utero.

Prenatal Diagnosis of Aberrant Right Subclavian Artery: Association with Genetic Abnormalities

OBJECTIVE

 The objective of the present study was to determine the frequency of malformations and chromosomal abnormalities in a population of fetuses with an aberrant right subclavian artery (ARSA).

METHODS

 This is a 6-year retrospective study of fetuses with a prenatal diagnosis of ARSA conducted during the period between September 2013 and June 2019 at a fetal medicine unit. Data were collected from ultrasound, fetal echocardiograms, genetic studies, and neonatal records.

RESULTS

 An ARSA was diagnosed in 22 fetuses. An ARSA was an isolated finding in 18 out of 22 cases (82%). Associated abnormal sonographic findings were found in 4 cases. All cases underwent invasive testing. In 1 of the cases, a chromosomal abnormality was detected (mos 45,X [13]/46,X,e(X) (p22.1q22.1)). No cases of congenital heart disease were found in any of these fetuses. There were two cases in which the postnatal evaluation revealed a malformation: one case of hypospadias and 1 case of cleft palate.

CONCLUSION

 The presence of an isolated ARSA is benign and is not associated with chromosomal abnormalities. The finding of ARSA, however, warrants a detailed fetal ultrasound in order to exclude major fetal abnormalities and other soft markers.

Comparative clinical genetic testing in spontaneous miscarriage: Insights from a study in Southern Chinese women

Single nucleotide polymorphism (SNP) array and karyotype analyses were conducted on 441 spontaneous miscarriage placental villous tissues collected from women from southern China. Subsequently, the results from these two analyses were compared to evaluate the best diagnostic strategy for subsequent pre‐pregnancy planning. Here, the success rate of genetic testing using karyotyping and SNP array analysis was 78.46% (346/441) and 100.0% (441/441), respectively. The abnormality rate estimated by both methods was 54.9% (242/441). Three hundred and forty‐six cases were successfully detected via both SNP array and karyotype analyses; the rate of consistent detection was 96.24% (333/346), whereas 13 cases were not consistent. There was no substantial positive correlation between age and genetic abnormalities such as Turner syndrome, structural variation or euploidy state in the different age groups studied. However, the aneuploidy rate was significantly different in each age group. Thus, although SNP array has higher success rate and resolution in genetic abnormality detection, supplementary karyotype analysis is needed for a more accurate revelation of the genetic aetiology of miscarriages. Therefore, this study indicates that simultaneous karyotype and SNP array analyses should be performed for spontaneous miscarriages. Furthermore, miscarriages irrespective of maternal age must be genetically analysed.

Endoluminal tumor implant of a colorectal cancer in an anal fistula detected by FISH techniques: a case report

Intraluminal shedding of tumor cells is a rare infrequent sporadic colorectal cancer (sCRC) mechanism of spreading. Less than 30 cases of sCRC metastasis into anal fistula have been reported. Here, we study a 72-year-old male with an adenocarcinoma arising in an anal fistula. Subsequent studies revealed another tumor in the rectum without distant metastatic disease; therefore, a curative-intent abdominoperineal resection was performed. The histologic study showed a moderately differentiated adenocarcinoma in both locations. No perineural or lymphovascular invasion was observed, and all the lymphatic nodes resected were negative for malignancy. Both tumors showed positive CK20 and negative CK7 immunostaining, but KRAS G12D mutation was only detected in the rectal tumor. After those conventional studies, a cytogenetic profile of both tumors was performed by interphase fluorescence in situ hybridization (iFISH) techniques. The FISH study displayed an identical genetic profile in both tumors, loss of the chromosomes 8 and 18q, and no alteration in chromosome 7 and 13q. Based on pathological and genetic findings, we established the same clonal origin of both tumors. Currently, the diagnosis of an intraluminal CRC metastasis relies on histologic and immunohistochemistry findings. We suggest that genetic studies at the individual cell level by FISH techniques may be useful in order to differentiate synchronous from intraluminal metastasis.

Polycystic ovary syndrome: a contemporary clinical approach

Polycystic ovary syndrome (PCOS) is a frequent endocrine disease in women during reproductive period. It is considered a complex metabolic disorder with long-term metabolic, as well as reproductive consequences. Main pathophysiological pathways are related to the increased androgen levels and insulin resistance. Nowadays, genetic origins of PCOS are acknowledged, with numerous genes involved in the pathogenesis of hyperandrogenemia, insulin resistance, inflammation and disturbed folliculogenesis. Rotterdam diagnostic criteria are most widely accepted and four PCOS phenotypes have been recognized. Metabolic abnormalities are more common in phenotypes 1 and 2. Women with classic PCOS are more obese and typically have central type of obesity, more prevalently displaying dyslipidemia, insulin resistance and metabolic syndrome that could be associated with an increased risk of cardiovascular complications during life. Heterogeneity of phenotypes demands an individualized approach in the treatment of women with PCOS. Metabolic therapies involve a lifestyle intervention followed by the introduction of insulin sensitizers including metformin and inositols, glucagon-like peptide 1 receptor agonists (GLP-1 RA), as recently sodium glucose contransporter-2 (SGLT2) inhibitors. Addition of an insulin sensitizer to the standard infertility therapy such as CC improves ovulation and pregnancy rates. Our current review analyzes the contemporary knowledge of PCOS etiology and etiopathogenesis, its cardiometabolic risks and their outcomes, as well as therapeutic advances for women with PCOS.

The role of autophagy in targeted therapy for acute myeloid leukemia

Although molecular targeted therapies have recently displayed therapeutic effects in acute myeloid leukemia (AML), limited response and acquired resistance remain common problems. Numerous studies have associated autophagy, an essential degradation process involved in the cellular response to stress, with the development and therapeutic response of cancers including AML. Thus, we review studies on the role of autophagy in AML development and summarize the linkage between autophagy and several recurrent genetic abnormalities in AML, highlighting the potential of capitalizing on autophagy modulation in targeted therapy for AML.Abbreviations: AML: acute myeloid leukemia; AMPK: AMP-activated protein kinase; APL: acute promyelocytic leukemia; ATG: autophagy related; ATM: ATM serine/threonine kinase; ATO: arsenic trioxide; ATRA: all trans retinoic acid; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; BET proteins, bromodomain and extra-terminal domain family; CMA: chaperone-mediated autophagy; CQ: chloroquine; DNMT, DNA methyltransferase; DOT1L: DOT1 like histone lysine methyltransferase; FLT3: fms related receptor tyrosine kinase 3; FIS1: fission, mitochondrial 1; HCQ: hydroxychloroquine; HSC: hematopoietic stem cell; IDH: isocitrate dehydrogenase; ITD: internal tandem duplication; KMT2A/MLL: lysine methyltransferase 2A; LSC: leukemia stem cell; MDS: myelodysplastic syndromes; MTORC1: mechanistic target of rapamycin kinase complex 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NPM1: nucleophosmin 1; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PML: PML nuclear body scaffold; ROS: reactive oxygen species; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SAHA: vorinostat; SQSTM1: sequestosome 1; TET2: tet methylcytosine dioxygenase 2; TKD: tyrosine kinase domain; TKI: tyrosine kinase inhibitor; TP53/p53: tumor protein p53; ULK1: unc-51 like autophagy activating kinase 1; VPA: valproic acid; WDFY3/ALFY: WD repeat and FYVE domain containing 3.

Pediatric randomized trial EORTC CLG 58951: Outcome for adolescent population with acute lymphoblastic leukemia

Over the years, the prognosis of adolescents treated for acute lymphoblastic leukemia (ALL) has improved. However, this age group still represents a challenge with an overall survival (OS) of 60% compared to 85% in younger children. Herein, we report the outcome of adolescents treated in the European Organisation for Research and Treatment of Cancer (EORTC) 58951 clinical trial. EORTC 58951 clinical trial included patients with de novo ALL between 1998 and 2008. For this study, we analyzed data of all adolescents between 15 and under 18. Data from 97 adolescents were analyzed, 70 had B-lineage and 27 had T-lineage ALL. The 8-year event-free survival (EFS) and OS for the B-cell precursor ALL cases were 72.3% (59.4%-81.7%) and 80.8% (67.4%-89.1%), respectively. For the T-lineage, the 8-year EFS and OS were 57.4% (36.1%-74.0%) and 59.0% (36.1%-76.2%), respectively. "B-other" ALL, defined as BCP-ALL lacking any known recurrent genetic abnormalities were more frequent in our adolescent population (52.8%) than in younger children (27.1%). Outcome of adolescents in the EORTC 58951 study is supporting the findings that adolescents have better outcome in pediatric compared to adults' trials. Nevertheless, in pediatric studies, adolescents still have a worse prognosis than younger children. Despite the fact that specific unfavorable characteristics may be linked to the adolescent population, a careful study and characterization of adolescents "B-other" genetic abnormalities in ALL is critical to improve the outcome of this population.

Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR

Genomic integrity of human pluripotent stem cells (hPSCs) is essential for research and clinical applications. However, genetic abnormalities can accumulate during hPSC generation and routine culture and following gene editing. Their occurrence should be regularly monitored, but the current assays to assess hPSC genomic integrity are not fully suitable for such regular screening. To address this issue, we first carried out a large meta-analysis of all hPSC genetic abnormalities reported in more than 100 publications and identified 738 recurrent genetic abnormalities (i.e., overlapping abnormalities found in at least five distinct scientific publications). We then developed a test based on the droplet digital PCR technology that can potentially detect more than 90% of these hPSC recurrent genetic abnormalities in DNA extracted from culture supernatant samples. This test can be used to routinely screen genomic integrity in hPSCs.

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A meta-analysis was carried out to list genetic abnormalities detected in hPSCs

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Recurrent genetic abnormalities in hPSCs were precisely defined

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ddPCR is a robust and sensitive approach to screen these recurrent abnormalities

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In culture supernatant digital test can be used to rapidly screen iPSC clones

NOP53 as A Candidate Modifier Locus for Familial Non-Medullary Thyroid Cancer

Nonsyndromic familial non-medullary thyroid cancer (FNMTC) represents 3–9% of thyroid cancers, but the susceptibility gene(s) remain unknown. We designed this multicenter study to analyze families with nonsyndromic FNMTC and identify candidate susceptibility genes. We performed exome sequencing of DNA from four affected individuals from one kindred, with five cases of nonsyndromic FNMTC. Single Nucleotide Variants, and insertions and deletions that segregated with all the affected members, were analyzed by Sanger sequencing in 44 additional families with FNMTC (37 with two affected members, and seven with three or more affected members), as well as in an independent control group of 100 subjects. We identified the germline variant p. Asp31His in NOP53 gene (rs78530808, MAF 1.8%) present in all affected members in three families with nonsyndromic FNMTC, and not present in unaffected spouses. Our functional studies of NOP53 in thyroid cancer cell lines showed an oncogenic function. Immunohistochemistry exhibited increased NOP53 protein expression in tumor samples from affected family members, compared with normal adjacent thyroid tissue. Given the relatively high frequency of the variant in the general population, these findings suggest that instead of a causative gene, NOP53 is likely a low-penetrant gene implicated in FNMTC, possibly a modifier.

Update on the classification of T-cell lymphomas, Hodgkin lymphomas, and histiocytic/dendritic cell neoplasms

Introduction: The classification of lymphomas is based on the postulated normal counterparts of lymphoid neoplasms and currently constitutes over 100 definite or provisional entities. As this number of entities implies, lymphomas show marked pathological, genetic, and clinical heterogeneity. Recent molecular findings have significantly advanced our understanding of lymphomas. Areas covered: The World Health Organization (WHO) classification of lymphoid neoplasms was updated in 2017. The present review summarizes the new findings that have been gained in the areas of mature T-cell neoplasms, Hodgkin lymphomas, and histiocytic/dendritic cell neoplasms since the publication of the 2017 WHO classification. Expert opinion: Although formal revisions to the WHO classification are published only periodically, our understanding of the pathologic, genetic, and clinical features of lymphoid neoplasms is constantly evolving, particularly in the age of -omics technologies and targeted therapeutics. Even in the relatively short time since the publication of the 2017 WHO classification, many significant findings have been identified in the entities covered in this review.

Current Knowledge of Germline Genetic Risk Factors for the Development of Non-Medullary Thyroid Cancer

The thyroid is the most common site of endocrine cancer. One type of thyroid cancer, non-medullary thyroid cancer (NMTC), develops from follicular cells and represents approximately 90% of all thyroid cancers. Approximately 5%–15% of NMTC cases are thought to be of familial origin (FNMTC), which is defined as the occurrence of the disease in three or more first-degree relatives of the patient. It is often divided into two groups: Syndrome-associated and non-syndromic. The associated syndromes include Cowden syndrome, familial adenomatous polyposis, Gardner syndrome, Carney complex and Werner syndrome. The hereditary factors contributing to the unfavorable course of FNMTC remain poorly understood; therefore, considerable effort is being expended to identify contributing loci. Research carried out to date identifies fourteen genes (DICER1, FOXE1, PTCSC2, MYH9, SRGAP1, HABP2, BRCA1, CHEK2, ATM, RASAL1, SRRM2, XRCC1, TITF-1/NKX2.1, PTCSC3) associated with vulnerability to FNMTC that are not related to hereditary syndromes. In this review, we summarize FNMTC studies to date, and provide information on genes involved in the development of non-syndromic familial non-medullary thyroid cancers, and the significance of mutations in these genes as risk factors. Moreover, we discuss whether the genetic polymorphism rs966423 in DIRC3 has any potential as a prognostic factor of papillary thyroid cancer.

MicroRNAs and their target mRNAs as potential biomarkers among smokers and non-smokers with lung adenocarcinoma

Lung adenocarcinoma is one of the major causes of mortality. Current methods of diagnosis can be improved through identification of disease specific biomarkers. MicroRNAs are small non-coding regulators of gene expression, which can be potential biomarkers in various diseases. Thus, the main objective of this study was to gain mechanistic insights into genetic abnormalities occurring in lung adenocarcinoma by implementing an integrative analysis of miRNAs and mRNAs expression profiles in the case of both smokers and non-smokers. Differential expression was analysed by comparing publicly available lung adenocarcinoma samples with controls. Furthermore, weighted gene co-expression network analysis is performed which revealed mRNAs and miRNAs significantly correlated with lung adenocarcinoma. Moreover, an integrative analysis resulted in identification of several miRNA-mRNA pairs which were significantly dysregulated in non-smokers with lung adenocarcinoma. Also two pairs (miR-133b/Protein Kinase C Zeta (PRKCZ) and miR-557/STEAP3) were found specifically dysregulated in smokers. Pathway analysis further revealed their role in important signalling pathways including cell cycle. This analysis has not only increased the authors' understanding about lung adenocarcinoma but also proposed potential biomarkers. However, further wet laboratory studies are required for the validation of these potential biomarkers which can be used to diagnose lung adenocarcinoma.

Genetic abnormalities seen on CVS in early pregnancy failure

Objective: To determine the frequency and distribution of chromosome abnormalities in women with early pregnancy failure (EPF) detected by cytogenetic testing on chorionic villus sampling.Method: Retrospective observational cohort study of chromosomal analysis from transvaginal chorionic villus sampling (CVS) or reflex products of conception (POC) karyotype. CVS was offered as a training tool for Maternal Fetal Medicine fellows prior to manual vacuum aspiration for EPF 9-week gestation. POC were analyzed for cytogenetics if no results were obtained on CVS.Results: One hundred thirty samples were collected from December 2011 to April 2015. 33 (27.3%) cases had a normal karyotype and 88 (73.0%) cases had an abnormal karyotype. The most common group of abnormalities were trisomy, (n = 50, 41.3%), triploidy/tetraploidy, (n = 17, 14.0%), monosomy (n = 15, 12.4%), and structural rearrangements (n = 6, 5.0%). Nine (6.9%) samples were maternal decidua only. Abnormal karyotype in EPF was significantly increased in women by age group (p < .01) but not in women with a history of prior miscarriage (p = .5).Conclusion: Our cohort had a high detection rate of aneuploidy. The most common chromosomal abnormalities in EPF were: trisomy, followed by triploidy/tetraploidy, monosomy, and structural rearrangements. Maternal age had the strongest correlation with EPF associated with aneuploidy.

Genetic and epigenetic factors which modulate differentiation propensity in human pluripotent stem cells

BACKGROUND

Human pluripotent stem cell (hPSC) lines are known to have a bias in their differentiation. This gives individual cell lines a propensity to preferentially differentiate towards one germ layer or cell type over others. Chromosomal aberrations, mitochondrial mutations, genetic diversity and epigenetic variance are the main drivers of this phenomenon, and can lead to a wide range of phenotypes.

OBJECTIVE AND RATIONALE

Our aim is to provide a comprehensive overview of the different factors which influence differentiation propensity. Specifically, we sought to highlight known genetic variances and their mechanisms, in addition to more general observations from larger abnormalities. Furthermore, we wanted to provide an up-to-date list of a growing number of predictive indicators which are able to identify differentiation propensity before the initiation of differentiation. As differentiation propensity can lead to difficulties in both research as well as clinical translation, our thorough overview could be a useful tool.

SEARCH METHODS

Combinations of the following key words were applied as search criteria in the PubMed database: embryonic stem cells, induced pluripotent stem cells, differentiation propensity (also: potential, efficiency, capacity, bias, variability), epigenetics, chromosomal abnormalities, genetic aberrations, X chromosome inactivation, mitochondrial function, mitochondrial metabolism, genetic diversity, reprogramming, predictive marker, residual stem cell, clinic. Only studies in English were included, ranging from 2000 to 2017, with a majority ranging from 2010 to 1017. Further manuscripts were added from cross-references.

OUTCOMES

Differentiation propensity is affected by a wide variety of (epi)genetic factors. These factors clearly lead to a loss of differentiation capacity, preference towards certain cell types and oftentimes, phenotypes which begin to resemble cancer. Broad changes in (epi)genetics, such as aneuploidies or wide-ranging modifications to the epigenetic landscape tend to lead to extensive, less definite changes in differentiation capacity, whereas more specific abnormalities often have precise ramifications in which certain cell types become more preferential. Furthermore, there appears to be a greater, though often less considered, contribution to differentiation propensity by factors such as mitochondria and inherent genetic diversity. Varied differentiation capacity can also lead to potential consequences in the clinical translation of hPSC, including the occurrence of residual undifferentiated stem cells, and the transplantation of potentially transformed cells.

WIDER IMPLICATIONS

As hPSC continue to advance towards the clinic, our understanding of them progresses as well. As a result, the challenges faced become more numerous, but also more clear. If the transition to the clinic is to be achieved with a minimum number of potential setbacks, thorough evaluation of the cells will be an absolute necessity. Altered differentiation propensity represents at least one such hurdle, for which researchers and eventually clinicians will need to find solutions. Already, steps are being taken to tackle the issue, though further research will be required to evaluate any long-term risks it poses.

Multicenter study of genetic abnormalities associated with severe oligospermia and non-obstructive azoospermia

Objective

*

Chong Xie, Xiangfeng Chen, and Yulin Liu contributed equally to this work.

Genetic defects are identified in nearly 20% of infertile males. Determining the frequency and types of major genetic abnormalities in severe male infertility helps inform appropriate genetic counseling before assisted reproductive techniques.

Methods

Cytogenetic results of 912 patients with non-obstructive azoospermia (NOA) and severe oligozoospermia (SOS) in Eastern China were reviewed in this multicenter study from January 2011 to December 2015. Controls were 215 normozoospermic men with offspring.

Results

Among all patients, 22.6% (206/912) had genetic abnormalities, including 27.3% (146/534) of NOA patients and 15.9% (60/378) of SOS patients. Chromosomal abnormalities (all autosomal) were detected in only 1.9% (4 /215) of controls. In NOA patients, sex chromosomal abnormalities were identified in 25.8% (138/534), of which 8% (43/534) had a 47,XXY karyotype or its mosaic; higher than the SOS group prevalence (1.1%; 4/378). The incidence of Y chromosome microdeletions was lower in the SOS group (13.2%; 50/378) than in the NOA group (17.8%; 95/534).

Conclusions

The high prevalence of genetic abnormalities in our study indicates the importance of routine genetic testing in severe male infertility diagnosis. This may help determine the choice of assisted reproductive technique and allow specific pre-implantation genetic testing to minimize the risk of transmitting genetic defects.

High-grade serous carcinoma of tubo-ovarian origin: recent developments

Extra-uterine high-grade serous carcinoma (HGSC) accounts for most of the morbidity and mortality associated with ovarian carcinoma, and is one of the leading causes of cancer death in women. Until recently our understanding of HGSC was very limited compared to other common cancers, and it has only been during the last 15 years that we have learned how to diagnose this ovarian carcinoma histotype accurately. Since then, however, there has been rapid progress, with identification of a precursor lesion in the fallopian tube, development of prevention strategies for both those with inherited susceptibility (hereditary breast and ovarian cancer syndrome) and without the syndrome, and elucidation of the molecular events important in oncogenesis. This molecular understanding has led to new treatment strategies for HGSC, with the promise of more to come in the near future. In this review we focus on these recent changes, including diagnostic criteria/differential diagnosis, primary site assignment, precursor lesions and the molecular pathology of HGSC.

Microcephaly

Microcephaly is defined as a head circumference more than two standard deviations below the mean for gender and age. Congenital microcephaly is present at birth, whereas postnatal microcephaly occurs later in life. Genetic abnormalities, syndromes, metabolic disorders, teratogens, infections, prenatal, perinatal, and postnatal injuries can cause both congenital and postnatal microcephaly. Evaluation of patients with microcephaly begins with a thorough history and physical examination. In cases of worsening microcephaly or neurological signs or symptoms, neuroimaging, metabolic, or genetic testing should be strongly considered. Any further studies and workup should be directed by the presence of signs or symptoms pointing to an underlying diagnosis and are usually used as confirmatory testing for certain conditions. Neuroimaging with magnetic resonance imaging (MRI) is often the first diagnostic test in evaluating children with microcephaly. Genetic testing is becoming more common and is often the next step following neuroimaging when there is no specific evidence in the history or physical examination suggesting a diagnosis. Microcephaly is a lifelong condition with no known cure. The prognosis is usually worse for children who experienced an intrauterine infection or have a chromosomal or metabolic abnormality. Zika virus has rapidly spread since 2015, and maternal infection with this virus is associated with microcephaly and other serious brain abnormalities. Microcephaly has become much more prevalent in the news and scientific community with the recent emergence of Zika virus as a cause of congenital microcephaly.

High-grade serous carcinoma of tubo-ovarian origin: recent developments

Extra-uterine high-grade serous carcinoma (HGSC) accounts for most of the morbidity and mortality associated with ovarian carcinoma, and is one of the leading causes of cancer death in women. Until recently our understanding of HGSC was very limited compared to other common cancers, and it has only been during the last 15 years that we have learned how to diagnose this ovarian carcinoma histotype accurately. Since then, however, there has been rapid progress, with identification of a precursor lesion in the fallopian tube, development of prevention strategies for both those with inherited susceptibility (hereditary breast and ovarian cancer syndrome) and without the syndrome, and elucidation of the molecular events important in oncogenesis. This molecular understanding has led to new treatment strategies for HGSC, with the promise of more to come in the near future. In this review we focus on these recent changes, including diagnostic criteria/differential diagnosis, primary site assignment, precursor lesions and the molecular pathology of HGSC.

Recent advances in prenatal genetic screening and testing

The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.

Genetic abnormalities associated with acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) occurs with high frequency in childhood and is associated with high mortality in adults. Recent technical advances in next‐generation sequencing have shed light on genetic abnormalities in hematopoietic stem/progenitor cells as the precursor to ALL pathogenesis. Based on these genetic abnormalities, ALL is now being reclassified into newly identified subtypes. Philadelphia chromosome‐like B‐lineage ALL is one of the new high‐risk subtypes characterized by genetic alterations that activate various signaling pathways, including those involving cytokine receptors, tyrosine kinases, and epigenetic modifiers. Philadelphia chromosome‐like ALL is essentially heterogeneous; however, deletion mutations in the IKZF1 gene encoding the transcription factor IKAROS underlie many cases as a key factor inducing aggressive phenotypes and poor treatment responses. Whole‐genome sequencing studies of ALL patients and ethnically matched controls also identified inherited genetic variations in lymphoid neoplasm‐related genes, which are likely to increase ALL susceptibility. These findings are directly relevant to clinical hematology, and further studies on this aspect could contribute to accurate diagnosis, effective monitoring of residual disease, and patient‐oriented therapies.

Retrospective analysis of genetic abnormalities and survival in 131 patients with multiple myeloma

Genetic abnormalities in patients with multiple myeloma (MM) are important risk factors in terms of prognosis. In the present study, the prognostic value of several common MM genetic abnormalities was investigated. Interphase fluorescence in situ hybridization (iFISH) was used to detect genetic abnormalities, including 1q21 gain, t(4;14), t(11;14), t(14;16) and 17p13 deletion in 131 patients. A total of 46.6% patients were detected with one or more abnormalities using iFISH analysis. The 1q21 gain, t(4;14), t(11;14), t(14;16) and 17p13 deletion abnormalities were detected in 42.5, 6.9, 17.5, 0.8 and 10.7% of patients, respectively. Patients with t(4;14) commonly exhibited lower levels of albumin and hemoglobin. The progression-free survival (PFS) and overall survival times of iFISH-positive patients (particularly patients with two or more iFISH abnormalities) were significantly shorter than those of the patients without detectable abnormalities. The 1q21 gain and 17p13 deletion were also adverse prognostic factors for MM. Bortezomib-based therapies improved the PFS times in the patients with unfavorable iFISH abnormalities. These findings demonstrate that patients with two or more iFISH abnormalities, a gain of the 1q21 region or a 17p13 deletion were more likely to have a poor prognosis; however, bortezomib treatment improved the outcome for MM patients with unfavorable iFISH abnormalities.

Genetic abnormalities and challenges in the treatment of acute myeloid leukemia

Acute myeloid leukemia (AML) is a hematopoietic disorder in which there are too many immature blood-forming cells accumulating in the bone marrow and interfering with the production of normal blood cells. It has long been recognized that AML is a clinically heterogeneous disease characterized by a multitude of chromosomal abnormalities and gene mutations, which translate to marked differences in responses and survival following chemotherapy. The cytogenetic and molecular genetic aberrations associated with AML are not mutually exclusive and often coexist in the leukemic cells. AML is a disease of the elderly, with a mean age of diagnosis of 70 years. Adverse cytogenetic abnormalities increase with age, and within each cytogenetic group, prognosis with standard treatment worsens with age. In the past 20 years, there has been little improvement in chemotherapeutic regimens and hence the overall survival for patients with AML. A huge unmet need exists for efficacious targeted therapies for elderly patients that are less toxic than available chemotherapy regimens. The multitude of chromosomal and genetic abnormalities makes the treatment of AML a challenging prospect. A detailed understanding of the molecular changes associated with the chromosomal and genetic abnormalities in AML is likely to provide a rationale for therapy design and biomarker development. This review summarizes the variety of cytogenetic and genetic changes observed in AML and gives an overview of the clinical status of new drugs in development.

Genetic and molecular mechanisms in multiple myeloma: a route to better understand disease pathogenesis and heterogeneity

Multiple myeloma (MM) is a heterogeneous plasma cell neoplasm presenting with a wide range of clinical manifestations. In spite of the availability of very performing treatment modalities, survival is highly varying, ranging from a few months to several years. Underlying genetic and microenvironmental mechanisms are thought to be responsible for clinical heterogeneity. Disease etiology is unknown but progresses in the understanding of its pathogenesis have shown that MM precursor cell transformation into a malignant one occurs in a multistep process. Possibly during class switch recombination a primary genetic event takes place. With the occurrence of additional events and the support of bone marrow microenvironmental cells, neoplastic plasma cells actively proliferate and disease behavior may change. Recurrent translocations involving the IgH locus (11q13, 4p16, 16q23, 21q12, and 6p21), deletions of chromosome 13, trisomies of chromosomes 3, 5, 9, 11, 15, 19, and 21, and dysregulated expression of cyclin D genes, are considered initiating or primary events. Alterations related to further disease transformation and adverse prognosis are deletion of 17p13, c-myc translocations, and gains of chromosome 1q21. In relation to the underlying genetic defects, disease subgroups are recognized. Accordingly treatment effectiveness may differ among groups. Intense research is ongoing in this field.

Her-2 immunohistochemical expression in oral squamous cell carcinomas is associated with polysomy of chromosome 17, not Her-2 amplification

Based on the prognostic role of Her-2 amplification and protein overexpression in breast cancer, various studies have been performed in oral squamous cell carcinomas (OSCC) with inconsistent results. As in invasive breast carcinomas Her-2 overexpression has been related to an increased number of chromosome 17 copies, a common chromosomal alteration in OSCC, we evaluated the association between polysomy 17 and Her-2 protein expression in a series of primary OSCC. Forty-one incisional biopsies of primary OSCC were included in the study. Protein expression was evaluated immunochistochemically with CB11 mouse monoclonal anti-human antibody. The reaction was arbitrarily characterized as absent, faint, moderate, and strong, and staining pattern as cytoplasmic and membranous. Positive cases were analyzed by chromogenic in situ hybridisation (CISH) to access Her-2 status. The association between polysomy 17 and Her-2 expression was checked by Fisher's exact test. Four cases were negative and 37 cases were positive for Her-2. Staining was faint in 15 cases and moderate in 22 cases. CISH showed that all cases with faint staining were diploid, while from the cases with moderate staining 10 were diploid and 12 polysomic for chromosome 17. Thirteen cases showed purely cytoplasmic staining, while in 24 there were areas of both cytoplasmic and membranous staining. There was a statistically significant correlation between intensity of the reaction and polysomy 17 (P = 0.0036), in particular for cases with both cytoplasmic and membranous staining (P = 0.0128). In some OSCC Her-2 immunohistochemical expression may be associated with chromosome 17 polysomy and not Her-2 amplification.