Direct embryonic biopsy with transcervical embryoscopy is an effective method for karyotyping and morphology assessment in miscarriages

PURPOSE

The main purpose of this study is to compare the validity of transcervical embryoscopy method with standard uterine evacuation method in detecting more accurate karyotypes in miscarriages below tenth week of pregnancy. Additionally, the frequency and distribution of fetal morphological abnormality were evaluated.

METHODS

A prospective study was carried out at the Gazi University Faculty of Medicine, Department of Obstetrics and Gynecology. Patients with missed abortions between sixth and tenth gestational weeks were included in the study group, and fetal morphological examination and direct embryonic biopsy were performed by transcervical embryoscopy. The control group consisted of patients who experienced miscarriage and genetic material obtained from routine uterine evacuation between February and October 2023.

RESULT

A total of 60 patients in the study group and 189 patients in the control group were evaluated. The median ages, previous miscarriage numbers, median gravida numbers, and median gestational weeks were comparable between groups. Chromosomal abnormality was detected in 24 (42.8%) and 52 embryos (29.9%) in the study and control groups, respectively (p = 0.004). Culture failure rates were 6.6% (n = 4) and 7.9% (n = 15) in the study and control groups, respectively. In the study group, 12 embryos had a morphological abnormality in which 6 of them had normal karyotype.

CONCLUSION

Direct embryonic biopsy with transcervical embryoscopy is an effective method to exclude maternal decidual cell contamination and placental mosaicism in miscarriages for karyotype analysis. In addition, detecting anomalies in morphology might contribute our understanding in the process of miscarriages which arises independent from structural/numerical chromosomal abnormalities.

Meiotic drive against chromosome fusions in butterfly hybrids

Species frequently differ in the number and structure of chromosomes they harbor, but individuals that are heterozygous for chromosomal rearrangements may suffer from reduced fitness. Chromosomal rearrangements like fissions and fusions can hence serve as a mechanism for speciation between incipient lineages, but their evolution poses a paradox. How can rearrangements get fixed between populations if heterozygotes have reduced fitness? One solution is that this process predominantly occurs in small and isolated populations, where genetic drift can override natural selection. However, fixation is also more likely if a novel rearrangement is favored by a transmission bias, such as meiotic drive. Here, we investigate chromosomal transmission distortion in hybrids between two wood white (Leptidea sinapis) butterfly populations with extensive karyotype differences. Using data from two different crossing experiments, we uncover that there is a transmission bias favoring the ancestral chromosomal state for derived fusions, a result that shows that chromosome fusions actually can fix in populations despite being counteracted by meiotic drive. This means that meiotic drive not only can promote runaway chromosome number evolution and speciation, but also that it can be a conservative force acting against karyotypic change and the evolution of reproductive isolation. Based on our results, we suggest a mechanistic model for why chromosome fusion mutations may be opposed by meiotic drive and discuss factors contributing to karyotype evolution in Lepidoptera.

Noninvasive prenatal testing for the detection of fetal chromosome 17 microduplication: clinical implications and findings

BACKGROUND

 Noninvasive prenatal testing (NIPT) is widely used to screen for fetal aneuploidies. However, there are few reports of using NIPT for screening chromosomal microduplications and microdeletions. This study aimed to investigate the application efficiency of NIPT for detecting chromosomal microduplications.

METHODS

Four cases of copy number gains on the long arm of chromosome 17 (17q12) were detected using NIPT and further confirmed using copy number variation (CNV) analysis based on chromosome microarray analysis (CMA).

RESULTS

The prenatal diagnosis CMA results of the three cases showed that the microduplications in 17q12 (ranging from 1.5 to 1.9 Mb) were consistent with the NIPT results. The karyotypic analysis excluded other possible unbalanced rearrangements. The positive predictive value of NIPT for detecting chromosomal 17q12 microduplication was 75.0%.

CONCLUSIONS

 NIPT has a good screening effect on 17q12 syndrome through prenatal diagnosis, therefore it could be considered for screening fetal CNV during the second trimester. With the clinical application of NIPT, invasive prenatal diagnoses could be effectively reduced while also improving the detection rate of fetal CNV.

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution

BACKGROUND

Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.

RESULTS

Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.

CONCLUSION

Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.

A working model for the formation of Robertsonian chromosomes

Robertsonian chromosomes form by fusion of two chromosomes that have centromeres located near their ends, known as acrocentric or telocentric chromosomes. This fusion creates a new metacentric chromosome and is a major mechanism of karyotype evolution and speciation. Robertsonian chromosomes are common in nature and were first described in grasshoppers by the zoologist W. R. B. Robertson more than 100 years ago. They have since been observed in many species, including catfish, sheep, butterflies, bats, bovids, rodents and humans, and are the most common chromosomal change in mammals. Robertsonian translocations are particularly rampant in the house mouse, Mus musculus domesticus, where they exhibit meiotic drive and create reproductive isolation. Recent progress has been made in understanding how Robertsonian chromosomes form in the human genome, highlighting some of the fundamental principles of how and why these types of fusion events occur so frequently. Consequences of these fusions include infertility and Down's syndrome. In this Hypothesis, I postulate that the conditions that allow these fusions to form are threefold: (1) sequence homology on non-homologous chromosomes, often in the form of repetitive DNA; (2) recombination initiation during meiosis; and (3) physical proximity of the homologous sequences in three-dimensional space. This Hypothesis highlights the latest progress in understanding human Robertsonian translocations within the context of the broader literature on Robertsonian chromosomes.

Growth Hormone Treatment to Final Height in Turner Syndrome: Systematic Review

PURPOSE

Turner syndrome (TS) is the most common sex chromosomal abnormality found in female subjects. It is a result of a partial or complete loss of one of the X chromosomes. Short stature is a hallmark of TS. Attainment of adult height (AH) within the normal range for height within the general female population represents the usual long-term goal of growth hormone (GH) treatment. The aim of this systematic review was to understand the efficacy of GH therapy on AH of patients with TS.

METHODS

The literature review yielded for analysis 9 articles published from 2010 to 2021. Using the data from this literature search, the goal was to answer 5 questions: (1) What is the efficacy of GH on AH of girls with TS?; (2) Is AH influenced by the age at initiation of GH treatment?; (3) What is the optimal dose of GH to improve AH?; (4) Can the timing of either spontaneous or induced puberty influence AH?; and (5) Can the karyotype influence AH in patients with TS?

FINDINGS

GH therapy and adequate dose could enable patients with TS to achieve appropriate AH compared with the possible final height without therapy. The greatest increase in height during GH therapy occurs in the prepubertal years, and if therapy is continued to AH, there is no further increase. Furthermore, karyotype did not show a predictive value on height prognosis and did not affect the outcome of GH administration or the height gain in girls with TS.

IMPLICATIONS

Even if GH therapy is safe, close monitoring is indicated and recommended. Further evidence is needed to understand what other parameters may influence AH in patients undergoing GH therapy.

Hedysarumqilianshanense sp. nov. (Fabaceae, Hedysareae), a new species from the Qilianshan Mountains in Gansu, China

Hedysarumqilianshanensesp. nov. (Fabaceae, Hedysareae) is described and illustrated from the Qilianshan Mountains in Gansu, China. This new species is similar to H.przewalskii, but can be distinguished by its corolla being light purple to purple, standard 15-19 mm long, wings 14-16 mm long, keels 16-19 mm long, and the ovary and legume being glabrous. The new species can be easily distinguished from H.neglectum Ledeb. by its bract being shorter than the pedicel, and the ovary and legume being glabrous. Phylogenetic tree based on the nuclear ITS and ETS sequences shows that H.qilianshanense is sister to H.przewalskii, while the tree based on the plastid psbA-trnH, trnC-petN, trnL-F, trnS-G and petN-psbM sequences shows H.qilianshanense as sister to a clade consisting of H.hedysaroides, H.inundatum, H.americanum and H.neglectum. The new species is a diploid with the chromosome number 2n = 14. Based on morphological, phylogenetic and karyotypic evidence, the new species may originate from an ancient homoploid hybrid speciation event.

Reciprocal natural hybridization between Lycoris aurea and Lycoris radiata (Amaryllidaceae) identified by morphological, karyotypic and chloroplast genomic data

BACKGROUND

Hybridization is considered as an important model of speciation, but the evolutionary process of natural hybridization is still poorly characterized in Lycoris. To reveal the phylogenetic relationship of two new putative natural hybrids in Lycoris, morphological, karyotypic and chloroplast genomic data of four Lycoris species were analyzed in this study.

RESULTS

Two putative natural hybrids (2n = 18 = 4 m + 5t + 6st + 3 T) possessed obvious heterozygosity features of L. radiata (2n = 22 = 10t + 12st) and L. aurea (2n = 14 = 8 m + 6 T) in morphology (e.g. leaf shape and flower color), karyotype (e.g. chromosome numbers, CPD/DAPI bands, 45S rDNA-FISH signals etc.) and chloroplast genomes. Among four Lycoris species, the composition and structure features of chloroplast genomes between L. radiata and the putative natural hybrid 1 (L. hunanensis), while L. aurea and the hybrid 2, were completely the same or highly similar, respectively. However, the features of the cp genomes between L. radiata and the hybrid 2, while L. aurea and the hybrid 1, including IR-LSC/SSC boundaries, SSRs, SNPs, and SNVs etc., were significantly different, respectively. Combining the karyotypes and cp genomes analysis, we affirmed that the natural hybrid 1 originated from the natural hybridization of L. radiata (♀) × L. aurea (♂), while the natural hybrid 2 from the hybridization of L. radiata (♂) × L. aurea (♀).

CONCLUSION

The strong evidences for natural hybridization between L. radiata (2n = 22) and L. aurea (2n = 14) were found based on morphological, karyotypic and chloroplast genomic data. Their reciprocal hybridization gave rise to two new taxa (2n = 18) of Lycoris. This study revealed the origin of two new species of Lycoris and strongly supported the role of natural hybridization that facilitated lineage diversification in this genus.

Case report: Pai syndrome with multiple ventricular septal defect and without cleft palate

Pai syndrome is described as the association of a midline cleft lip, midline facial polyps, and lipoma of the central nervous system. However, only a few patients present the full triad, and most exhibit a wide spectrum of phenotypic variability. Its entire clinical spectrum is still poorly delineated and the etiology remains unknown. In this report, a newborn was presented with congenital nasal septal lipoma, lipoma of the corpus callosum, multiple ventricular septal defect, and additional minor facial dysmorphism. This entity, multiple ventricular septal defect, which has never been reported in PS. Cytogenetic analysis showed normal male 46, XY karyotype. Chromosomal microarray analysis (750 K array) was also unremarkable. This case draws attention with the presence of multiple ventricular septal defect in Pai syndrome and is important in terms of providing phenotypic diversity. To our knowledge, this is also the first genetically evaluated case of Pai syndrome from Turkey.

Chromosome analysis of 303 pregnancy losses in Mexico

BACKGROUND

Chromosomal abnormalities are present in 50 to 60% of miscarriages and in 6 to 19% of stillbirths. Although microarrays are preferred for studying chromosomal abnormalities, many hospitals cannot offer this methodology.

OBJECTIVE

To present the results of the cytogenetic analysis of 303 products of conception (POC), which included 184 miscarriages, 49 stillbirths and 17 cases of undefined age.

MATERIAL AND METHODS

Karyotyping, fluorescence in situ hybridization, short tandem repeats and microarrays were used, depending on the type of loss and available sample.

RESULTS

In 29 POCs we found maternal tissue and were eliminated from the analyses. Informative results were obtained in 250 (91.2 %)/274 cases; the karyotyping success rate was 80.7%; that of single nucleotide polymorphism microarrays, 94.5%; and that of fluorescence in situ hybridization and short tandem repeat, 100%. Cytogenetic abnormalities were observed in 57.6% of miscarriages and in 24.5% of stillbirths; 94% of total anomalies were numerical and 6% were submicroscopic.

CONCLUSIONS

Karyotyping with simultaneous short tandem repeat study to rule out contamination of maternal cells is effective for studying miscarriages; in stillbirths, microarrays are recommended.

A reliable technique for karyotyping mouse oocytes prepared by a gradual fixation/air-drying method followed by multicolour FISH

Chromosome segregation errors during oocyte meiosis increase with age and lead to aneuploidy; hence, the mechanism has been studied extensively. The mouse is the most widely used experimental animal for this purpose. However, the lack of a reliable and efficient technique for karyotyping mouse oocytes has limited comprehensive studies of chromosome-specific segregation errors in this animal model. Here, we developed a novel karyotyping technique for mouse oocytes by applying multicolour fluorescence in situ hybridisation (FISH) to chromosome slides prepared by a gradual fixation/air-drying method, which is best suited to avoid rupture of oocyte membrane and artificial loss of chromosomes. The success rate of karyotyping meiosis I and II oocytes was about 30%, which improved to over 90% when the oocytes were 'flattened' during fixation and the chromosome specimens were denatured at 4°C. When this technique was applied to the karyotyping of meiosis II oocytes from aged female mice and from young female mice injected with colchicine, more than 80% of the oocytes were successfully karyotyped and the number of chromosomes was identified on all aberrant chromosomes. In conclusion, our technique allows for the efficient and reliable karyotyping of mouse oocytes.

Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing

BACKGROUND

Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples.

RESULTS

In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data.

CONCLUSIONS

This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.

Diagnosis of 22q11.2 deletion syndrome in children with congenital heart diseases and facial dysmorphisms

Background

Congenital heart diseases (CHDs) are the leading cause of birth defects. Approximately, 30% of CHDs are related to genetic syndromes accompanied by extracardiac anomalies. Aneuploidies and 22q11.2 deletions account for majority of cases. 22q11.2 deletion involves deletion of 30-40 genes, and varying deletions in this region lead to different phenotypes. Fluorescent in situ hybridization probes span a narrow region on chromosome 22 as compared to other recent techniques like multiplex ligation probe amplification assay (MLPA) which may also identify any gene duplications if present.

Methods

Present study was a cross-sectional descriptive study. In total, 350 children with CHD reported to pediatric cardiology clinic during the study period. Of these, 60 children had associated facial dysmorphism. Out of these 60 children, 18 children had clinical phenotype characteristic of Down syndrome and hence these children were excluded from the study. Forty-two children with CHDs (conotruncal and other defects) and craniofacial features (subtle or obvious) suggestive of 22q11.2 deletion spectrum disorder were included in this study.

Results

Nineteen percent of children presenting with CHDs and facial dysmorphisms had 22q11.2 deletion syndrome. All the samples were subjected to karyotyping.

Conclusion

Metaphase FISH has been the method of choice for microdeletions. However, apart from technical challenges and longer turnaround time, FISH probes span a very narrow region in 22q11.2 chromosome (LCR22 D) and provide information about DiGeorge syndrome (DGS) only. Take home message is that patients of CHDs with facial dysmorphism should be investigated in an approach-based manner.

Klinefelter syndrome in primary care: A case and review

Reviewed here is a case of Klinefelter Syndrome (KS) diagnosed by a primary care physician after recognition of key features of KS, confirmed by karyotype, along with a discussion of factors associated with this patient's diagnosis and care. Recognition of the key features of this syndrome is important in order to provide proper screening, risk mitigation and treatment to these patients.

Comparative Cytogenetic Analysis of Diploid and Triploid Pacific Abalone, Haliotis discus hannai

INTRODUCTION

The Pacific abalone, Haliotis discus hannai, is one of the most commercially important marine shellfish in China. Cell engineering breeding is an important tool in abalone genetic breeding, and the triploids obtained through this method have high commercial value. However, current research mainly focuses on establishing induction methods and evaluating the growth traits of triploids, while there is a lack of basic research on triploid cytogenetics.

METHOD

In this study, Cytogenetic analysis of triploid Haliotis discus hannai larvae (produced by chemical treatment) and diploid larvae was performed.

RESULT

The results showed that triploid H. discus hannai had a chromosome number of 3n = 54, consisting of 30 metacentric (m) and 24 submetacentric (sm) chromosomes, while the diploids had a chromosome number of 2n = 36, consisting of 20 metacentric (m) and 16 submetacentric (sm) chromosomes. Notably, both triploids and diploids displayed variation in the number of NORs and/or their diameter. The average number of NORs in triploid was significantly higher than that in diploids (p < 0.05), but the average diameter of NORs of triploid was no significant different from that of diploid (p > 0.05). Additionally, 5S rDNA localization to 3 submetacentric chromosomes was observed in triploids, compared to 2 submetacentric chromosomes in diploids. The number of 18S rDNA sites displayed positional conservancy and quantitative variability in both diploids and triploids. Specifically, 18S rDNA was found at the end of the chromosome in both groups, with triploids exhibiting a significantly higher number of loci than diploids (p < 0.01).

CONCLUSION

This study provides valuable insights into the cytogenetic characteristics of triploid H. discus hannai, which could facilitate further research on the stability of the chromosome set in this species.

[Assessment of the man in the infertile couple]

BACKGROUND

Among couples consulting for infertility, there is a male component, either alone or associated with a female aetiology in around one in 2 cases.

MATERIAL AND METHODS

Bibliographic search in PubMed using the keywords "male infertility", "diagnosis", "management" and "evaluation" limited to clinical articles in English and French prior to 1/01/2023.

RESULTS

The AFU recommends: (1) a complete medical history including: family history, patient history affecting fertility, lifestyle habits (toxicity), treatments, symptoms, sexual dysfunctions; (2) a physical examination including: BMI, signs of hypogonadism, secondary sexual characteristics, scrotal examination (volume and consistency of testes, vas deferens, epididymal or testicular nodules, presence of varicocele); (3) two spermograms, if abnormal on the first; (4) a systematic scrotal ultrasound,± an endorectal ultrasound depending on the clinic; (5) a hormonal work-up (testosterone, FSH; if testosterone is low: LH assay to differentiate between central or peripheral hypogonadism); (6) karyotype if sperm concentration≤10 million/mL; (7) evaluation of Y chromosome microdeletions if concentration≤1 million/mL; (8) evaluation of the CFTR gene in cases of suspected bilateral or unilateral agenesis of the vas deferens and seminal vesicles. The role and usefulness of direct and indirect tests to assess the effects of oxidative stress on sperm DNA will also be explained.

CONCLUSION

This review complements and updates the AFU/SALF 2021 recommendations.

Ovotesticular disorder of sex development in a 46 XY adolescent: a rare case report with review of the literature

INTRODUCTION

Ovotestis is a rare cause of sexual ambiguity characterized by the presence in a patient of both testicular and ovarian tissue, leading to the development of both male and female structures. We report a case of ovotestis diagnosed in an adolescent, with a review of the literature.

CASE REPORT

A 15-year-old patient presented with a right scrotal swelling associated with gynecomastia. Histology showed a juxtaposition of ovarian stroma with ovarian follicle and seminiferous tubules. Karyotype revealed a male subject (XY). We have therefore retained the diagnosis of ovotesticular disorders of sex development.

CONCLUSION

Ovotestis is a rare finding, heterogeneous in its genetic etiology and clinical presentation. While many patients are diagnosed during infancy or childhood, we presented a case diagnosed in a 15-year-old adolescent.

Chromosome analysis and the occurrence of B chromosomes in fish parasite Acanthocephalus anguillae (Palaeacanthocephala: Echinorhynchida)

The cytogenetics of Acanthocephala is a neglected area in the study of this group of endoparasites. Chromosome number and/or karyotypes are known for only 12 of the 1,270 described species, and molecular cytogenetic data are limited to rDNA mapping in two species. The standard karyological technique and mapping of 18S rRNA and H3 histone genes on the chromosomes of Acanthocephalus anguillae individuals from three populations, one of which originated from the unfavorable environmental conditions of the Zemplínska Šírava reservoir in eastern Slovakia, were applied for the first time. All specimens had 2n = 7/8 (male/female); n = 1m + 1m-sm + 1a + 1a (X). Fluorescence in situ hybridization (FISH) revealed three loci of 18S rDNA on two autosomes and dispersion of H3 histone genes on all autosomes and the X chromosome. In addition to the standard A chromosome set, 34% of specimens from Zemplínska Šírava possessed a small acrocentric B chromosome, which was always found to be univalent, with no pairing observed between the B chromosome and the A complement. The B chromosome had a small amount of heterochromatin in the centromeric and telomeric regions of the chromosomal arms and showed two clusters of H3 genes. It is well known that an environment permanently polluted with chemicals leads to an increased incidence of chromosomal rearrangements. As a possible scenario for the B chromosome origin, we propose chromosomal breaks due to the mutagenic effect of pollutants in the aquatic environment. The results are discussed in comparison with previous chromosome data from Echinorhynchida species.

Fecundity, in vitro early larval development and karyotype of the zoonotic nematode Anisakis pegreffii

The in vitro life cycle of zoonotic helminths is an essential tool for -omic translational studies focused on disease control and treatment. Anisakiosis is an emerging zoonosis contracted by the ingestion of raw or undercooked fish infected with the third stage larvae (L3) of two sibling species Anisakis simplex sensu stricto (s.s.) and Anisakis pegreffii, the latter being the predominant species in the Mediterranean basin. Recently, in vitro culture of A. pegreffii has been developed to enable fast and large-scale production of fertile adults. However, the conditions for larval development from hatching to infective L3 were not fulfilled to complete the cycle. Herein, we used a Drosophila medium supplemented with chicken serum and adjusted different osmolarities to maintain the culture of L3 hatched from eggs for up to 17 weeks. The highest survival rate was observed in the medium with the highest osmolarities, which also allowed the highest larval exsheathment rate. Key morphological features of embryogenesis and postembryogenesis studied by transmission electron microscopy revealed that the excretory gland cell is differentiated already up to 48 h post-hatching. Extracellular vesicles and cell-free mitochondria are discharged between the two cuticle sheets of the second stage larvae (L2). Contemporarly cultivated, two populations of adult A. simplex s.s. and A. pegreffii reached an average production of 29,914.05 (± 27,629.36) and 24,370.96 (± 12,564.86) eggs/day/female, respectively. The chromosome spreads of A. pegreffii obtained from mature gonads suggests a diploid karyotype formula of 2n = 18. The development of a reliable protocol for the in vitro culture of a polyxenous nematode such as Anisakis spp. will serve to screen for much needed novel drug targets, but also to study the intricated and unknown ecological and physiological traits of these trophically transmitted marine nematodes.

Cytogenetics in the management of T-cell acute lymphoblastic leukemia (T-ALL): Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH)

Molecular analysis is the hallmark of T-cell acute lymphoblastic leukemia (T-ALL) categorization. Several T-ALL sub-groups are well recognized based on the aberrant expression of specific transcription factors. This recently resulted in the implementation of eight provisional T-ALL entities into the novel 2022 International Consensus Classification, albeit not into the updated World Health Organization classification system. Despite this extensive molecular characterization, cytogenetic analysis remains the backbone of T-ALL diagnosis in many countries as chromosome banding analysis and fluorescence in situ hybridization are relatively inexpensive techniques to obtain results of diagnostic, prognostic and therapeutic interest. Here, we provide an overview of recurrent chromosomal abnormalities detectable in T-ALL patients and propose guidelines regarding their detection. By referring in parallel to the more general molecular classification approach, we hope to offer a diagnostic framework useful in a broad clinical genetic setting.

Cytogenetics in the management of mature B-cell non-Hodgkin lymphomas: Guidelines from the Groupe Francophone de Cytogénétique Hematologique (GFCH)

Non-Hodgkin lymphomas (NHL) consist of a wide range of clinically, phenotypically and genetically distinct neoplasms. The accurate diagnosis of mature B-cell non-Hodgkin lymphoma relies on a multidisciplinary approach that integrates morphological, phenotypical and genetic characteristics together with clinical features. Cytogenetic analyses remain an essential part of the diagnostic workup for mature B-cell lymphomas. Karyotyping is particularly useful to identify hallmark translocations, typical cytogenetic signatures as well as complex karyotypes, all bringing valuable diagnostic and/or prognostic information. Besides the well-known recurrent chromosomal abnormalities such as, for example, t(14;18)(q32;q21)/IGH::BCL2 in follicular lymphoma, recent evidences support a prognostic significance of complex karyotype in mantle cell lymphoma and Waldenström macroglobulinemia. Fluorescence In Situ Hybridization is also a key analysis playing a central role in disease identification, especially in genetically-defined entities, but also in predicting transformation risk or prognostication. This can be exemplified by the pivotal role of MYC, BCL2 and/or BCL6 rearrangements in the diagnostic of aggressive or large B-cell lymphomas. This work relies on the World Health Organization and the International Consensus Classification of hematolymphoid tumors together with the recent cytogenetic advances. Here, we review the various chromosomal abnormalities that delineate well-established mature B-cell non-Hodgkin lymphoma entities as well as newly recognized genetic subtypes and provide cytogenetic guidelines for the diagnostic management of mature B-cell lymphomas.

Swyer Syndrome: A Case Report

Swyer syndrome is a rare form of primary amenorrhea resulting from gonadal dysgenesis. It is characterized by the presence of a female phenotype with a 46, XY karyotype. In our case, CT scans revealed the absence of the uterus and bilateral ovaries of the 16-year-old female patient. Calcific nodules were found in both inguinal areas, which were suspected to be calcified atrophic testes. A chromosomal study confirmed the diagnosis of Swyer syndrome. Herein, we report a rare case of Swyer syndrome.

Multiparametric Flow Cytometry in Newly Diagnosed Multiple Myeloma Patients: An Italian Monocentric Experience

Multiple myeloma (MM) is a heterogeneous malignancy characterized by the proliferation of abnormal plasma cells in the bone marrow. Multiparametric flow cytometry (MFC) plays a role in the work-up of the disease in view of the aberrant expression of surface antigens. Our study aimed at describing the antigenic profile detected by MFC in a series of newly diagnosed MM patients to correlate the level of expression with other features of the disease. Between April 2018 and June 2022, 84 consecutive MM patients were studied at presentation. CD56 and CD117 were commonly detected, while CD45, CD28, CD20, CD19, CD13 and CD33 were less recurrent. CD20 expression was associated with the type of secretory MM (p=0.041) and with a higher disease burden (p=0.038). CD28 positivity correlated with a lower platelet count at baseline (p=0.005) and with a lower rate of complete response (p=0.038). Furthermore, CD28 positivity and a lower CD138 expression tended to associate with the high-risk chromosomal translocations t(14;16) and t(4;14). The results of this study indicate that in the diagnostic work-up of MM, MFC may help to identify different patient subsets and improve risk stratification. These observations need to be validated in larger series of patients with a longer follow-up.

High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

BACKGROUND

Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics.

RESULTS

The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function.

CONCLUSIONS

Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).

Unique Roberts syndrome with bilateral congenital glaucoma: A case report

BACKGROUND

Congenital glaucoma associated with Roberts syndrome (RS) is an unusual and unique condition. No previous report describes this association. A multidisciplinary approach including molecular studies were conducted to reach the final diagnosis.

CASE SUMMARY

We present a rare case of a 1-wk-old male with RS associated with bilateral congenital glaucoma, left ectopic kidney, and left-hand rudimentary digits. A comprehensive approach was applied by which bilateral non-penetrating glaucoma surgery was performed with good control of intraocular pressure for more than 6 mo. Cytogenetic and molecular testing were conducted and revealed normal measurements.

CONCLUSION

This report described a case of a male baby with clinical features of RS but with a negative molecular analysis, presenting with left-hand rudimentary digits, bilateral congenital glaucoma, and left ectopic kidney. To the best of our knowledge, this is the first case reported with phocomelia, bilateral congenital glaucoma, and unilateral ectopic kidney.

Monorchidism in a Phenotypic Mare With a 64,XY, SRY-Positive Karyotype

Disorders of sexual development (DSD) are associated with atypical chromosomal, gonadal, or phenotypic sex. It is likely that the number of cases of DSD are underestimated in the equine population. Monorchidism in the horse is very rare. This case report describes the clinical assessment of a phenotypic mare with stallion-like behavior which led to the diagnosis of a DSD. A 4-year-old Quarter Horse mare presented in good body condition, with normal external genitalia for a mare, and normal mammary glands with two bilaterally symmetric teats. No uterus, cervix, or gonads were detected on transrectal palpation. Transrectal ultrasonography revealed a single gonad in the right dorsal abdomen with the morphologic appearance of a testicle. Presurgical hormonal evaluation revealed elevated serum testosterone and anti-Müllerian hormone (AMH) concentrations. The right gonad was successfully removed via standing exploratory laparoscopy and submitted for histopathology. No gonad was identified on the left side during laparoscopy. Histopathologic examination confirmed that the excised gonad was a testicle. Cytogenetic and molecular analysis revealed a 64,XY, SRY-positive chromosomal constitution. Hormonal evaluation 5 weeks after surgery revealed low serum testosterone and AMH levels. A diagnosis of monorchidism was based on ultrasound examination, laparoscopic exploration of the abdomen, removal of a single gonad, and a subsequent decrease in serum testosterone and AMH concentrations to basal levels. In summary, a combination of clinical signs, endocrine evaluation, chromosomal and molecular analysis, and histopathology can be used in the diagnosis of DSD conditions.

Exploration of Parascaris species in three different Equus populations in China

BACKGROUND

The roundworms, Parascaris spp., are important nematode parasites of foals and were historically model organisms in the field of cell biology, leading to many important discoveries. According to karyotype, ascarids in Equus are commonly divided into Parascaris univalens (2n = 2) and Parascaris equorum (2n = 4).

METHODS

Here, we performed morphological identification, karyotyping and sequencing of roundworms from three different hosts (horses, zebras and donkeys). Phylogenetic analysis was performed to study the divergence of these ascarids based on cytochrome c oxidase subunit I (COI) and internal transcribed spacer (ITS) sequences.

RESULTS

Karyotyping, performed on eggs recovered from worms of three different Equus hosts in China, showed two different karyotypes (2n = 2 in P. univalens collected from horses and zebras; 2n = 6 in Parascaris sp. collected from donkeys). There are some differences in the terminal part of the spicula between P. univalens (concave) and Parascaris sp. (rounded). Additionally, it was found that the egg's chitinous layer was significantly thicker in Parascaris sp. (> 5 μm) than P. univalens (< 5 μm) (F₍₂₅₃₇₎ = 1967, P < 0.01). Phylogenetic trees showed that the sequences of Parascaris from Equus hosts were divided into two distinct lineages based on sequences of the COI and ITS.

CONCLUSIONS

Comparing the differences in roundworms collected from three different Equus hosts, this study describes a Parascaris species (Parascaris sp.) with six chromosomes in donkeys. It is worth noting that the thickness of the chitinous layer in the Parascaris egg may serve as a diagnostic indicator to distinguish the two roundworms (P. univalens and Parascaris sp.). The Parascaris sp. with six chromosomes in donkeys in the present study may be a species of P. trivalens described in 1934, but the possibility that it is a new Parascaris species cannot be ruled out. Both karyotyping and molecular analysis are necessary to solve the taxonomic problems in Parascaris species.

Chromosomal aberrations and prognostic analysis of secondary acute myeloid leukemia-a retrospective study

Background

Secondary acute myeloid leukemia (S-AML) patients generally have a poor prognosis, but the chromosomal aberrations of S-AML have been rarely reported. We aimed to explore the chromosomal aberrations and clinical significance in patients with S-AML.

Patients and methods

The clinical characteristics and karyotypes of 26 patients with S-AML were retrospectively analyzed. The overall survival (OS) was measured from the time of the patients' transition to AML (i.e., at S-AML diagnosis).

Results

The study included 26 S-AML patients (13 males and 13 females), with a median age of 63 years (range, 20-77 years). They transformed from various hematologic malignancies or solid tumors; most of them were secondary to myelodysplastic syndrome (MDS). About 62% of the S-AML patients showed chromosomal aberrations. The serum lactate dehydrogenase (LDH) level in S-AML patients with abnormal karyotype was higher than those with normal karyotype. Apart from the differences in treatment regimens, S-AML patients with chromosomal aberrations had shorter OS (P < 0.05).

Conclusion

S-AML patients with abnormal karyotype have higher LDH levels and shorter OS than normal karyotype patients, and the OS of hypodiploidy was much shorter than hyperdiploid.

Assessing ploidy levels and karyotype structure of the fire ant Solenopsissaevissima Smith, 1855 (Hymenoptera, Formicidae, Myrmicinae)

The family Formicidae is composed of ants that organize themselves into castes in which every individual has a joint organizational function. Solenopsis Westwood, 1840 is an ant genus with opportunistic and aggressive characteristics, known for being invasive species and stings that cause burning in humans. This genus is particularly difficult to classify and identify since its morphology provides few indications for species differentiation. For this, a tool that has been useful for evolutionary and taxonomic studies is cytogenetics. Here, we cytogenetically studied Solenopsissaevissima Smith, 1855 from Ouro Preto, Minas Gerais, Brazil. We evaluated the occurrence of polyploid cells in individuals and colonies by conventional cytogenetics. A total of 450 metaphases were analyzed and counted. Chromosome counts of individuals and colonies showed varied numbers of ploidies, from n = 16 to 8n = 128. The karyomorphometrical approach allowed determination of the following karyotypes: n = 10 m + 4 sm + 2 st, 2n = 20 m + 8 sm + 4 st, and 4n = 40 m + 16 sm + 8 st. Polyploidy can be found naturally in individuals and colonies and may represent an adaptative trait related to widespread distribution and invasion ability of new habitats.

From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci

There is a growing need of alternative experimental models that avoid or minimize the use of animals due to ethical, economical, and scientific reasons. Surprisingly, the stable embryonic cell lines representing Nothobranchius spp., emerging vertebrate models in aging research, regenerative medicine, ecotoxicology, or genomics, have been not derived so far. This paper reports establishment and deep characterization of ten continuous cell lines from annual killifish embryos of N. furzeri and N. kadleci. The established cell lines exhibited mostly fibroblast- and epithelial-like morphology and steady growth rates with cell doubling time ranging from 27 to 40 h. All cell lines retained very similar characteristics even after continuous subcultivation (more than 100 passages) and extended storage in liquid nitrogen (∼3 years). The cytogenetic analysis of the cell lines revealed a diploid chromosome number mostly equal to 38 elements (i.e., the native chromosome count for both killifish species), with minor but diverse line/passage-specific karyotype changes compared to the patterns observed in non-cultured N. furzeri and N. kadleci somatic cells. Based on transcriptional analysis of marker genes, the cell lines displayed features of an undifferentiated state without signs of senescence even in advanced passages. We confirmed that the cell lines are transfectable and can form viable 3-D spheroids. The applicability of the cell lines for (eco)toxicological surveys was confirmed by assessing the effect of cytotoxic and growth inhibitory agents. Properties of established Nothobranchius embryonic cell lines open new possibilities for the application of this model in various fields of life sciences including molecular mechanisms of aging, karyotype (in)stability or differences in lifespan.

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

BACKGROUND

Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining.

RESULTS

We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids.

CONCLUSIONS

Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.

Integrated genetic profiling of archival pediatric high-grade glial tumors and reassessment with 2021 WHO classification of paediatric CNS tumours

Though rare, pediatric high-grade gliomas (pHGG) are a leading cause of cancer-related mortality in children. We wanted to determine whether our currently available clinical laboratory methods could better define diagnosis for pHGG that had been archived at our institution for the past 20 years (1998 to 2017). We investigated 33 formalin-fixed paraffin-embedded pHGG using ThermoFisher Oncoscan SNP microarray with somatic mutation analysis, Sanger sequencing, and whole genome sequencing. These data were correlated with historical histopathological, chromosomal, clinical, and radiological data. Tumors were subsequently classified according to the 2021 WHO Classification of Paediatric CNS Tumours. All 33 tumors were found to have genetic aberrations that placed them within a 2021 WHO subtype and/or provided prognostic information; 6 tumors were upgraded from WHO CNS grade 3 to grade 4. New pHGG genetic features were found including two small cell glioblastomas with H3 G34 mutations not previously described; one tumor with STRN-NTRK2 fusion; and a congenital diffuse leptomeningeal glioneuronal tumor without a chromosomal 1p deletion but with KIAA1549-BRAF fusion. Overall, the combination of laboratory methods yielded key information for tumor classification. Thus, even small studies of these uncommon tumor types may yield new genetic features and possible new subtypes that warrant future investigations.

Cytogenetic Analysis of the Fungus-Farming Ant Cyphomyrmex rimosus (Spinola, 1851) (Formicidae: Myrmicinae: Attini) Highlights Karyotypic Variation

The fungus-farming ant genus Cyphomyrmex (subtribe Attina, clade Neoattina) comprises 23 described species that are widely distributed throughout the Neotropics. Species within Cyphomyrmex have taxonomic issues such as Cyphomyrmex rimosus (Spinola, 1851) which is likely a species complex. Cytogenetics is a useful tool for evolutionary studies and understanding species with dubious taxonomy. In this study, we characterized the karyotype of C. rimosus from Viçosa, Minas Gerais State, southeastern Brazil using classical and molecular cytogenetic techniques to enrich the chromosomal information about Cyphomyrmex. The karyotype of C. rimosus from the rainforest of southeastern Brazil (2n = 22, 18m + 4sm) notably contrasts with that previously described for this species in Panama (2n = 32). This intraspecific chromosomal variation suggests the existence of a species complex within this taxon according to the previous hypothesis derived from morphological analysis. We detected GC-rich heterochromatic regions in C. rimosus and, using repetitive DNA probes, showed that this heterochromatin shares repetitive sequences with other Neoattina species already studied, enhancing the importance of this specific genome region in the understanding of Attina evolution. Mapping of microsatellite (GA)15 on C. rimosus was restricted to the euchromatic regions of all chromosomes. The single intrachromosomal rDNA sites observed in C. rimosus follow the general genomic organization trend of ribosomal genes in Formicidae. Our study extends the data of chromosome mapping on Cyphomyrmex and reinforces the importance of cytogenetic studies in different localities to better understand taxonomic issues in widely distributed taxa such as C. rimosus.

Prenatal diagnosis of ultrasound soft markers in a single medical center of mainland China

BACKGROUND

There are a few studies on the chromosomal aberration of Ultrasound soft markers (USMs). The aim of this study was to determine the detection rate of clinically significant chromosomal abnormalities (CSCA) in fetuses with different USMs.

METHODS

This study included fetuses with USMs who underwent invasive prenatal diagnosis for karyotype and/or chromosomal microarray (CMA) by categorizing into two groups: a single USM (SUSM) and multiple USMs (MUSMs).

RESULTS

Of the 358 cases with USMs, CSCA occurred in 3.09% (8/259) and 8.08% (8/99) of the SUSM and MUSM groups, respectively (P < 0.05). Of 16 cases identified with CSCA, theoretically 68.75% (11/16) could be detected by karyotype, while 31.25% (5/16) could be recognized only by CMA. Among CSCA cases, the most frequent USM was an absent or hypoplastic nasal bone (62.5%, 10/16). In cases with negative karyotypes and/or CMA, follow-up results were available in 307 cases, including 292 term deliveries, 6 preterm deliveries, 8 terminations of pregnancy due to USMs, and 1 still birth.

CONCLUSION

MUSMs increased the risk of chromosomal abnormalities. An absent or hypoplastic nasal bone was the most clinically significant marker either alone or in combination with other USMs. Most of SUSM had a good prognosis.

Array study in fetuses with nuchal translucency above the 95th percentile: a 4-year observational single-centre study

PURPOSE

To evaluate the performance of chromosomal microarray analysis (CMA) in fetuses with nuchal translucency (NT) > 95th percentile. Secondary objectives were to analyze these results according to NT thickness, below or above 3.5 mm, and those without associated anomalies.

METHODS

This observational single-cohort study was conducted between 2015 and 2018 in fetuses with NT > 95th percentile. Following an invasive test, quantitative fluorescence-polymerase chain reaction (QF-PCR) was performed, and if normal, CMA was performed. Pathogenic copy number variants (CNVs), non-reported pathogenic CNV, pathogenic autosomal recessive variants and variants of unknown significance (VUS) were analysed.

RESULTS

One-hundred and sixty-two fetuses with NT > 95th percentile, normal QF-PCR and CMA were included. Amongst 128 fetuses with NT between the 95th percentile and 3.5 mm, one (0.8%) had a pathogenic CNV, four (3.1%) had non-reported pathogenic CNV, one (0.8%) had pathogenic autosomal recessive variant and 13 (10.2%) had VUS. Amongst 34 fetuses with NT ≥ 3.5 mm, four (11.8%) had pathogenic CNV, one (2.9%) had non-reported pathogenic CNV, one (2.9%) had pathogenic autosomal recessive variant and four (11.8%) had VUS. Four in 162 (2.5%) fetuses had CNVs at the chromosome 16p13.11 region. Amongst 154 fetuses without structural abnormalities and normal QF-PCR, three (1.9%) had a pathogenic CNV, 5 (3.2%) had non-reported pathogenic CNV, one (0.6%) autosomal recessive pathogenic CNV and 16 (10.4%) had VUS.

CONCLUSION

Pathogenic CNVs were found in 1% of fetuses with an NT thickness between the 95^th percentile and 3.5 mm and in 12% of fetuses with NT ≥ 3.5 mm. CNVs were found at the 16p13.11 region in 2.5% of cases.

Release 4.0 of the Plant rDNA Database: A Database on Plant Ribosomal DNA Loci Number, Their Position, and Organization: An Information Source for Comparative Cytogenetics

This paper presents the latest update to the Plant rDNA database (Release 4.0), a valuable resource for researchers in the field of plant cytogenetics. The database provides information on the number, position, and arrangement of ribosomal DNA loci in plants, including angiosperms, gymnosperms, bryophytes, and pteridophytes. The new release includes new data for 820 species coming from additional 173 papers. In the updated version of the Plant rDNA database, 4948 entries comprising 2760 organisms can be found. A brief guide on how to navigate the database and obtain the desired information is also provided. The regular updating of the database is important for ensuring the information it contains is accurate, up-to-date, and useful for the research community. The Plant rDNA database continues to be beneficial for phylogenetic and cytogenetic studies in a wide range of taxa including angiosperms, gymnosperms, and early diverging groups, such as bryophytes and lycophytes.

Bridging the Gap between AZF Microdeletions and Karyotype: Twelve Years' Experience of an Infertility Center

PURPOSE

Despite all past efforts, the current guidelines are not explicit enough regarding the indications for performing azoospermia factor (AZF) screening and karyotype, burdening clinicians with the decision to assess whether such tests are meaningful for the infertile male patient. These assessments can be costly and it is up to the healthcare practitioner to decide which are necessary and to weigh the benefits against economic/psychological harm. The aim of this study is to address such gaps and provide update on current management options for this group of patients.

MATERIALS AND METHODS

To address such gaps in male infertility management and to elucidate whether AZF screening is indicated in individuals who concomitantly harbor chromosomal abnormalities we conducted a retrospective cohort analysis of 10,388 consecutive patients with non-obstructive azoospermia (NOA) and severe oligozoospermia.

RESULTS

Previously, it has been suggested that all NOA cases with chromosomal defects, except males with 46,XY/45,X karyotype, have no indication for AZF screening. Our findings revealed that cases carrying the following chromosomal abnormalities inv(Y)(p11.2q12); idic(Y)(q11.2); 46,XY,r(Y); idic(Y)(p11.2) and der(Y;Autosome) (76/169; 44.9%; 95% CI, 37.7-52.5) should also be referred for AZF deletion screening. Here, we also report the correlation between sperm count and AZF deletions as a secondary outcome. In accordance with previously reported data from North America and Europe, our data revealed that only 1% of cases with >1×10⁶ sperm/mL had Y chromosome microdeletions (YCMs).

CONCLUSIONS

In the era of assisted reproduction, finding cost-minimization strategies in infertility clinics without affecting the quality of diagnosis is becoming one of the top prioritized topics for future research. From a diagnostic viewpoint, the results reflect a need to reconsider the different karyotype presentations and the sperm count thresholds in male infertility guidelines as indicators for YCM screening during an infertility evaluation.

South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent

Chromosome numbers have been used in plant taxonomy, and they are still fundamental for taxon delimitation and genome evolution studies. South America is one of the most diverse continents in terms of plant species and there is a considerable number of species not yet analyzed. Accumulated knowledge about plant chromosome numbers has been compiled from online databases, and here we present an overview. The CCDB is one of the largest plant cytological databases and includes data for around 18% of known vascular plants in the world. In this work, we review the information contained in CCDB and in three databases with exclusive information for South America. At present, the three existing databases comprise information on around 1800 plant taxa related to specific regions, countries, or biomes. Efforts are necessary to expand cytological knowledge and to collect all the available information in a plant chromosome database for this continent.

First Update to B-Chrom: A Database on B-Chromosomes

The supernumerary mostly dispensable B chromosomes are nuclear components of about 15% of eukaryotic phyla. For a long time, B chromosomes have been studied, generating an enormous bulk of knowledge, diluted in the vastness of the scientific literature. In order to provide better access to this information, we created B-chrom ( www.bchrom.csic.es ), an online database with comprehensive information on Bs for plants, animals, and fungi. It was released in 2017 and first updated in 2021, by adding 334 entries and 123 new species. Currently, the resource provides information for 2951 species coming from 3292 sources. During this time, the usefulness of this database has been proven by the number of visits (more than 207,000 since its release) and by the scientific community, having been cited in more than 60 publications until present. This chapter explains the database composition and tips on how to use it.

Online Resources Useful for Plant Cytogenetics and Cytogenomics Research

The advancements in research in the field of plant cytogenetics and genomics in recent decades have led to a significant increase in publications. To simplify access to the widely dispersed data, there has been a rise in the number of online databases, repositories, and analytical tools. This chapter presents a comprehensive overview of these resources, which can be beneficial to researchers in these areas. It includes, among others, databases on chromosome numbers, special chromosomes (such as B chromosomes or sex chromosomes), some of which are taxon-specific; genome sizes, cytogenetics; and online applications and tools for genomic analysis and visualization.

First Trimester Screening Tests Pregnancy and Trisomy 13 Syndrome, Sex Chromosome Aneuploidy in Iran: A Cross-Sectional Study

BACKGROUND

Trisomy 13 (T13) and sex chromosome aneuploidies (SCA) are the vital causes of congenital malformations. This study was performed to identify the T13 and SCA with screening tests in the first trimester of pregnancy.

MATERIALS AND METHODS

In this cross-sectional study, first-trimester combined screening was conducted on 2100 pregnant women referred to Narges Genetics Laboratory, Ahvaz, Iran. Evaluating the first trimester screening tests, including nuchal translucency (NT), crown-rump length (CRL) and pregnancy-associated plasma protein-A (PAPP-A), and free beta of human chorionic gonadotropin (fβhCG) was performed. For a definitive diagnosis of T13 and SCA syndrome, fetal karyotype was evaluated.

RESULTS

The average NT and CRL in high-risk group for T13 were 5.96 mm and 61.7 mm respectively and in high-risk groups for SCA were 3.7 mm and 75.9 mm, respectively. Significant correlation was observed among NT, CRL and T13, SCA (P<0.05). The average serum fβhCG and PAAP-A levels in high-risk group for T13 were 0.42 and 0.31, respectively. Significant correlation was observed between decrease fβhCG, PAPP-A and T13 levels and increase fβhCG levels and SCA levels (P<0.05). No Significant correlation was observed between PAPP-A levels and SCA levels (P>0.05).

CONCLUSION

Using special software and karyotype testing, the prenatal screening tests based on the maternal age and gestational age in the first trimester of pregnancy may determine the major risk of fetal chromosomal abnormalities.

Plant Cytogenetics: From Chromosomes to Cytogenomics

Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical development of preparation methods, microscopes, and chemicals to stain them, with latest continuing developments described in this volume. At the end of the twentieth and beginning of the twenty-first centuries, DNA technology, genome sequencing, and bioinformatics have revolutionized how we see, use, and analyze chromosomes. The advent of in situ hybridization has shaped our understanding of genome organization and behavior by linking molecular sequence information with the physical location along chromosomes and genomes. Microscopy is the best technique to accurately determine chromosome number. Many features of chromosomes in interphase nuclei or pairing and disjunction at meiosis, involving physical movement of chromosomes, can only be studied by microscopy. In situ hybridization is the method of choice to characterize the abundance and chromosomal distribution of repetitive sequences that make up the majority of most plant genomes. These most variable components of a genome are found to be species- and occasionally chromosome-specific and give information about evolution and phylogeny. Multicolor fluorescence hybridization and large pools of BAC or synthetic probes can paint chromosomes and we can follow them through evolution involving hybridization, polyploidization, and rearrangements, important at a time when structural variations in the genome are being increasingly recognized. This volume discusses many of the most recent developments in the field of plant cytogenetics and gives carefully compiled protocols and useful resources.

The Use of Ribosomal DNA for Comparative Cytogenetics

Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA₃ banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.

Chilean Plants Cytogenetic Database: An Online Resource for Embryophytes of the Southern Cone

Chilean Plants Cytogenetic Database (CPCD) is a resource available online in electronic format, providing a cytogenetics catalog for continental and insular Chilean plants that are representative of the floras of the Southern Cone. In the last update carried out in 2021, we increased the cytogenetic data for 499 Chilean native species, and from here on we will include a new section with chromosome number data for 683 exotic species classified as invaders in Chile. Aspects on the coverage, features, and uses of the CPCD are presented here, including background information accumulated since its inception in 2010 to the present. With the new update, the database currently stores cytogenetic information for species belonging to the divisions Bryophyta, Pteridophyta, Pinophyta, and Magnoliophyta, thus contributing to the largest community resource on plant cytogenetics in the world.

Study of the biological characteristics of human umbilical cord mesenchymal stem cells after long-time cryopreservation

Human umbilical cord mesenchymal stem cells (hUC-MSCs) have considerable potential in cell therapy. Cryopreservation represents the gold standard in cell storage, but its effect on hUC-MSCs is still not well understood. The aim of this study was to investigate the effect of one year of cryopreservation and thawing on the biological characteristics of hUC-MSCs from the same donors. Fresh hUC-MSCs were cryopreserved in commercial freezing medium (serum-free CellBanker 2) at passage 2. After one year of cryopreservation, the hUC-MSCs were thawed and subcultured to passage 4. The comparison was performed in terms of followings: cell count, viability, morphology, proliferation capacity, differentiation potential and chromosomal stability. The total cell count and viability of hUC-MSCs before and after one year of cryopreservation were 1 × 107 and 96.34% and 0.943 × 107 and 93.81%, respectively. Cryopreserved and fresh hUC-MSCs displayed a similar cell doubling times, expressed the markers CD73, CD90, CD105 and were negative for the markers CD34, CD45, and HLA-DR. Karyotypes were found to be normal after one year of cryopreservation. The trilineage differentiation properties were maintained after cryopreservation. However, when compared to freshly isolated hUC-MSCs from the same donor, cryopreserved hUC-MSCs exhibited decreased expression of osteogenesis- and chondrogenesis-related genes including Runx2, Sox9, and Col1a1, and increased expression of adipogenesis-related genes. These results demonstrated that cryopreservation did not affect cell morphology, surface marker expression, cell viability, proliferative capacity, or chromosomal stability. However, the osteogenic and chondrogenic differentiation capacities of cryopreserved hUC-MSCs were slightly reduced compared with those of fresh cells from the same donor.

Karyotyping of Lymphocytes and Epithelial Cells of Distinct Embryonic Origin Does Not Help to Predict the Turner Syndrome Features

BACKGROUND

In Turner syndrome (TS), fluorescent in situ hybridization (FISH) karyotyping offers an alternative to classical karyotyping.

OBJECTIVE

We tested the added value of FISH karyotyping from lymphocytes (mesodermal origin), buccal cells (ectodermal origin), and a rear-tongue smear (endodermal origin) to determine the 45,X cell line fraction and its impact on patient phenotype.

DESIGN AND PATIENTS

Classical karyotyping and three FISH assays were done in 153 girls and women previously diagnosed with TS in four university hospitals. The 45,X cell line fraction was determined for each method and correlated with the major phenotypic signs.

RESULTS

Classical karyotyping identified 45,X/46,XX mosaicism in 77/153 subjects (50%), 45,X monosomy in 52/153 (34%), and other karyotypes in 24/153 (16%). FISH from lymphocytes verified 45,X in 47/52 original cases, whereas 4/52 had 45,X/46,XX and 1/52 45,X/47,XYY mosaicism. The 45,X cell line fraction was higher in FISH from lymphocytes compared to classical karyotyping (median 86.4% vs. 70.0%; p < 0.001), while there was no difference for FISH from buccal or rear-tongue smear cells. The mean 45,X cell line fraction was more abundant in patients with several of the characteristic phenotypic signs compared to patients without them (p < 0.01), but the predictive power was insufficient.

CONCLUSION

FISH analysis confirmed the findings of classical karyotyping; only a few 45,X monosomy cases were reclassified as mosaics. The 45,X cell line fraction did not show clinically meaningful prediction of the phenotype. FISH analysis of buccal or rear-tongue epithelial cells may be a non-inferior, less invasive alternative to classical karyotyping.

Molecular evaluation of gene mutation profiles and copy number variations in pediatric acute myeloid leukemia

BACKGROUND

The objectives of this study were to investigate the mutation profiles of targeted genes and copy number variations (CNVs) in normal cytogenetics (CN) pediatric acute myeloid leukemia (AML).

METHODS

This prospective study was conducted from October 2018 to December 2020. The next-generation sequencing (NGS) and chromosomal microarray analyses (CMA) were performed in pediatric CN-AML patients.

RESULTS

Out of 94 children (aged ≤18 years), 70 patients with AML (24 excluded) underwent conventional karyotyping/cytogenetic analyses. Forty-five (64.3%) of patients had abnormal/ recurrent cytogenetic abnormalities and 25 (35.7%) had normal cytogenetics. Twenty-three out of 25 CN-AML were further processed for gene mutation profile and CNVs using NGS and CMA, respectively. Twenty-two out of 23 (95.7%) patients were detected to have mutations in various genes. The common mutations were: NRAS, NPM1, CEBPA, KRAS, KIT, RUNX1, NOTCH1, WT1, GATA1, GATA2, FLT3, KMT2D, FLT3-TKD, and PHF6. Copy number variations (CNVs) were detected in nine patients (39%), and eight (34.8%) had a long contiguous stretch of homozygosity (LCSH) /loss of heterozygosity (LOH). An LCSH was detected on chromosomes 5, 7, 11, and 19. The gains were more common than losses (8 vs 2). The gains were observed on chromosomes 8, 9, 14, 19, 21, and 22, and the losses were detected on chromosomes 7 and 10. Monosomy was observed in three patients. Three patients (monosomy7, n = 2, and FLT-ITD, n = 1) were reclassified into the high-risk category. Post-induction, complete remission was achieved in all evaluable patients.

CONCLUSION

CN-AML patients have genetic abnormalities that can be detected by more advanced techniques like NGS and CMA. These genetic abnormalities play a role in risk stratification that may remain hidden in otherwise CN-AML.

Establishing and characterising a new cell line from Calliphora vicina (diptera: calliphoridae) fly embryonic tissues

Insect cell lines represent a promising and expanding field as they have several research applications including biotechnology, virology, immunity, toxicology, cell signalling mechanisms and evolution. They constitute a powerful tool having a direct impact on human and veterinary medicine and agriculture. Although more than 1000 cell lines have currently been established from various insect species, Calliphora vicina-derived fly cell lines are lacking. This study was aimed at establishing a new C. vicina embryonic tissue-derived cell line. Adult flies were collected and embryonated eggs were mechanically homogenised and seeded in four types of culture media (L15, Grace's insect medium, Grace's/L15 and DMEM). Cell growth and morphological characteristics were recorded and cytogenetic and molecular patterns were determined. The CV-062020-PPB cell line was established and was shown to have optimal growth in Grace's/L15 medium. CV-062020-PPB cell monolayers that had been sub-cultured over 16 times consisted of firmly adhering cells having different morphologies; a fibroblast-like shape dominated and the karyotype had a 12-chromosome diploid number. RAPD-PCR analysis of the CV-062020-PPB cell line revealed a high similarity index and strong intraspecific relationship with C. vicina adult flies and a weaker relationship with the Lutzomyia longipalpis-derived cell line (Lulo). The CV-062020-PPB cell line constitutes the first cell line obtained from C. vicina embryonic tissues and represents an important basic and applied research tool.

•

A new C. vicina embryonic tissue-derived cell line is here reported.

•

Fibroblast-like cells were predominant.

•

The cell-line karyotype was 2n = 12 diploid chromosomes.

•

The DNA profile enabled discriminating its molecular identity.

The significance of karyotyping and azoospermia factor analysis in patients with nonobstructive azoospermia or oligozoospermia

OBJECTIVE

We present our study about the significance of karyotyping and azoospermia factor(AZF) analysis in patients with azoospermia or oligozoospermia.

MATERIALS AND METHODS

We retrospectively reviewed 141 Taiwanese patients with nonobstructive azoospermia and 45 Taiwanese patients with oligozoospermia at MacKay Memorial Hospital, Taiwan, from 2010 to 2021 to determine the significance of karyotyping and azoospermia factor analysis. The karyotyping was analyzed using the Giemsa banding method. The AZF microdeletions were determined using multiplex polymerase chain reaction using primers specifically flanking the AZF subregions.

RESULTS

We found that 7.80% of patients with nonobstructive azoospermia had AZF microdeletions and 19.86% of patients with nonobstructive azoospermia had chromosomal anomalies or polymorphic variations. Furthermore, 4.44% of patients with oligozoospermia had AZF microdeletions, and 4.44% of patients with oligozoospermia had chromosomal anomalies or polymorphic variations.

CONCLUSION

In this study, 25.53% of patients with nonobstructive azoospermia and 8.88% of patients with oligozoospermia had abnormal findings. The significance of karyotyping and azoospermia factor analysis is more critical in patients with nonobstructive azoospermia than patients with oligozoospermia. Both karyotyping and AZF analysis could prevent delayed treatment for male infertility through accurate diagnosis and appropriate treatment. The number of our patients with AZFc microdeletion was also higher than that of patients with AZFa or AZFb. The spermatogenic potential may gradually decline in patients with AZFc microdeletion. The earlier is the diagnosis, the earlier will be the retrieval of testicular spermatozoa.