Karyotypic Changes Research Articles

Out of the Himalaya-Hengduan Mountains: Phylogenomics, biogeography and diversification of Polygonatum Mill. (Asparagaceae) in the Northern Hemisphere

Clarifying the process of formation of diversity hotspots and the biogeographic connection between regions is critical in understanding the impact of environmental changes on organismal evolution. Polygonatum (Asparagaceae) is distributed across the Northern Hemisphere. It displays an uneven distribution, with more than 50% of its species occurring in the Himalaya-Hengduan Mountains (HHM). Here, we generated a time-calibrated phylogeny of Polygonatum, based on whole-plastome data, to reconstruct the genus’ biogeographical history and morphological/chromosomal evolution. Our phylogenetic analyses strongly support the monophyly of Polygonatum and its division into three sections (i.e., Verticillata, Sibirica, and Polygonatum). Polygonatum originated from the HHM region during the early-Miocene (c. 20.10 Ma), and began to radiate since the mid-Miocene, driven by the uplift of the Qinghai–Tibet Plateau (QTP), increasingly colder/arid climates following the mid-Miocene Climatic Optimum (MMCO), and intensification of the East Asian winter monsoon. Dispersal from the HHM region to other regions was facilitated by the intensification of East Asian summer monsoon in response to global climatic warming during the MMCO. Decreasing dysploidy accompanied by karyotype change and polyploidization in Polygonatum appears to be associated with its diversification and colonization of new ecological niches. Our results highlight the importance of regional tectonic activities and past climatic changes from the Neogene onwards to the spatial–temporal diversification and distribution patterns of plant lineages with a wide distribution in the Northern Hemisphere. They also contribute to the knowledge of the uneven species richness between East Asia and other regions.

Chromosome Painting in Lonchorhina aurita Sheds Light onto the Controversial Phylogenetic Position of Sword-Nosed Bats (Chiroptera, Phyllostomidae)

The subfamily Lonchorhininae encompasses 6 species of sword-nosed bats (Lonchorhina) and is one of the most problematic lineages in the Neotropical leaf-nosed bats (Phyllostomidae) phylogeny. There are at least 5 different hypotheses to explain when the subfamily diverged from the remaining phyllostomids, but none with robust statistical support. Here, we generated a chromosome painting homology map of Lonchorhina aurita karyotype (2n = 32 and FN = 60) using whole-chromosome probes of Macrotus californicus (MCA; 2n = 40 and FN = 60). We placed the karyotype changes of L. aurita in a phylogenetic context to discuss the most likely branching position of Lonchorhininae based on karyotypic evolution. We show that L. aurita has a derived karyotype with 24 segments homologous to the 20 MCA chromosomes used as probes. Comparative analyses between 7 published painted bats species across 4 phyllostomid subfamilies (Macrotinae, Phyllostominae, Glossophaginae, and Lonchophyllinae) revealed that one inversion (MCA 4inv) and one fusion (MCA 17 + 18) are shared derived features between the karyotypes of L. aurita and species of Phyllostominae not yet observed in other bats. Our data show that chromosomal homology maps may contribute with new insights into a long-standing phylogenetic debate that has endured for decades.

Nuclear–plastid discordance indicates past introgression inEpidendrumspecies (Laeliinae: Orchidaceae) with highly variable chromosome numbers

AbstractHere we study a challenging group of karyotypically highly variable Epidendrum spp. using phylogenetic methods to help understand how hybridization/introgression contributes to karyotype evolution. We hypothesize that species with great chromosome number variation are a result of past hybridization/introgression. Conflicting topologies in trees constructed using separate plastid and nuclear datasets suggest past hybridization events that occurred most probably at least 3.7 Mya. A basic number x = 14 and substantial karyotype change followed by species divergence are suggested. Descending dysploidy and polyploidy were the most frequent changes estimated across the phylogenetic tree of the group. Two species, Epidendrum secundum and E. xanthinum, have probably experienced unidirectional gene flow involving their ancestors (the pollen recipients) and ancestors of E. puniceoluteum and E. denticulatum/E. flammeum, respectively, the pollen donors. However, it is not possible to say whether hybridization participated in the origin of E. secundum and E. xanthinum or merely contributed to their genomic divergence and karyotype change through introgression as has been observed in modern hybrid zones in Epidendrum. This pattern of introgression causing karyotype disruption and divergence could help explain the enigma of some highly diverse genera, such as Epidendrum. Further studies using a wider sampling of the genus could test if gene flow and karyotype variability are associated with the increase of speciation rates.

High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani.

Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two clonal populations of Leishmania promastigotes representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations, affecting a defined subset of chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.

Karyotype Diversity, Mode, and Tempo of the Chromosomal Evolution of Attina (Formicidae: Myrmicinae: Attini): Is There an Upper Limit to Chromosome Number?

Simple SummaryAnts are an important insect group that includes a considerable number of species. Along with this diversity in species, they also exhibit a wide variation in chromosome numbers, from 1 up to 60 chromosomes. DNA molecules can be counted in a specific stage of the cell life cycle and quantified. These DNA molecules are very tightly packed together with several proteins and are called chromosomes. Each species shows a specific number of chromosomes with different shapes and sizes, as well as different quantities of DNA. We can use such information (the number of chromosomes, shape of the chromosomes, and quantity of DNA) as morphological attributes to study evolution at the species level. In this study, we describe new karyotypes of several ant species. In addition, from previous studies, we have compiled all the available information regarding the chromosome number and DNA quantity in fungus-farming ant cells. Different processes, called rearrangements, can change chromosomes over time, producing new character states. Such states can be tracked, along with the species and groups of similar species, using their relationships to identify patterns. We use DNA sequences to reconstruct the relationships of fungus-farming ant species (molecular phylogeny). By comparing such phylogeny with the chromosome number and DNA quantity, we discuss the evolution of chromosomes and DNA quantity (or genome size), and the potential limits to these features across fungus-farming ants. Ants are an important insect group that exhibits considerable diversity in chromosome numbers. Some species show only one chromosome, as in the males of the Australian bulldog ant Myrmecia croslandi, while some have as many as 60 chromosomes, as in the males of the giant Neotropical ant Dinoponera lucida. Fungus-growing ants are a diverse group in the Neotropical ant fauna, engaged in a symbiotic relationship with a basidiomycete fungus, and are widely distributed from Nearctic to Neotropical regions. Despite their importance, new chromosome counts are scarcely reported, and the marked variation in chromosome number across species has been poorly studied under phylogenetic and genome evolutionary contexts. Here, we present the results of the cytogenetic examination of fungus-farming ants and compile the cytogenetic characteristics and genome size of the species studied to date to draw insights regarding the evolutionary paths of karyotype changes and diversity. These data are coupled with a fossil-calibrated phylogenetic tree to discuss the mode and tempo of chromosomal shifting, considering whether there is an upper limit for chromosome number and genome size in ants, using fungus-farming ants as a model study. We recognize that karyotypes are generally quite variable across fungus-farming ant phylogeny, mostly between genera, and are more numerically conservative within genera. A low chromosome number, between 10 and 12 chromosomes, seems to present a notable long-term evolutionary stasis (intermediate evolutionary stasis) in fungus-farming ants. All the genome size values were inside a limited spectrum below 1 pg. Eventual departures in genome size occurred with regard to the mean of 0.38 pg, indicating that there is a genome, and likely a chromosome, number upper limit.

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs’ recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.

Molecular genetic characterization of acute myeloid leukemia with isolated trisomy of chromosomes 4, 11, and 21.

Autosomal trisomy is a relatively rare abnormality observed in AML, occurring singly or as a secondary event in association with other karyotypic changes, and associated with prognosis. The molecular genetic and clinical characterizations of acute myeloid leukemia (AML) with isolated trisomy 4, 11, or 21 have been poorly investigated. Interphase fluorescence in situ hybridization, reverse transcriptase-quantitative polymerase chain reaction for 41 chromosomal gene translocations/fusion genes, and next-generation sequencing (NGS) were performed on 29 AML patients with trisomy 4, 11, or 21 as the sole chromosomal anomaly. Of the 29 patients, one or more mutations were detected in 93.1% of patients. CEBPA had the highest mutation frequency, followed by TET2, NPM1, DNMT3A, and FLT3-ITD. The sole +11 AML patients exhibited more mutations in FLT3-ITD (P=.031) than the sole +21 AML patients, while CEBPA mutation was more frequently found in the sole +21 AML patients than that in the sole +11 AML patients(P=.07). The median overall survival (OS) and disease-free survival (DFS) for patients with +11 were shorter than those with +4(P=.015, 0.046) or +21 (0.057, 0.064), but no difference was found between +4 patients and +21 patients. In the whole cohort, only the FLT3-ITD mutation was significantly associated with inferior OS (18 vs. 35months, P=.023) and DFS (12months vs. NR, P=.046). There were no significant differences in OS and DFS according to the gene mutation status of CEBPA, TET2, NPM1, DNMT3A, and IDH1/2. There was a significantly different mutation profile among the sole +4, +11, +21 AML patients. Our research provided new insight into the molecular characteristics of AML with isolated trisomy.

Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing

Karyotype alterations have emerged as on-target complications from CRISPR-Cas9 genome editing. However, the events that lead to these karyotypic changes in embryos after Cas9-treatment remain unknown. Here, using imaging and single-cell genome sequencing of 8-cell stage embryos, we track both spontaneous and Cas9-induced karyotype aberrations through the first three divisions of embryonic development. We observe the generation of abnormal structures of the nucleus that arise as a consequence of errors in mitosis, including micronuclei and chromosome bridges, and determine their contribution to common karyotype aberrations including whole chromosome loss that has been recently reported after editing in embryos. Together, these data demonstrate that Cas9-mediated germline genome editing can lead to unwanted on-target side effects, including major chromosome structural alterations that can be propagated over several divisions of embryonic development.

Eosinophilic solid and cystic renal cell carcinoma: a clinicopathological analysis of four cases

Objective: To study the clinicopathological characteristics and prognosis of eosinophilic solid and cystic renal cell carcinoma (ESC RCC). Methods: The clinical pathologic data of 4 cases of ESC RCC diagnosed and treated from 2017 to 2019 at the Second Hospital of Longyan City, the Second Affiliated Hospital of Fujian Medical University, and the Zhangzhou Municipal Hospital were collected. The expression of different antibodies was detected by immunohistochemistry, and the diagnosis and differentiate diagnosis were investigated. Results: The 4 ESC RCC cases included 2 males and 2 females, the average age of these patients was 40 years, ranged from 31 to 51 years. The tumors were composed of solid area mixed with giant vesicles and microcapsules of varying sizes. The cyst cavity was lined by neoplastic cells with voluminous eosinophilic cytoplasm and hobnail arrangement. The solid area appeared as diffuse flaky, dense acinar or nested arrangement, the local area was island-shaped and tubular, mixed with a small amount of histiocytes and lymphocytes. Neoplastic cells contained voluminous eosinophilic cytoplasm with obvious fine or coarse particles, eosinophilic globules in part of the cytoplasm, and intracytoplasmic vacuoles in some areas. Immunohistochemical results showed that tumor cells were CK20 expressed (3/3, 2 cases were sparsely positive and 1 case was patched strongly positive), Vimentin (4/4) and CD10 (4/4) sparsely positive, while Actin, HMB45, Melan-A, CD117 and CK7 were negative in all cases. Ki-67 proliferation index was about 1%. Two cases were followed up and the progression free survival were 18 and 24 months, respectively. Conclusions: ESC RCC has unique histomorphological manifestations, CK20(+ ) and CK7(-) are helpful for its diagnosis, and it has common molecular karyotype changes, supporting it as a unique tumor entity. The overall prognosis of the patient is good.

Prognostic significance of chromosomal abnormalities at relapse in children with relapsed acute myeloid leukemia: A retrospective cohort study of the Relapsed AML 2001/01 Study.

In addition to treatment response, cytogenetic and molecular aberrations are the most important prognostic factors in children with de novo acute myeloid leukemia (AML). However, little is known about cytogenetics at the time of relapse. This international study analyzed the prognostic value of cytogenetic profiles and karyotypic changes in pediatric relapsed AML in relation to the probability of event-free (pEFS) and overall survival (pOS). For this purpose, cytogenetic reports from all patients registered on the Relapsed AML 2001/01 Study were reviewed and classified. Cytogenetic information at relapse was available for 403 (71%) of 569 registered patients. Frequently detected aberrations at relapse were t(8;21)(q22;q22) (n = 60) and inv(16)(p13.1q22)/t(16;16)(p13.1;q22) (n = 24), both associated with relatively good outcome (4-year pOS 59% and 71%, respectively). Monosomy 7/7q-, t(9;11)(p22;q23), t(10;11)(p12;q23), and complex karyotypes were associated with poor outcomes (4-year pOS 17%, 19%, 22%, and 22%, respectively). Of 261 (65%) patients for whom cytogenetic data were reliable at both diagnosis and relapse, pEFS was inferior for patients with karyotypic instability (n = 128, 49%), but pOS was similar. Unstable karyotypes with both gain and loss of aberrations were associated with inferior outcome. Early treatment response, time to relapse, and cytogenetic profile at time of relapse were the most important prognostic factors, both outweighing karytoypic instability per se. The cytogenetic subgroup at relapse is an independent risk factor for (event-free) survival. Cytogenetic assessment at the time of relapse is of high importance and may contribute to improved risk-adapted treatment for children with relapsed AML.

Generating CRISPR-Cas9-Mediated Null Mutations and Screening Targeting Efficiency in Human Pluripotent Stem Cells.

CRISPR-Cas9 mutagenesis facilitates the investigation of gene function in a number of developmental and cellular contexts. Human pluripotent stem cells (hPSCs), either embryonic or induced, are a tractable cellular model to investigate molecular mechanisms involved in early human development and cell fate decisions. hPSCs also have broad potential in regenerative medicine to model, investigate, and ameliorate diseases. Here, we provide an optimized protocol for efficient CRISPR-Cas9 genome editing of hPSCs to investigate the functional role of genes by engineering null mutations. We emphasize the importance of screening single guide RNAs (sgRNAs) to identify those with high targeting efficiency for generation of clonally derived null mutant hPSC lines. We provide important considerations for targeting genes that may have a role in hPSC maintenance. We also present methods to evaluate the on-target mutation spectrum and unintended karyotypic changes. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Selecting and ligating sgRNAs into expression plasmids Basic Protocol 2: Validation of sgRNA via in vitro transcription and cleavage assay Basic Protocol 3: Nucleofection of primed human embryonic stem cells Basic Protocol 4: MiSeq analysis of indel mutations Basic Protocol 5: Single cell cloning of targeted hPSCs Basic Protocol 6: Karyotyping of targeted hPSCs.

Interphase FISH Analysis Reveals High Frequence of Partial 6q Deletions in Adult Acute Lymphoblastic Leukemia (ALL) with Normal or Failed Karyotype.

Karyotypic analysis in adult ALL has provided relevant insights in the prognostic significance of chromosome abnormalities, which in turn become of potential importance for the design of risk-adapted therapeutic strategies for newly diagnosed cases. Among structural karyotypic changes, partial deletions of the long arm of chromosome 6 (6q) are reported to be between 4 and 6% of cases of adult ALL by conventional cytogenetics and depict a subset of patients with strict correlation with T-lineage ALL and an unfavorable prognostic likelihood. Recent studies at the molecular level in childhood ALL have shown 6q deletions in up to 30% of the investigated cases. With the aim of more precisely defining the exact incidence of 6q deletions in adult ALL, we started to investigate by interphase FISH patients with normal or failed karyotype included in the GIMEMA 0496 and 2000 protocols. These trials contemplated a central handling of bone marrow samples of the enrolled patients at presentation. We identified the following bacteria-derived artificial chromosome (BAC) clones with a known map location within the most common deleted region of 6q: 90G9 (6q13), 12B13 (6q15), 465M14 (6q21), 81H16 (6q26), 91016 (6q27). BAC clones were obtained from the Children's Hospital Oakland Research Institute (CHORI).Twenty-seven consecutive ALL patients have so far been analyzed by interphase FISH, 16 with T- and 11 with B-cell phenotype. Eleven cases had a normal karyotype and 16 a failed cytogenetic analysis. Among the cases with normal karyotype, 2 cases with T-cell phenotype showed a deletion in the 6q21 and 6q15 regions, whereas in the group with failed cytogenetics 1 case with B- and 3 cases with T-cell phenotype harbored deletions spanning respectively the 6q13-15 (2), 6q13-q21 and 6q15-21 regions. The median percentage of nuclei with 6q deletion was 30% (range 7–75%). T-ALL deleted cases showed the absence of the most frequent fusion genes detectable with molecular analysis, whereas a BCR-ABL rearrangement was identified in the only B-lineage ALL deleted case. Overall, partial 6q deletions were observed in 22% of the cases analyzed and in 31% of cases with T-cell phenotype. The present study shows that the probe set we have utilized is a useful tool for providing accurate cytogenetic diagnosis of partial 6q deletions and indicates that this abnormality is a frequent karyotypic change in adult ALL, particularly in T-lineage cases where it appears to represent the most relevant genetic anomaly. Since this abnormality is underestimated by conventional cytogenetic analysis, interphase FISH for 6q deletions should be included in the routine genetic screening of the ALL patients with failed or normal cytogenetics

Two-phased evolution: Genome chaos-mediated information creation and maintenance

Cancer is traditionally labeled a “cellular growth problem.” However, it is fundamentally an issue of macroevolution where new systems emerge from tissue by breaking various constraints. To study this process, we used experimental platforms to “watch evolution in action” by comparing the profiles of karyotypes, transcriptomes, and cellular phenotypes longitudinally before, during, and after key phase transitions. This effort, alongside critical rethinking of current gene-based genomic and evolutionary theory, led to the development of the Genome Architecture Theory. Following a brief historical review, we present four case studies and their takeaways to describe the pattern of genome-based cancer evolution. Our discoveries include 1. The importance of non-clonal chromosome aberrations or NCCAs; 2. Two-phased cancer evolution, comprising a punctuated phase and a gradual phase, dominated by karyotype changes and gene mutation/epigenetic alterations, respectively; 3. How the karyotype codes system inheritance, which organizes gene interactions and provides the genomic basis for physiological regulatory networks; and 4. Stress-induced genome chaos, which creates genomic information by reorganizing chromosomes for macroevolution. Together, these case studies redefine the relationship between cellular macro- and microevolution: macroevolution does not equal microevolution + time. Furthermore, we incorporate genome chaos and gene mutation in a general model: genome reorganization creates new karyotype coding, then diverse cancer gene mutations can promote the dominance of tumor cell populations. Finally, we call for validation of the Genome Architecture Theory of cancer and organismal evolution, as well as the systematic study of genomic information flow in evolutionary processes.

Karyotypic Changes of Apoptosis-Resistant Rat Cells HindIIIG during Prolonged Cultivation after Exposure to Ionizing Irradiation

Karyotypic Changes of Apoptosis-Resistant Rat Cells HindIIIG during Prolonged Cultivation after Exposure to Ionizing Irradiation

Expression of Hedgehog signalling molecules inmicrocystic adnexal carcinoma.

Microcystic adnexal carcinoma (MAC) is a rare skin neoplasm that has not been characterized on a molecular basis. To assess expression profiles of Hedgehog (HH) signalling molecules in MAC and control tumours. Immunohistochemistry was performed for Sonic Hedgehog (SHH), Indian Hedgehog (IHH), Patched 1 (PTCH1) and Smoothened (SMO) on patient MAC tissue (n=26) and control tumour tissue, including syringoma (SyG; n=11), trichoepithelioma (TE; n=11) and basal cell carcinoma (BCC; n=12) tissues. Patched 1 and SMO immunoreactivity was significantly higher in BCC than in SyG, TE or MAC (P<0.001 and P<0.03, respectively). The highest IHH expression was observed in BCC and TE compared with SyG and MAC (P<0.04). Notably, the highest SHH protein expression was observed in SyG compared with MAC, TE and even BCC (P<0.001). In patients with MAC, SMO immunoreactivity significantly (r=0.51; P<0.01) correlated with PTCH1 expression. Further correlation studies did not show significant associations between the HH expression markers assessed (P>0.05). Our results indicate that alterations of the HH signalling are unlikely to play a major role in the pathogenesis of MAC, which is in contrast to the morphologically similar BCC and TE. Our observation provides additional information to the limited molecular pathology knowledge on this rare tumour.

What can evolutionary biology learn from cancer biology?

Detecting and treating cancer effectively involves understanding the disease as one of somatic cell and tumor macroevolution. That understanding is key to avoid triggering an adverse reaction to therapy that generates an untreatable and deadly tumor population. Macroevolution differs from microevolution by karyotype changes rather than isolated localized mutations being the major source of hereditary variation. Cancer cells display major multi-site chromosome rearrangements that appear to have arisen in many different cases abruptly in the history of tumor evolution. These genome restructuring events help explain the punctuated macroevolutionary changes that mark major transitions in cancer progression. At least two different nonrandom patterns of rapid multisite genome restructuring – chromothripsis (“chromosome shattering”) and chromoplexy (“chromosome weaving”) – are clearly distinct in their distribution within the genome and in the cell biology of the stress-induced processes responsible for their occurrence. These observations tell us that eukaryotic cells have the capacity to reorganize their genomes rapidly in response to calamity. Since chromothripsis and chromoplexy have been identified in the human germline and in other eukaryotes, they provide a model for organismal macroevolution in response to the kinds of stresses that lead to mass extinctions.

Chromosome number is key to longevity of polyploid lineages.

Polyploidy is ubiquitous and often recursive in plant lineages, most frequently resulting in extinction but occasionally associated with great evolutionary success. However, instead of chromosome numbers exponentially increasing due to recurrent polyploidy, most angiosperm species have fewer than 14 chromosome pairs. Following genome duplication, diploidisation can render one copy of essential genes nonfunctional without fitness cost. In isolated subpopulations, alternate (homoeologous) gene copies can be lost, creating incompatibilities that reduce fitness of hybrids between subpopulations, constraining exchange of favourable genetic changes and reducing species fitness. When multiple sets of incompatible genes are genetically linked, their deleterious effects are not independent. The effective number of independently acting sets of incompatible loci in hybrids is limited by chromosome number and recombination. Therefore, species with many chromosomes are subject to a higher fitness penalty during diploidisation. Karyotypic changes, especially fusions, that reduce gene flow are normally fitness disadvantages, but during the diploidisation process, can increase fitness by reducing mixing of differentially diploidised alleles. Fitness penalties caused by diploidisation favour accelerated karyotypic change, with each change increasing barriers to gene flow, contributing to speciation. Lower chromosome numbers and increased chromosome fusions confer advantages to surviving the diploidisation process following polyploid formation, by independent mechanisms.

Adaptation to the dietary sugar D-tagatose via genome instability in polyploid Candida albicans cells.

The opportunistic fungal pathogen Candida albicans undergoes an unusual parasexual cycle wherein diploid cells mate to form tetraploid cells that can generate genetically diverse progeny via a nonmeiotic program of chromosome loss. The genetic diversity afforded by parasex impacts clinically relevant features including drug resistance and virulence, and yet the factors influencing genome instability in C. albicans are not well defined. To understand how environmental cues impact genome instability, we monitored ploidy change following tetraploid cell growth in a panel of different carbon sources. We found that growth in one carbon source, D-tagatose, led to high levels of genomic instability and chromosome loss in tetraploid cells. This sugar is a stereoisomer of L-sorbose which was previously shown to promote karyotypic changes in C. albicans. However, while expression of the SOU1 gene enabled utilization of L-sorbose, overexpression of this gene did not promote growth in D-tagatose, indicating differences in assimilation of the two sugars. In addition, genome sequencing of multiple progenies recovered from D-tagatose cultures revealed increased relative copy numbers of chromosome 4, suggestive of chromosome-level regulation of D-tagatose metabolism. Together, these studies identify a novel environmental cue that induces genome instability in C. albicans, and further implicate chromosomal changes in supporting metabolic adaptation in this species.

22. Masked hypodiploid B-Cell Lymphoblastic Leukemia (B-ALL) characterized by SNP microarray in a Li Fraumeni syndrome patient with post therapy karyotype changes

Cases of B-ALL with chromosome counts of >60 and tetrasomic for chromosomes 6, 18, 21 and X are suspicious for “masked hypodiploidy” in that the theoretic hypodiploid stemline is present as a doubled clone only. To characterize and define these cases when FISH and chromosomes show no evidence of the hypodiploid clone, our laboratory utilizes the IlluminaⓇ Cyto-SNP 850K microarray to recognize the loss of heterozygosity (LOH) of the disomic chromosomes. We report an 18yo female with a known diagnosis of Li Fraumeni syndrome, referred to Cytogenetics with pancytopenia and circulating blasts. Cytogenetic results at diagnosis revealed three hyperdiploid clones with counts of 62-64, tetrasomy for X, 1, 6, 18, and 21, with additional trisomies and structural rearrangements including a derivative 17p with 11q. No evidence for monosomy was observed by FISH or chromosomes. Microarray results confirmed loss of heterozygosity (LOH) for those chromosomes present in 2 copies. Genes associated with low hypodiploid B-ALL include TP53, IKZF1 and RB1 which were present in 2 copies on the isodisomic chromosomes in this specimen. This patient was in remission for several months, but with reemergence of B-ALL, underwent CD19 directed CAR-T therapy which resulted in deep remission (by NGS-MRD). Recent surveillance studies showed a karyotype change to loss of 5q and TP53 by FISH and a dic(5;17)(q11.2;p11.2) consistent with MDS. Microarray studies confirm the MDS genetic findings and were negative for the masked hypodiploid findings present at diagnosis. This strategy has been useful to report chromosome results with confidence for cases of masked hypodiploidy that may have been otherwise misinterpreted.

Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level.

Karyotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result in genome instability. However, the complex chromosome end structures and the other possible consequences of telomere dysfunction have rarely been resolved at the nucleotide level due to the lack of the high-throughput methods needed to analyse these highly repetitive regions. Here we applied long-read sequencing technology to Caenorhabditis elegans survivor lines that emerged after telomere dysfunction. The survivors have preserved traces of DDRs in their genomes and our data revealed that variants generated by telomere dysfunction are accumulated along all chromosomes. The reconstruction of the chromosome end structures through de novo genome assemblies revealed diverse types of telomere damage processing at the nucleotide level. When telomeric repeats were totally eroded by telomere dysfunction, DDRs were mostly terminated by chromosome fusion events. We also partially reconstructed the most complex end structure and its DDR signatures, which would have been accumulated via multiple cell divisions. These finely resolved chromosome end structures suggest possible mechanisms regarding the repair processes after telomere dysfunction, providing insights into chromosome evolution in nature.