The current state of molecular cytogenetics in cancer diagnosis

Minimal residual disease detection in lymphoma: methods, procedures and clinical significance

Lymphoma is a highly heterogeneous lymphohematopoietic tumor. As our understanding of the biological and pathological characteristics of lymphoma improves, we are identifying an increasing number of lymphoma subtypes. Genotyping has enhanced our ability to diagnose, treat, and monitor the prognosis of lymphoma. Despite significant improvements in treatment effectiveness, traditional methods for assessing disease response and monitoring prognosis are imperfect, and there is no significant improvement in overall remission rates for lymphoma patients. Minimal Residual Disease (MRD) is often indicative of refractory disease or early relapse. For lymphoma patients, personalized MRD monitoring techniques offer an efficient means to estimate disease remission levels, predict early relapse risk, and assess the effectiveness of new drug regimens. In this review, we delve into the MRD procedures in lymphoma, including sample selection and requirements, detection methods and their limitations and advantages, result interpretation. Besides, we also introduce the clinical applications of MRD detection in lymphoma.

FISH-Banding for Characterization of Simple and Complex Chromosomal Rearrangements in Cancer

While interphase and metaphase-directed molecular cytogenetics is a standard technique in routine tumor (cyto)genetics, fluorescence in situ hybridization-based banding (FISH-banding) approaches are less commonly applied. In research FISH-banding showed its excellence in the characterization of simple and complex chromosomal aberrations; however, in routine settings, it is still only little applied. The main argument against FISH-banding is, that it shall be associated with comparatively high costs. However, if applied advisedly FISH-banding can even save costs, as in one or two chromosome-specific FISH experiments; otherwise, cryptic, not resolvable chromosomal rearrangements may be resolved quickly. Here the protocol for the only yet commercially available FISH-banding approach-the multicolor banding (MCB/ mBAND)-is outlined.

Identification of a novel recurrent EEF2 gene amplification in familial prostate tumors

Recurrent tumor copy number variations (CNVs) in prostate cancer (PrCa) have predominantly been discovered in sporadic tumor cohorts. Here, we examined familial prostate tumors for novel CNVs as prior studies suggest these harbor distinct CNVs. Array comparative genomic hybridization of 12 tumors from an Australian PrCa family, PcTas9, highlighted multiple recurrent CNVs, including amplification of EEF2 (19p13.3) in 100% of tumors. The EEF2 CNV was examined in a further 26 familial and seven sporadic tumors from the Australian cohort and in 494 tumors unselected for family history from The Cancer Genome Atlas (TCGA). EEF2 overexpression was observed in seven PcTas9 tumors, in addition to seven other predominantly familial tumors (n_total  = 34%). EEF2 amplification was only observed in 1.4% of TCGA tumors, however 7.5% harbored an EEF2 deletion. Analysis of genes co-expressed with EEF2 revealed significant upregulation of two genes, ZNF74 and ADSL, and downregulation of PLSCR1 in both EEF2 amplified familial tumors and EEF2 deleted TCGA tumors. Furthermore, in TCGA tumors, EEF2 amplification and deletion were significantly associated with a higher Gleason score. In summary, we identified a novel PrCa CNV that was predominantly amplified in familial tumors and deleted in unselected tumors. Our results provide further evidence that familial tumors harbor distinct CNVs, potentially due to an inherited predisposition, but also suggest that regardless of how EEF2 is dysregulated, a similar set of genes involved in key cancer pathways are impacted. Given the current lack of gene-based biomarkers and clinical targets in PrCa, further investigation of EEF2 is warranted.

Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches

Here the role of molecular cytogenetics in the context of yet available all other cytogenomic approaches is discussed. A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). The latter contains the methodology itself, the types of probe- and target-DNA, as well as probe sets. The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. Overall, molecular cytogenetics is far from being outdated and actively involved in up-to-date diagnostics and research.

Cryptic t(15;17) acute promyelocytic leukemia with a karyotype of add(11)(p15) and t(13,20)- A case report with a literature review

Most acute promyelocytic leukemias (APL) are characterized by reciprocal translocations t(15;17)(q22;21), which results in the fusion of the promyelocytic leukemia protein (PML) gene at 15q22 with retinoic acid receptor a (RARα) gene at 17q21. However, several complex variant translocations also have been reported. Here, we report a 62-year-old man with typical morphology and clinical features of APL with a complex karyotype including add(11)(p15) and t(13;20)(q12;q11.2) without typical t(15;17) assayed by the G-banding analysis. The fluorescence in situ hybridization with a PML/RARα dual-color DNA probe showed an atypical fusion signal, quantitative real-time polymerase chain reaction analysis showed PML/RARα fusion transcripts, and NGS detected FLT3, WT1, and KRAS mutations. The patient achieved complete remission after treatment with conventional chemotherapy combined with all-trans retinoic acid (ATRA) and arsenic trioxide (ATO). Although the mechanism of this kind of cryptic variant remains unknown, we conclude that the cryptic PML/RARα fusion with add(11)(p15) and t(13;20)(q12;q11.2) seems not to alter the effectiveness of chemotherapy combined with ATRA and ATO.

From Human Cytogenetics to Human Chromosomics

BACKGROUND

The concept of "chromosomics" was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a "chromosomic view" of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945⁻20 July 2008).

RECENT FINDINGS

Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches.

CONCLUSION

Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.

Chromosomes in the DNA era: Perspectives in diagnostics and research

Chromosomes were discovered more than 130 years ago. The implementation of chromosomal investigations in clinical diagnostics was fueled by determining the correct number of human chromosomes to be 46 and the development of specific banding techniques. Subsequent technical improvements in the field of genetic diagnostics, such as fluorescence in situ hybridization (FISH), chromosomal microarrays (CMA, array CGH) or next-generation sequencing (NGS) techniques, partially succeeded in overcoming limitations of banding cytogenetics. Consequently, nowadays, higher diagnostic yields can be achieved if new approaches such as NGS, CMA or FISH are applied in combination with cytogenetics. Nonetheless, high-resolution DNA-focused techniques have dominated clinical diagnostics more recently, rather than a “chromosomic view,” including banding cytogenetics as a precondition for the application of higher resolution methods. Currently, there is a renaissance of this “chromosomic view” in research, understanding chromosomes to be an essential feature of genomic architecture, owing to the discovery of (i) higher order chromosomal sub-compartments, (ii) chromosomal features that influence genomic architecture, gene expression, and evolution, and (iii) 3D and 4D chromatin organization within the nucleus, including the complex way in which chromosomes interact with each other. Interestingly, in many instances research was triggered by specific clinical diagnostic cases or diseases that contributed to new and fascinating insights, not only into disease mechanisms but also into basic principles of chromosome biology. Here we review the role, the intrinsic value, and the perspectives of chromosomes in a molecular genetics-dominated human genetics diagnostic era and make comparison with basic research, where these benefits are well-recognized.

Characterization of RB1 Deletions in Interphase and Metaphase by Molecular Cytogenetics Exemplified in Chronic Lymphatic Leukemia

In chronic lymphatic leukemia (CLL), detection and characterization of prognostic relevant chromosomal alterations is optimally done by interphase-fluorescence in situ hybridization (iFISH). Interphase nuclei derived from blood smears, bone marrow smears or from cultivated and conventionally prepared blood or bone marrow cells can be used. In CLL heterozygous or even homozygous deletion of RB1 can be found. Interestingly an iFISH diagnostic result with RB1 deletion as sole aberration is indicative for a favorable course of the disease. Here we describe the best way how to detect RB1 deletion in CLL.

Molecular Cytogenetic Characterization Identified the Murine B-Cell Lymphoma Cell Line A-20 as a Model for Sporadic Burkitt's Lymphoma

Here, we report the first molecular cytogenetic characterization of the BALB/cAnN mouse derived B-cell non-Hodgkin lymphoma (B-cell NHL) cell lines A-20. Even though previously used as a model for testing of, for example, dexametason, up to present, no data in the genetic properties of A-20 were available. The present study closed this gap and provides evidence that A-20 is a model for B-cell NHL subgroup sporadic Burkitt's lymphoma. C-myc oncogene is involved in a translocation and copy number alterations as gain of murine 14q material could be observed. Interestingly, the cell line showed the karyotype 39,X,-X or -Y,t(2;15)(qE5;qD2),del(6)(qB3qC3),del(9)(qA3qA4),dup(14)(qE1qE4) in ~95% of the cells, being exceptionally stable for cell lines being established 38 years ago. Still, ~5% of the cells showed polyploidization followed by chromothripsis. It remains to be determined if this can be observed also in other cell lines, just has not been reported yet, and/or if it is a unique feature of A-20. Overall, finally here, the necessary genetic data to identify A-20 as a model for human sporadic Burkitt's lymphoma are provided.

Genetics of Cutaneous T Cell Lymphoma: From Bench to Bedside

OPINION STATEMENT

Cutaneous T cell lymphomas (CTCLs) are non-Hodgkin lymphomas of skin homing T cells. Although early-stage disease may be limited to the skin, tumor cells in later stage disease can populate the blood, the lymph nodes, and the visceral organs. Unfortunately, there are few molecular biomarkers to guide diagnosis, staging, or treatment of CTCL. Diagnosis of CTCL can be challenging and requires the synthesis of clinical findings, histopathology, and T cell clonality studies; however, none of these tests are entirely sensitive or specific for CTCL. Treatment of CTCL is often empiric and is not typically based on specific molecular alterations, as is common in other cancers. In part, limitations in diagnosis and treatment selection reflect the limited insight into the genetic basis of CTCL. Recent next-generation sequencing has revolutionized our understanding of the mutational landscape in this disease. These analyses have uncovered ultraviolet radiation and recombination activating gene (RAG) endonucleases as important mutagens. Furthermore, these studies have revealed potentially targetable oncogenic mutations in the T cell receptor complex, NF-κB, and JAK-STAT signaling pathways. Collectively, these somatic mutations drive lymphomagenesis via cancer-promoting changes in proliferation, apoptosis, and T cell effector function. We expect that these genetic findings will launch a new era of precision medicine in CTCL.

Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications

Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.