Long Arm Of Chromosome Research Articles

Apert syndrome: modern aspects of diagnosis and treatment

The purpose of this review is to raise awareness of medical professionals about the features of the clinical picture, the possibilities of diagnosis (including prenatal) and therapy of patients with Apert syndrome to further improve the prognosis and improve the quality of life. Acrocephalosyndactyly is a group of rare congenital syndromes characterized by the presence of acrocephaly, craniofacial anomalies, syndactyly of the hands and feet. According to the literature, the most common form of аcrocephalosyndactyly is Apert syndrome (acrocephalosyndactyly type I, Apert syndrome, ICD 10 Q 87.0, OMIM 101200). This is a genetic disease inherited by an autosomal dominant type. CA is caused by a mutation of the fibroblast growth factor receptor type 2 gene (FGFR2) located on the long arm of chromosome 10, which leads to increased bone metabolism and impaired bone synthesis. The frequency of Apert syndrome is about 15 cases per 1,000,000 live births. Wheaton first reported this pathology in 1894, and in 1906 the French pediatrician Eugene Apert published a series of nine clinical cases with a characteristic triad of symptoms. Apert syndrome is characterized by craniosynostosis, bilateral symmetrical limb syndactyly and dysmorphic facial features. Hypoplasia of the upper jaw and bicoronal synostosis are two noticeable craniofacial defects that lead to a flat, deepened appearance of the forehead and the middle part of the face. Hypertelorism and excessive orbitality, low-set ears, flat nose and cleft palate are often found. Cardiovascular, neurological and genitourinary abnormalities may be present. Diagnosis is based on clinical criteria and molecular genetic testing. There is a possibility of prenatal detection of Apert syndrome.

The first description of a rare monogenic disease with polymicrogyria caused by a pathogenic variant in the gene WASF1 in monozygotic twins

Neurodevelopmental disorder without speech and variable seizures (NEDALVS) is a rare autosomal dominant inherited disorder, characterized by motor development delay, mental retardation, wide-based gait, autism spectrum disorders and seizures. 
 Currently, fifteen cases of NEDALVS have been described worldwide.
 NEDALVS caused by mutations in the WASF1 gene, located on the long arm of chromosome 6. Nonsense-, missense-, frameshift mutations and large deletion have been described in WASF1 gene. 
 We present the clinical case of 9-year monozygotic NEDALVS twins, accompanied by cerebral pachygyria/polymicrogyria. DNA diagnostic was performed using full genome sequencing, followed by validation using Sanger sequencing. A previously described heterozygous pathogenic variant c.1516C>T (p.R506*) in the WASF1 gene was identified.
 We performed the results of a comparative analysis based on the literature and our patients. All patients had delayed motor and psycho-speech development, severe mental retardation was in 53% of cases, lack of speech — 18%, autistic manifestations and seizures — 41%, wide-based gait — 29%, strabismus and feeding problems — 35%.
 Conclusion. WASF1 gene mutations caused a rare form of mental retardation in children. We present the first case of NEDALVS in Russian Federation and the world’s first description of pachygyria in patients, caused by WASF1 gene mutations. The use of NGS as a first-line test for research and diagnostic of neurodevelopmental disorder is determined by their non-specific clinical features.

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.MethodsFour 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).ResultsThe 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.

Myelodysplastic Neoplasms (MDS): The Current and Future Treatment Landscape.

Myelodysplastic neoplasms (MDS) are a heterogenous clonal disorder of hemopoietic stem cells characterized by cytomorphologic dysplasia, ineffective hematopoiesis, peripheral cytopenias and risk of progression to acute myeloid leukemia (AML). Our understanding of this disease has continued to evolve over the last century. More recently, prognostication and treatment have been determined by cytogenetic and molecular data. Specific genetic abnormalities, such as deletion of the long arm of chromosome 5 (del(5q)), TP53 inactivation and SF3B1 mutation, are increasingly associated with disease phenotype and outcome, as reflected in the recently updated fifth edition of the World Health Organization Classification of Hematolymphoid Tumors (WHO5) and the International Consensus Classification 2022 (ICC 2022) classification systems. Treatment of lower-risk MDS is primarily symptom directed to ameliorate cytopenias. Higher-risk disease warrants disease-directed therapy at diagnosis; however, the only possible cure is an allogenic bone marrow transplant. Novel treatments aimed at rational molecular and cellular pathway targets have yielded a number of candidate drugs over recent years; however few new approvals have been granted. With ongoing research, we hope to increasingly offer our MDS patients tailored therapeutic approaches, ultimately decreasing morbidity and mortality.

HSPA9/mortalin inhibition disrupts erythroid maturation through a TP53-dependent mechanism in human CD34+ hematopoietic progenitor cells.

Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic stem cell malignancies characterized by abnormal hematopoietic cell maturation, increased apoptosis of bone marrow cells, and anemia. They are the most common myeloid blood cancers in American adults. The full complement of gene mutations that contribute to the phenotypes or clinical symptoms in MDS is not fully understood. Around 10%-25% of MDS patients harbor an interstitial heterozygous deletion on the long arm of chromosome 5 [del(5q)], creating haploinsufficiency for a large set of genes, including HSPA9. The HSPA9 gene encodes for the protein mortalin, a highly conserved heat shock protein predominantly localized in mitochondria. Our prior study showed that knockdown of HSPA9 induces TP53-dependent apoptosis in human CD34+hematopoietic progenitor cells. In this study, we explored the role of HSPA9 in regulating erythroid maturation using human CD34+cells. We inhibited the expression of HSPA9 using gene knockdown and pharmacological inhibition and found that inhibition of HSPA9 disrupted erythroid maturation as well as increased expression of p53 in CD34+cells. To test whether the molecular mechanism of HSPA9 regulating erythroid maturation is TP53-dependent, we knocked downHSPA9 and TP53 individually or in combination in human CD34+cells. We found that the knockdown of TP53 partially rescued the erythroid maturation defect induced by HSPA9 knockdown, suggesting that the defect in cells with reduced HSPA9 expression is TP53-dependent. Collectively, these findings indicate that reduced levels of HSPA9 may contribute to the anemia observed in del(5q)-associated MDS patients due to the activation of TP53.

Family case of cystic fibrosis

Cystic fibrosis is an autosomal recessively inherited monogenic disease caused by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, located on the long arm of chromosome 7 (7q31.2). This mutation results in a disruption in the transport of sodium and chloride ions between intercellular fluid and the epithelial cells of the excretory ducts of the exocrine glands. This paper presents the description of a family case of cystic fibrosis involving two patients who have been under observation since birth and are sisters (patient A – 4 years 10 months, patient B – 1 year 11 months). In both patients, neonatal screening and sequential diagnosis of cystic fibrosis identified the DF508/CFTRdele2.3(21kb) mutation, the most prevalent among the Caucasian population in the Russian Federation. The primary concern in managing both patients is the correction of nutritional status and minimization of exacerbations of chronic bronchopulmonary inflammation. To determine the management strategy for these patients, a consultation was held with Dr. E.I. Kondratyeva, a leading cystic fibrosis expert and professor at the MGSC Institute, who serves as the head of the Scientific and Clinical Department of Cystic Fibrosis and the Department of Genetics of Respiratory System Diseases, an expert of the European Society for Cystic Fibrosis Committee on Diagnostics and Registry, and Deputy Chief for Scientific Work of Research Clinical Institute of Childhood of the Ministry of Health of the Moscow Region. The peculiarity of the presented clinical cases lies in the fact that within one family, with an interval of 3 years, two girls with severe disease were born. Early diagnosis was performed for both, which has allowed for the slowing down of the pathology's progression.

Abstract 248: HSPA9/mortalin regulates erythroid maturation through a TP53-dependent mechanism in human CD34+ hematopoietic progenitor cells

Abstract Mortalin, encoded by the HSPA9 gene, is a highly conserved heat-shock chaperone belonging to the HSP70 family. It is predominantly presented in the mitochondria, and is critical in regulating a variety of cell physiological functions such as response to cell stress, control of cell proliferation, and inhibition/prevention of apoptosis. Myelodysplastic syndromes (MDS) are a group of hematopoietic stem cell malignancies characterized by ineffective hematopoiesis, increased apoptosis of bone marrow cells, and anemia. Up to 25% of MDS patients harbor an interstitial deletion on the long arm of chromosome 5, also known as del(5q), creating haploinsufficiency for multiple genes including HSPA9. Our prior study showed that knockdown of HSPA9 induces TP53-dependent apoptosis in human CD34+ hematopoietic progenitor cells, consistent with cytopenia observed in MDS patients. Since anemia is another featured symptom of MDS, we hypothesize that HSPA9 plays a role in regulating erythroid maturation. To test our hypothesis, we inhibited the expression of HSPA9 using various methods and measured the erythroid maturation in human CD34+ cells. We used siRNA targeting HSPA9 and found that HSPA9 siRNA significantly inhibited the cell growth, increased cell apoptosis, inhibited erythroid maturation (using CD71 as a surrogate marker), and increased p53 expression (p<0.01) compared to control siRNA in human CD34+ cells. Pharmacologic inhibition of HSPA9 by the chemical MKT-077, an inhibitor of HSP70 protein family members including mortalin, also increased p53 expression and inhibited erythroid maturation in human CD34+ cells. In addition, knockdown of HSPA9 by shRNA showed significant inhibition of erythroid maturation in human CD34+ cells compared to control shRNA. In order to test whether the regulation of erythroid maturation by HSPA9 is TP53-dependent or not, we constructed shRNAs targeting TP53 genes and simultaneously transduced lentivirus containing shRNAs targeting HSPA9 and TP53 respectively in human CD34+ cells using double antibiotics selection (puromycin for shRNA targeting HSPA9 and hygromycin for shRNA targeting TP53). We found that TP53 knockdown partially rescued the erythroid maturation defect caused by HSPA9 inhibition, suggesting that erythroid maturation inhibition by HSPA9 knockdown is partly mediated through a TP53 mechanism. Collectively, our results suggest that the increased apoptosis and reduced erythroid maturation observed in del(5a)-associated MDS is TP53-dependent. HSPA9/mortalin may be a potential target to treat anemia in del(5q) MDS patients, although simultaneous loss of multiple genes on del(5q) likely contributes to the complex phenotypes observed in MDS. Thus, our study not only uncovers some underlying mechanisms of del(5q) MDS, but also provides potential therapeutic indications through gene targeting in clinical MDS treatment. Citation Format: Tuoen Liu, Christopher Butler, Morgan Dunmire, Gabor Szalai, Anissa Johnson, Jaebok Choi, Matthew Walter. HSPA9/mortalin regulates erythroid maturation through a TP53-dependent mechanism in human CD34+ hematopoietic progenitor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 248.

Abstract 1762: Characterization of somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma

Abstract Deletion in the long arm of chromosome 22 (22qDEL) is the most prevalent somatic copy number alteration (SCNA) observed in papillary thyroid carcinoma (PTC). Despite its recurrence, the specific characteristics and role of 22qDEL in PTC have not been fully studied. We conducted a pooled analysis of 22qDEL by integrating patient and clinical information and molecular profiles from 1,094 primary PTC tumors across four major published PTC genomic studies: The Cancer Genome Atlas (TCGA) PTC profile study, the National Cancer Institute (NCI) post-Chornobyl PTC study, the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets (MSKCC-IMPACT) PTC cases, and the Seoul National University (SNU) thyroid cancer profile study. The majority of PTC with 22qDEL demonstrated arm-level loss of heterozygosity (86%). Even in PTC cases with partial 22qDEL, we observed a loss across 70% of chromosome 22, encompassing regions 22q12 and 22q13, which harbors known cancer genes (NF2 and CHEK2). More than 90% of 22qDEL co-occurred with established oncogenic drivers of PTC, though a full assessment of PTC drivers was not available for all cases. 22qDEL occurred more frequently with RAS point mutations (50.4%) than other drivers (9.3%). A higher fraction of 22qDEL was clonal in RAS-driven PTCs (78.3%), suggesting 22qDEL occurs early in RAS-driven tumor development. We did not observe any association between 22qDEL and established PTC risk factors such as age, sex, and radiation, nor with clinical features including tumor size, multifocality, and metastasis (p-values>0.22). RNA sequencing gene expression analysis based on 22qDEL status revealed downregulation of most genes residing on chromosome 22q and significant differential expression activity of immune-related genes, further implicating a role of immune dysregulation in PTC. Our study suggests that 22qDEL may not act as a primary driver of PTC but plays an important role as a co-factor of RAS point mutations, which could further drive PTC development. Citation Format: Olivia W. Lee, Danielle Karyadi, Stephen Hartley, Weyin Zhou, Mitchell Machiela, Mykola Tronko, Tetiana Bogdanova, Liudmyla Zurnadzhy, Lindsay Morton, Stephen Chanock. Characterization of somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1762.

Clinical and molecular cytogenetic studies of five new patients with 20q11q12 deletion and review of the literature: Proposition of two critical regions.

Deletions of the long arm of chromosome 20 (20q) are rare, with only 16 reported patients displaying a proximal interstitial 20q deletion. A 1.62 Mb minimal critical region at 20q11.2, encompassing three genes GDF5, EPB41L1, and SAMHD1, is proposed to be responsible for this syndrome. The leading clinical features include growth retardation, intractable feeding difficulties with gastroesophageal reflux, hypotonia and psychomotor developmental delay. Common facial dysmorphisms including triangular face, hypertelorism, and hypoplastic alae nasi were additionally reported. Here, we present the clinical and molecular findings of five new patients with proximal interstitial 20q deletions. We analyzed the phenotype and molecular data of all previously reported patients with 20q11.2q12 microdeletions, along with our five new cases. Copy number variation analysis of patients in our cohort has enabled us to identify the second critical region in the 20q11.2q12 region and redefine the first region that is initially identified. The first critical region spans 359 kb at 20q11.2, containing six MIM genes, including two disease-causing genes, GDF5 and CEP250. The second critical region spans 706 kb at 20q12, encompassing four MIM genes, including two disease-causing genes, MAFB and TOP1. We propose GDF5 to be the primary candidate gene generating the phenotype of patients with 20q11.2 deletions. Moreover, we hypothesize TOP1 as a potential candidate gene for the second critical region at 20q12. Of note, we cannot exclude the possibility of a synergistic role of other genes involved in the deletion, including a contiguous gene deletion syndrome or position effect affecting both critical regions. Further studies focusing on patients with proximal 20q deletions are required to support our hypothesis.

Factor VIII as a Novel Biomarker for Diagnosis, Prognosis, and Therapy Prediction in Human Cancer and Other Disorders.

Coagulation factor VIII (FVIII) is an essential cofactor in the coagulation cascade, encoded by the F8 gene on the long arm of chromosome X (Xq28). FVIII is normally circulated in complex with Von Willebrand factor (VWF) and has relevant emerging extracoagulative functions. Dysregulation of FVIII is associated with tumor progression, and could be used as a novel biomarker for tumor screening and monitoring. In breast cancer, bladder cancer, colorectal carcinoma, esophageal carcinoma, hepatocellular carcinoma and lung cancer, F8 is regarded as an oncogene. In coronary heart disease, hemophilia A and liver disease, F8 dysregulation has been recognized as a potential biomarker for disease diagnosis and prognosis. However, the basis of these differential expression levels remains to be understood. In this review, which is a mixture of literature review and bioinformatics analysis we described the biological functions and characteristics of FVIII, and also its expression level in non-malignant disorders and various cancers.

Identification of a complex intrachromosomal inverted insertion in the long arm of chromosome 9 as a cause of tuberous sclerosis complex in a Korean family.

Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder, caused by a loss-of-function of either TSC1 or TSC2 gene. However, in 10%-15% TSC patients there is no pathogenic variant identified in either TSC1 or TSC2 genes based on standard clinical testing. In this study, genome sequencing was performed for families with clinical diagnosis of TSC with negative results from TSC1 and TSC2 single-gene tests. Herein, we report a family presenting a classical TSC phenotype with an unusual, complex structural variant involving the TSC1 gene: an intrachromosomal inverted insertion in the long arm of chromosome 9. We speculate that the inverted 9q33.3q34.13 region was inserted into the q31.2 region with the 3'-end of the breakpoint of the inversion being located within the TSC1 gene, resulting in premature termination of TSC1. In this study, we demonstrate the utility of genome sequencing for the identification of complex chromosomal rearrangement. Because the breakpoints are located within the deep intronic/intergenic region, this copy-neutral variant was missed by the TSC1 and TSC2 single-gene tests and contributed to an unknown etiology. Together, this finding suggests that complex structural variants may be underestimated causes for the etiology of TSC.

Three-way Philadelphia Translocation [t(46, XX, t(9;22;16) (q34;q11.2;q24)] in Chronic Myeloid Leukemia: A Report of Two Cases with Review of the Literature.

Chronic myeloid leukemia (CML) is a clonal myeloproliferative neoplasm that is genetically characterized by the presence of the Philadelphia (Ph) chromosome. Variant Ph translocation has been observed in 5% to 10% of the CML cases. In the previous studies, many different types of variant Ph translocations have been observed involving chromosomes 1p36, 3p21, 5q13, 6p21, 9q22, 11q13, 12p13, 17p13, and 10p15. According to the published literature, only two cases with the complex translocations involving long arm of chromosome 16 at band q24 have been reported. We report two female patients with complex translocation (three-way) involving chromosomes 9, 22, and 16 at breakpoint q24 and both patients responded well to Imatinib. The present study included 469 patients of clinically diagnosed CML patients who were referred for cytogenetic analysis to our laboratory. Cytogenetic analysis was performed by GTG banding, and the karyotype was designated according to the International System for Human Cytogenetic Nomenclature. Fluorescence in situ hybridization (FISH) analysis was performed for complex and variant BCR-ABL cases. Of total 469 cases, 248 patients showed classical Ph chromosome [t(9;22)(q34;q11.2)], 198 cases were normal, and 23 patients had variant and complex Ph chromosome translocation. Two patients showed three-way translocation involving long arm of chromosomes 9, 22, and 16 at band 9q34, 22q11.2, and 16q24. In this report, patients with variant Ph translocation did not have a significantly different outcome as compared to the classical translocation. Both cases responded well to Imatinib.

Identification and evolution of a diterpenoid phytoalexin oryzalactone biosynthetic gene in the genus Oryza.

The natural variation of plant-specialized metabolites represents the evolutionary adaptation of plants to their environments. However, the molecular mechanisms that account for the diversification of the metabolic pathways have not been fully clarified. Rice plants resist attacks from pathogens by accumulating diterpenoid phytoalexins. It has been confirmed that the composition of rice phytoalexins exhibits numerous natural variations. Major rice phytoalexins (momilactones and phytocassanes) are accumulated in most cultivars, although oryzalactone is a cultivar-specific compound. Here, we attempted to reveal the evolutionary trajectory of the diversification of phytoalexins by analyzing the oryzalactone biosynthetic gene in Oryza species. The candidate gene, KSLX-OL, which accounts for oryzalactone biosynthesis, was found around the single-nucleotide polymorphisms specific to the oryzalactone-accumulating cultivars in the long arm of chromosome 11. The metabolite analyses in Nicotiana benthamiana and rice plants overexpressing KSLX-OL indicated that KSLX-OL is responsible for the oryzalactone biosynthesis. KSLX-OL is an allele of KSL8 that is involved in the biosynthesis of another diterpenoid phytoalexin, oryzalexin S and is specifically distributed in the AA genome species. KSLX-NOL and KSLX-bar, which encode similar enzymes but are not involved in oryzalactone biosynthesis, were also found in AA genome species. The phylogenetic analyses of KSLXs, KSL8s, and related pseudogenes (KSL9s) indicated that KSLX-OL was generated from a common ancestor with KSL8 and KSL9 via gene duplication, functional differentiation, and gene fusion. The wide distributions of KSLX-OL and KSL8 in AA genome species demonstrate their long-term coexistence beyond species differentiation, suggesting a balancing selection between the genes.

Diffuse CNS cortical vein malformations with chromosome 17q microduplication: Possible link to SEC14L1.

Partial trisomy of the long arm of chromosome 17 (17q) is a rare but clinically recognized syndrome that involves facial dysmorphisms, skeletal abnormalities, and global developmental delay, as well as various reports of cardiovascular, renal, and central nervous system abnormalities. This report presents a novel neuroradiologic finding of diffuse enlarged, tortuous cortical veins with physiological antegrade flow in a child with a microduplication of the distal end of 17q. To our knowledge, this finding has not been described previously. Although the exact cause for the cortical vascular anomaly is currently unknown, this duplicated region contains genes of interest for future studies that focus on normal and abnormal angiogenesis.

Unraveling Diverse Mechanisms of Complex Structural Variant Interactions through Multiomic Data in Multiple Myeloma

Introduction: Structural variants (SVs) play a role in proliferation of plasma cells that characterizes multiple myeloma (MM). Several hallmark SVs have been identified in MM, including translocations involving the immunoglobulin heavy chain locus and several partner genes, as well as deletions and duplications affecting key genes such as TP53, RB1, and MYC. Complex SVs such as templated insertions, chromothripsis, and chromoplexy are associated with disease progression but have not yet systematically been studied. Methods: Paired short-read (Illumina, average depth 75x), long-read HiFi (PacBio, 16x), optical genome mapping (OGM; Bionano Genomics, 341x) and Micro-C (Cantata Bio, 45x) data were sequenced from 8 relapsed MM patient-derived xenograft samples and 2 cell lines, covering t(11;14), t(4;14), and hyperdiploid subgroups. Reads were aligned to the hg38 reference genome while complex SVs (chromothripsis, chromoplexy and templated insertion) were systematically identified and accurately reconstructed by combining short-read (Manta), HiFi (pbsv), OGM, and Micro-C data (EagleC). Chromosome organization including loops, topologically associated domains (TADs) and A/B compartments were called from Micro-C data (Mustache and Juicer). Haplotype phasing was conducted using small variants detected from HiFi data. De novo assembly of the genome was conducted using HiFi and Micro-C data and compared to the reference genome. Reconstructed derivative chromosome interactions due to complex SVs were further identified by aligning Micro-C reads to the newly assembled genomes. Previously identified super-enhancers from H3K27Ac ChIP-seq from MM cell lines were mapped onto these SVs and expression of target genes assessed by RNA-seq. Results: 1,340 SVs were found in 10 samples using OGM of which 828 were identified in short-read WGS data. 16 complex SVs including chromothripsis, chromoplexy and templated insertions were detected in 10 samples, and we describe two (Fig.1) in detail here. A complex templated insertion consisting of a t(2;6;8) was found in a t(11;14) PDX sample with copy number gains at breakpoints which could not be resolved from short-read data alone. OGM data revealed a single contig consisting of DNA from chromosomes 2, 6, and 8. Micro-C data revealed interactions between these chromosomes, specifically the gained regions on chromosomes 2 and 8 showed more interactions with chromosome 6 than with other chromosomes, indicating insertions into chromosome 6. As a result, both MYC at chromosome 8 and GALM at chromosome 2 were inserted into the TXNDC5 locus, containing a known MM super-enhancer, leading to the over-expression of both MYC and GALM (log 2FC=1.7 and 1.0) in this sample. A de novo genome assembly indicated neo-TAD formation encompassing the super-enhancer and both genes. In coMMpass dataset, high expression of GALM and MYC are significantly associated with inferior overall (p=0.002 and 0.05, logrank test) and progression-free survival (p=0.01 and 0.09). Another complex templated insertion consisting of a t(3;4;16) was identified in a hyperdiploid PDX sample, again with copy number gains at breakpoints. Although the short-read data indicated an assembly similar to the previous templated insertion SV, the OGM and Micro-C data indicated a 3-way chromosome swap where the short arm of chromosome 3 was translocated to the short arm of chromosome 4, the short arm of chromosome 4 was translocated to the long arm of chromosome 16, and the long arm of chromosome 16 was translocated to the short arm of chromosome 3. Separate contigs for the t(4;16), t(3;16) and t(3;4) were confirmed by OGM data and only 2-way chromosomal interactions were seen in the Micro-C data. This complex event led to numerous oncogenes juxtaposed to super-enhancers, which caused over-expression of target genes such as ACD and RANBP10 (log 2FC=1.0 and 0.4), both of which were on chromosome 16 and are significantly associated with inferior overall (p=0.02 and p=0.004) and progression-free survival (p=0.003 and p=0.005). Conclusion: By utilizing multiomic techniques we were able to reconstruct complex SV events, showing different mechanisms of generating templated insertion events and identifying their biological consequences. We demonstrated how these complex events could potentially facilitate tumor proliferation via engaging the super-enhancers and regulating the expression of key oncogenes.

A Potential Link between hnRNP K and Cebpα: Implications for Ribosomal Dysfunction in Acute Myeloid Leukemia (AML)

Deletion of the long arm of chromosome 9, del(9q), is a recurrent genetic abnormality involving the haploinsufficient loss of the RNA binding protein hnRNPK and is often associated with poor treatment responses in AML. In addition to reduced hnRNP K expression, other critical proteins, not localized to this locus, are also aberrantly expressed in del9q AML. One protein of critical interest is CEBPα, a well-established myeloid differentiation transcription factor. Recently, CEBPα was discovered to have a novel role in ribosomal RNA (rRNA) synthesis. However, as opposed to CEBPα, hnRNP K's role in RNA stability, rRNA processing, and ribosomal functions is already firmly rooted. Collectively, these results suggest that del(9q) AML dysregulations in hnRNP K and CEBPα expression may have a multi-faceted influence on ribosomal biogenesis and protein translation. Previously, we used animal models and patient samples to demonstrate that Hnrnpk haploinsufficiency alters CEBPa expression, suggesting that reduced hnRNP K expression contributes to decreased CEBPα levels and activity. These findings led us to hypothesize that these distinct, yet interconnected proteins, play a cooperative role in regulating rRNA synthesis in two major ways. Firstly, hnRNP K directly governs rRNA processing and ribosomal loading. And secondly, via hnRNP K's mediated regulation of the nucleolar-localized isoform of CEBPα (p42 isoform), which was recently shown to enhance recruitment of RNA polymerase I to rRNA genes. To explore these relationships, we used AML patient samples, Hnrnpk haploinsufficient animal models, si- and sh- HNRNPK AML cell lines, and biochemical analyses. Initially, RPPA, CyTOF, and western blot analyses were used to investigate how reduced hnRNP K levels affect proteins involved in ribogenesis and protein translation. Here, we observed a direct correlation between hnRNP K expression and defects in proteins and pathways involved in protein translation, such as mTOR, phos-S6, and eEF- and eIF-family members, and CEBPa (log 10pAdj < .0001). Subsequently, we performed polysome assays that revealed 40S and 60S subunit formation was impaired in AML cell lines with reduced hnRNP K levels. Across multiple cell lines, reduced hnRNP K expression directly led to a significant increase in monosomes (unbound/inactive ribosomes; p < 0.01) and a significant decrease in polysome-bound RNA (p < 0.05) . Critically, HNRNPK haploinsufficiency and si- and sh- HNRNPK knock down experiments disrupted the abundance and processing of the 47S transcript (p < 0.05). To understand the impact that hnRNP K has on CEBPα in the context of rRNA biology, we performed co-immunoprecipitation of hnRNP K followed by RNA-seq (RIP-Seq) in human AML cell lines KG-1 and KG-1a. 1076 interacting RNAs were identified, which were strongly enriched in transcription factors implicated in myeloid biology, including CEBPA (log 2pAdj < .0001). Biochemical analyses of sequence-specific motifs conferred direct and functional interactions between hnRNP K and the 5‘ and 3‘ UTRs of the human CEBPA. These interactions support our in vivo findings that del9q AML and Hnrnpk haploinsufficiency lead to reduced CEBPA expression, specifically in the p42 isoform, potentially impacting its role in nucleolar localization and rRNA transcription regulation. Currently, we are evaluating the significance of these interactions at both the biological and translational levels. Using biochemical and cell-based assays, we are evaluating the direct effect that Hnrnpk haploinsufficiency has on rRNA abundance and on the processing of ITS products in the context of CEBPA. Through the use of viability screens, we are examining the efficacy of inhibitors of protein translation, translation initiation, and RNA Pol I on leukemic cells with 9q deletions of reduced hnRNP K expression. Altogether, these findings identify an uncharacterized relationship between del9qAML ( HNRNPK haploinsufficiency), CEBPα expression, and ribogenesis, providing valuable insight towards mechanisms driving this subtype of leukemia. Collectively, these data also suggest that del9q AML represents a novel and currently uncharacterized ribosomopathy.

CUX1mut Acute Myeloid Leukemia As a Distinct Biological Entity: An Analysis of Clinical Outcomes and Implications

1. Introduction CUX1 is a tumor suppressor gene located on the long arm of chromosome 7. CUX1 mutations induce apoptosis evasion and are more commonly seen in therapy-related myeloid neoplasms. It is frequently mutated in myelodysplastic syndrome and less frequently in acute myeloid leukemia (AML). Preclinical investigations are ongoing to explore therapeutic approaches in CUX1-deficient leukemia cell lines. However, data on the clinical outcomes of patients with AML and mutated CUX1 are sparse. We aimed to characterize the biological and clinical outcomes of CUX1 mut AML. 2. Methods We analyzed next-generation sequencing from 318 patients in the Project ERIS database with newly diagnosed AML treated from January 1, 2013 to April 18, 2023 at VCU Massey Comprehensive Cancer Center. We identified 12 patients with CUX1 mut AML and compared them to a cohort of 306 CUX1 wild-type historical controls. We recorded baseline patient-related and disease characteristics, including age, ECOG, Charlson comorbidity index (CCI) scores, molecular profiling and ELN 2022 cytogenetic risk, dates of regimen initiation, and survival. We used the D'Agostino & Pearson method for normality testing and the t-test or Mann-Whitney (as applicable) tests for between-group comparisons. Categorical comparisons used Fischer's exact test. We applied the Bonferroni correction if multiple comparisons were made. The Wilson-Brown method was used for 95% confidence intervals. We analyzed survival by the Kaplan-Meier method with significance determined by the log-rank test. The event for calculating the overall survival (OS) was the date of death. Patients were otherwise censored at the date of last contact. 3. Results CUX1 mutations are found at a frequency of 3.9% (95% CI, 2.2-6.5) in AML. The median variant allele frequency of CUX1 mutations was 40.3% (range: 3.8-48.7), consistent with a heterozygous presentation. The median age at diagnosis of patients with CUX1 mut who received any anti-leukemic therapy was 57 years (range: 30-78 years), which was not significantly different from CUX1 wt at 65 years (range: 19-88, p = 0.312). Thirty-three (95% CI, 13.8-60.9) percent of patients had AML with myelodysplasia-related changes (AML-MRC) on the initial diagnostic bone marrow biopsy, compared with 29.2% (95% CI, 24.2-34.7, p=0.752) for CUX1 wt. CUX1 mut AML was found in cytogenetically normal specimens at a frequency of 30.0% compared with 49.3% for CUX1 wt (p = 0.337). The most frequent cytogenetic abnormality in CUX1 mut AML was -7 (20.0%), followed by +8 (10.0%) and complex cytogenetics (10.0%). The most frequent cooperating molecular lesions were RUNX1, SRSF2, STAG2, FLT3-ITD, and NRAS (25.0% each). Patients with CUX1 mutations were nonsignificantly more likely to have ELN 2022 adverse-risk disease (odds ratio: 2.013, p = 0.379). In patients treated with intensive cytarabine-based inductions, the median overall survival was 26.3 months in the CUX1 mut group and 17.6 months in the CUX1 wt cohort, which was not significantly different (p = 0.501). Two patients with CUX1 mut AML were treated with first-line venetoclax and a hypomethylating agent. The overall survival was 12.7 months in one patient and not reached at a follow-up time of 20.2 months in the second. 4. Discussion While definitive conclusions are limited by the rarity of the mutation, mutations in CUX1 are heterozygous and appear to be non-significantly more frequently associated with myelodysplastic-related changes and secondary-type mutations. These findings may explain a higher proportion of patients harboring CUX1 mutations that have ELN 2022 adverse-risk disease. While we did not detect any significant survival differences between patients with and without CUX1 mutations, larger cohorts are needed to confirm the prognostic impact of these rare mutations in AML.

Prognostic Impact of Chromosomal Abnormalities in TP53-Mutated Acute Myeloid Leukemia and High-Risk Myelodysplastic Syndromes

Background: Background: Acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) exhibit clinical heterogeneity, and genomic profiles play a crucial role in disease characteristics and survival outcomes. Elli Papaemmanuil et al. classified AML into 11 genomic subgroups (NEJM, 2016), where TP53 mutations and aneuploidy predicted dismal survival. Cases with TP53 mutations are often accompanied by complex chromosomal abnormalities (CAs), but the prognostic impact and target genes of CAs have not been fully studied. Methods: To clarify this issue, specimens of AML and MDS with excess blasts (MDS-EB) were collected from 1,001 patients enrolled at collaborating institutes of Kyoto Hematology Study Group between July 2017 and January 2023. Targeted capture sequencing with 1,216 single nucleotide polymorphism sites was used to analyze primary samples, allowing assessment of copy number alteration (CNA) profiles. The target gene panel included common mutations in myeloid neoplasms. Mutation calling was performed using the established pipeline Genomon 2. Prognostic impact of CNA, single nucleotide variants, and insertion/deletion with 10% or more frequency was evaluated, and the frequencies of CNA were calculated for the short and long arms of chromosomes 1-22 and the X chromosome. Univariate and multivariate analyses were conducted using statistical significance criteria of p < 0.05. Results: The average sequencing depth was 548. Among 1,001 patients, 224 (22.4%) harbored TP53 mutations. TP53-mutated cases had a median age of 70 (24-95) years old at diagnosis, with 117 (52.2%) being AML and 107 (47.8%) MDS-EB. TP53 biallelic mutation, defined by 2 or more mutations in TP53 or loss of heterogeneity of TP53 locus, was present in 200 (89.3%) of cases, more commonly associated with 3 or more CAs or CNA (complex karyotype (CK)-like) than monoallelic mutation (99% vs. 42%, p = 1.9x10 -13). The most frequent affected lesions were del(5q), del(7q), del(7p), del(12p), del(18q), gain(11q), and gain(21q) with frequencies of 76%, 59%, 34%, 33%, 28%, 27%, and 26%, respectively. In survival analysis, gain(21q), gain(19p), del(16q), del(3q), del(19p), del(13q), and del(4q), along with diagnosis of AML ( p = 2.0x10 -2), TP53 biallelic mutation ( p = 6.8x10 -3), and CK-like ( p = 3.4x10 -3), were associated with poor outcomes in univariate analysis. Multivariate analysis revealed gain(19p), del(3q), del(13q), del(4q), diagnosis of AML, and CK-like as independent poor prognostic factors. Here we have defined gain(19p), del(3q), del(13q), and del(4q) as “Risk CNA”. A significant difference in outcomes was observed between patients with and without Risk CNA (n = 110 and n = 114, respectively, Hazard ratio = 2.6, p = 6.0x10 -8): The 6-month survival rate was 70 (95% Confidence interval [60-79]) % for patients without Risk CNA and 42 [31-52] % for those with Risk CNA. Patients with two or more Risk CNAs had worse prognosis than those with one ( p = 2.7x10 -2), indicating independent or additive contributions to outcomes. Similar trends were observed when limiting the analysis to TP53-biallelic cases. Further investigation of Risk CNA target genes was performed by identifying commonly amplified/deleted lesions. Target genes of gain(19p) included DNM2, CARM1, SMARCA4, LDLR, and EPOR, while RB1 and TET2 were potential candidates of del(13q) and del(4q), respectively. Identification of candidate genes for del(3q) was challenging due to broad common deleted lesions. Conclusion: Chromosomal abnormalities stratify the prognosis of AML and MDS-EB with TP53 mutation. The number of Risk CNA also impacts survival. Investigation of target genes of Risk CNA suggests potential therapeutic targets for TP53-mutated myeloid neoplasms, warranting further study for treatment optimization.

Insight into the mechanism of AML del(9q) progression: hnRNP K targets the myeloid master regulators CEBPA (C/EBPα) and SPI1 (PU.1)

Deletions on the long arm of chromosome 9 (del(9q)) are recurrent abnormalities in about 2 % of acute myeloid leukemia cases, which usually involve HNRNPK and are frequently associated with other known aberrations. Based on an Hnrnpk haploinsufficient mouse model, a recent study demonstrated a function of hnRNP K in pathogenesis of myeloid malignancies via the regulation of cellular proliferation and myeloid differentiation programs. Here, we provide evidence that reduced hnRNP K expression results in the dysregulated expression of C/EBPα and additional transcription factors. CyTOF analysis revealed monocytic skewing with increased levels of mature myeloid cells. To explore the role of hnRNP K during normal and pathological myeloid differentiation in humans, we characterized hnRNP K-interacting RNAs in human AML cell lines. Notably, RNA-sequencing revealed several mRNAs encoding key transcription factors involved in the regulation of myeloid differentiation as targets of hnRNP K. We showed that specific sequence motifs confer the interaction of SPI1 and CEBPA 5′ and 3′UTRs with hnRNP K. The siRNA mediated reduction of hnRNP K in human AML cells resulted in an increase of PU.1 and C/EBPα that is most pronounced for the p30 isoform. The combinatorial treatment with the inducer of myeloid differentiation valproic acid resulted in increased C/EBPα expression and myeloid differentiation. Together, our results indicate that hnRNP K post-transcriptionally regulates the expression of myeloid master transcription factors. These novel findings can inaugurate novel options for targeted treatment of AML del(9q) by modulation of hnRNP K function.

NCMP-05. INTRACTABLE HEADACHE IN NEWLY DIAGNOSED AML WITH MIGRAINES AND CHIARI MALFORMATION- UNVEILING A COMPLEX SYMPTOM

Abstract Acute Myeloid Leukemia (AML) involvement in central nervous system (CNS) is poorly understood in pathophysiology, with reported incidence rates ranging from 1-33% of patients with relapsed AML. CNS involvement is uncommon in the early stages of AML. FLT3-ITD, chromosome 11 abnormalities, and inv(16) cytogenetics are known to have more potential to invade the CNS. A 28-year-old woman with recently diagnosed AML (FLT D835 mutation with deletion in the long arm of chromosome 11) and migraines was admitted for HIDAC consolidation #3. On day two, she started experiencing headaches in the bifrontal and bitemporal regions associated with photophobia, phonophobia, and nausea. Treatment for status migrainous provided little relief. MRI brain showed progression of Chiari malformation (CM) with tonsillar herniation from 16 to 19 mm, which precluded a lumbar puncture. On day 4, she was noted to have grade III papilledema and bilateral cranial nerve IV palsy with non-enhancing patchy increased FLAIR signal in dorsal pons, bilateral cerebral and middle cerebellar peduncles, without diffuse restriction on imaging. The patient underwent sub-occipital craniotomy and C1 laminectomy for decompression for chiari. On day 5, she developed cranial nerve palsies involving nerves VII, IV, and XII. Lumbar puncture (LP) performed after decompression demonstrated elevated opening pressure and 98% abnormal myeloid blast population, confirming CNS involvement of AML. 4 days before starting intrathecal chemotherapy, the patient was found to be in asystole (unclear etiology). This case highlights the range of differential diagnoses for headaches in a patient with multiple comorbidities, including obesity, migraine, Chiari malformation with tonsillar herniation, and cancer. It underscores the necessity for proactive screening of CNS invasion in AML patients with high-risk mutations and neurological symptoms. Moreover, it emphasizes the need to consider CNS involvement in AML patients with headaches, even if standard imaging does not show typical signs of leptomeningeal spread.