Interstitial Deletion Research Articles

Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma.

The aim of this study was to assess the performance of fluorescence in situ hybridization (FISH) in identifying the copy number profiles of the three key peritoneal mesothelioma tumor suppressor genes BAP1, CDKN2A, and NF2, with particular emphasis on minute homozygous deletions, a copy number abnormality recently unveiled at the 3p21 (BAP1) chromosomal region using high-throughput methods. FISH was performed on 75 formalin-fixed-paraffin-embedded peritoneal mesotheliomas and recognized two types of monoallelic loss (monosomy, and hemizygous deletion) and two types of biallelic loss (canonical homozygous deletion with a complete loss of FISH signal and homozygous deletion with diminished signal). Diminished FISH signals revealed deletions occurring within the genomic region covered by the gene-specific probe and affected all three tumor suppressors. BAP1 homozygous deletions with diminished signal outnumbered canonical homozygous deletions (13 vs 3): conversely, canonical homozygous deletions were prevalent for CDKN2A (2 vs 14). Diminished signal homozygous deletion was the only pattern of biallelic loss observed for NF2 (2 cases). Hemizygous deletion mainly affected BAP1 (21 vs 6), while monosomy was prevalent for CDKN2A (14 vs 7) and particularly for NF2 where it accounts for all monoallelic losses. FISH/immunohistochemistry (BAP1, CDKN2A, and MTAP) correlation showed that all homozygous deletions, including those with diminished signals, resulted in a null BAP1 and CDKN2A immunophenotype but only canonical CDKN2A homozygous deletions resulted in MTAP loss of expression. BAP1 hemizygous deletion, but not monosomy, was also invariably associated with loss of protein expression whereas neither type of CDKN2A monoallelic loss correlated with p16 or MTAPimmunohistochemistry. Array comparative genomic hybridization performed on a spontaneously emerging peritoneal mesothelioma cell line provided support for the interpretation of the FISH patterns and allowed us to extend the number of chromatin remodeling factors involved in mesothelioma to SETD7 and PCGF5, two previously unreported genes.

A 14q distal chromoanagenesis elucidated by whole genome sequencing

Chromoanagenesis represents an extreme form of genomic rearrangements involving multiple breaks occurring on a single or multiple chromosomes. It has been recently described in both acquired and rare constitutional genetic disorders. Constitutional chromoanagenesis events could lead to abnormal phenotypes including developmental delay and congenital anomalies, and have also been implicated in some specific syndromic disorders. We report the case of a girl presenting with growth retardation, hypotonia, microcephaly, dysmorphic features, coloboma, and hypoplastic corpus callosum. Karyotype showed a de novo structurally abnormal chromosome 14q31qter region. Molecular characterization using SNP-array revealed a complex unbalanced rearrangement in 14q31.1-q32.2, on the paternal chromosome 14, including thirteen interstitial deletions ranging from 33 kb to 1.56 Mb in size, with a total of 4.1 Mb in size, thus suggesting that a single event like chromoanagenesis occurred. To our knowledge, this is one of the first case of 14q distal deletion due to a germline chromoanagenesis. Genome sequencing allowed the characterization of 50 breakpoints, leading to interruption of 10 genes including YY1 which fit with the patient's phenotype. This precise genotyping of breaking junction allowed better definition of genotype-phenotype correlations.

A complex and cryptic intrachromosomal rearrangement generating the FIP1L1_PDGFRA in adult acute myeloid leukemia

Myeloid neoplasms with eosinophilia and abnormalities of the PDGFRA gene can benefit from therapy with tyrosine kinase inhibitors, therefore revealing the PDGFRA rearrangement is essential to ensure the best choice of treatment. The most common PDGFRA partner is the FIP1L1 gene, generating the oncoprotein FIP1L1/PDGFRA (F/P). In the majority of cases the F/P fusion gene originates from intrachromosomal rearrangement at band 4q12, and occasionally from chromosomal translocations. In both cases, the interstitial chromosomal deletion of a region involving the CHIC2 gene has been reported, which is cryptic by conventional karyotyping but detectable by Fluorescence In Situ Hybridization (FISH) analyses. Herein, we report an acute myeloid leukemia (AML) case presenting with eosinophilia; the F/P fusion gene originated from a new, cryptic and complex intrachromosomal rearrangement of 4q12. Classical FISH assay revealed abnormal hybridization signals, but the presence of the F/P chimaeric gene was demonstrated by molecular analysis. We performed molecular characterization of the chromosomal rearrangement and targeted Next-Generation Sequencing (NGS) analysis with a myeloid gene panel, revealing the presence of pathogenic genomic variants affecting the TET2 and ETV6 genes. These mutations were present as subclones at the disease onset and their clone size increased at relapse.

Novel de novo interstitial deletion in 2q36.1q36.3 causes syndromic hearing loss and further delineation of the 2q36 deletion syndrome

Background: Deletions of the interstitial 2q36 are uncommon and associated with varying phenotypes. However, the list of currently known phenotypes is still far complete for an understanding of the interstitial 2q36 deletion syndrome characteristics.Aims/Objectives: To identify the genetic and clinical characterization of a 6-year-old male patient suffering from a severe form of syndromic hearing loss, with brachydactyly family history.Material and Methods: We performed conventional cytogenetic analysis on the peripheral blood lymphocytes and whole exome sequencing and SNP array analysis on DNA samples from the family.Results: The proband showed signs such as bilateral sensorineural deafness, ocular hypertelorism, flat facial profile and several decayed teeth, slightly ulnar deviation of the hands, single transverse palmar crease, short stature and intellectual disability. Through cytogenetic and molecular genetic analysis, we discovered that the syndromic hearing loss was the result of a de novo 5.175-Mb microdeletion at chromosome 2q36.1q36.3 whose breakpoints had been precisely mapped by us.Conclusions and Significance: Our study warns that auditory assessment should be evaluated even if the patient with 2q36 deletion syndrome is not obviously presenting hearing loss. In addition, a comprehensive molecular genetics diagnosis involving multiple methods is important to support accurate genetic characterization of this syndrome.

S4A-01SESSION 4A: GENERALITIES IN CRANIOSYNOSTOSIS – PART I CLINICAL AND GENETIC CHARACTERIZATION OF CRANIOSYNOSTOSIS; A RETROSPECTIVE COHORT STUDY AT KING SAUD UNIVERSITY MEDICAL CITY

Introduction: Craniosynostosis (CS) is defined as premature fusion of one or more of the cranial sutures and is classified to either simple or complex.CS can present as a part of a syndrome or as isolated finding.The aim of this study was to evaluate the clinical and genetic pattern of CS among Saudi population. Methods: A retrospective cohort study has been conducted from February 2015 till February 2019 at King Saud University Medical City among patients diagnosed with CS. Results: A total of 31 patients with CS has been identified in our center, of which 26 patients were operated, 4 patients refused surgery, and 1 was operated outside. 58 % (18 cases) of patients were male and 42% (13 cases) were female. Mean age at surgery among the 26 patients was 16 months. Simple CS was observed in 19 cases and complex CS in 12 cases. In our population, the most common simple skull suture fusion was unilateral coronal (plageocephaly) followed by metopic (trigonocephaly). Raised intracranial pressure was detected in 35.4% of the patients especially among syndromic cases and the most common grade of Papilledema were grade I and grade II preoperatively. The Most common procedure done was cranial vault reconstruction with fronto-orbital advancement, followed by posterior vault distraction. Post-operatively, Papilledema resolved in all but one patient who had improvement and is still being followed up. Furthermore, we found that 77.4% of patients had normal development and 22.6% presented with developmental delay. Developmental delay was observed commonly among complex suture fusion patients followed by metopic suture fusion. Genetics etiology was identified either by whole exome sequencing, single gene testing or microarray. Testing revealed; FGFR2 (5 cases), TWIST1 (4 cases), ALPL (2 cases), FREM1 (1 case), TGFBR2 (1 case), TCF12 (1 case), MAN2B1 (1 case), SETD2 (1 case), Interstitial deletion of the short arm of chromosome 7 in one case, and dual genetic diagnoses in one patient with ALDOB and ADAT3 gene mutations. Genetic testing for the remaining 9 cases is still not finalized. Parental consanguinity presented in 25.8% of the patients. Conclusion: Worldwide, Sagittal suture is the most commonly affected suture in simple craniosynostosis, but in our population coronal suture fusion was observed to be affected the most. This is the first study conducted about this topic in Saudi Arabia and further studies needed to investigate the characteristics of CS in our population.

A 3.06-Mb interstitial deletion on 12p11.22-12.1 caused brachydactyly type E combined with pectus carinatum.

Brachydactyly, a developmental disorder, refers to shortening of hands/feet due to small or missing metacarpals/metatarsals and/or phalanges. Isolated brachydactyly type E (BDE), characterized by shortened metacarpals and/or metatarsals, consists in a small proportion of patients with Homeobox D13 (HOXD13) or parathyroid-hormone-like hormone (PTHLH) mutations. BDE is often accompanied by other anomalies that are parts of many congenital syndromes. In this study, we investigated a Chinese family presented with BDE combined with pectus carinatum and short stature. A four-generation Chinese family was recruited in June 2016. After informed consent was obtained, venous blood was collected, and genomic DNA was extracted by standard procedures. Whole-exome sequencing was performed to screen pathogenic mutation, array comparative genomic hybridization (Array-CGH) analysis was used to analyze copy number variations, and quantitative real-time polymerase chain reaction (PCR), stride over breakpoint PCR (gap-PCR), and Sanger sequencing were performed to confirm the candidate variation. A 3.06-Mb deletion (chr12:25473650-28536747) was identified and segregated with the phenotype in this family. The deletion region encompasses 23 annotated genes, one of which is PTHLH which has been reported to be causative to the BDE. PTHLH is an important regulator of endochondral bone development. The affected individuals showed bilateral, severe, and generalized brachydactyly with short stature, pectus carinatum, and prematurely fusion of epiphyses. The feature of pectus carinatum has not been described in the PTHLH-related BDE patients previously. The haploinsufficiency of PTHLH might be responsible for the disease in this family. This study has expanded the knowledge on the phenotypic presentation of PTHLH variation.

PS1330 VARIABILITY IN THE EXTENT OF DEL(5Q) AND ITS CLINICAL IMPLICATION IN MYELODYSPLASTIC SYNDROMES (MDS)

Background:The interstitial deletion of the long arm of chromosome 5—del(5q)—is the most common cytogenetic abnormality in MDS occurring either as a sole aberration or as a part of complex karyotypes (CK). MDS with isolated del(5q) are associated with a favorable outcome while MDS with CK relate to poor prognosis. Extent of deleted segment is highly variable. However, it remains unclear whether its size matters for the different MDS phenotypes.Aims:The aim was to compare the extent of deletion in 264 MDS patients [116 with isolated del(5q) and 148 with del(5q) involved in CK] and to assess the relationship of del(5q) extent and TP53 gene mutation.Methods:Extent of del(5q) was analyzed using I‐FISH (Abbott, MetaSystems), mBAND (MetaSystems) and array CGH/SNP (CytoChip Cancer SNP 180K, Illumina or SurePrint G3 Cancer CGH+SNP 4x180K, Agilent). CK were analyzed with mFISH (MetaSystems). Sequence analysis of TP53 gene was performed in 84 cases using amplicon deep sequencing (exons 4–11) on a 454 GS Junior system (Roche) or with TruSight Myeloid Panel Kit on MiSeq sequencing instruments (Illumina).Results:In the group with isolated del(5q), the most frequently deleted segment ranged between the bands 5q14 and 5q33.3, with the smallest deletion encompassing the 5q31.1–5q31.3 region (18.527 Mb). The TP53 mutation was proved in 19.4% cases. The size of the deletion did not significantly differ in patients with and without TP53 mutation. In the group with CK, the deletion often involved entire long arm including the telomeric region. In some cases, a part of short arm was also deleted, but we never observed the loss of the entire chromosome 5. The commonly conserved region (CCR) was localized in bands 5p12 to 5p14.1. In this group, the mutation of TP53 and/or LOH17p was detected in 49% of patients. The commonly deleted regions (CDR) were in the band 5q31.1 (5.522 Mb) in cases with isolated del(5q) and between the bands 5q31.1 and 5q31.3 (18.527 Mb) in patients with CK.Summary/Conclusion:Patients with isolated del(5q) had a smaller size of the deleted segment. More extensive 5q deletion was associated with higher karyotype complexity, increased frequency of TP53 aberrations and worse prognosis. Accurate analysis of breakpoints and range of del(5q) points out to the correlation of deletion size with increasing genomic instability in MDS and contributes to a better understanding of the MDS pathogenesis.Supported by RVO‐VFN64165, GACR P302/12/G157, ProgresQ28/LF1, MHCR 00023736.

First report of two successive deletions on chromosome 15q13 cytogenetic bands in a boy and girl: additional data to 15q13.3 syndrome with a report of high IQ patient

15q13.3 syndrome is associated with a wide spectrum of neurological disorders. Among a cohort of 150 neurodevelopmental cases, we identified two patients with two close proximity interstitial hemizygous deletions on chromosome 15q13. Using high-density microarrays, we characterized these deletions and their approximate breakpoints. The second deletion in both patients overlaps in a small area containing CHRNA7 where the gene is partially deleted. The CHRNA7 is considered a strong candidate for the 15q13.3 deletion syndrome’s pathogenicity. Patient 1 has cognitive impairment, learning disabilities, hyperactivity and subtle dysmorphic features whereas patient 2 has mild language impairment with speech difficulty, mild dysmorphia, heart defect and interestingly a high IQ that has not been reported in 15q13.3 syndrome patients before. Our study presents first report of such two successive deletions in 15q13.3 syndrome patients and a high IQ in a 15q13.3 syndrome patient. Our study expands the breakpoints and phenotypic features related to 15q13.3 syndrome.

Clinical and molecular cytogenetic characterization of a novel 10q interstitial deletion: a case report and review of the literature

BackgroundThere are only ten reported cases of interstitial deletions involving cytogenetic bands 10q21.3q22.2 in the literature. Of the ten patients with overlapping 10q21.3q22.2 interstitial deletions, only nine have been characterized by chromosomal microarray analysis. Here, we report a two-and-a-half-year-old patient with a de novo 10.2-Mb deletion that extends from 10q21.3 to 10q22.3 and contains 92 protein coding genes.Case presentationThe patient is the product of a 37-week dizygotic twin pregnancy and presented with global developmental delay, hypotonia, feeding difficulties, short stature, poor weight gain, scaphocephaly, retrognathia, hypoplasia of the optic nerves/chiasms, a distinctive facial gestalt, as well as additional minor dysmorphic features. The deletion identified in our patient is the second largest reported interstitial deletion involving the 10q21.3q22.2 region. Our patient presents with the generalized features observed in 10q21.3q22.2 deletion patients and also presents with several novel findings including scaphocephaly, hypoplasia of the optic nerves and chiasms, and a very distinctive facial gestalt.ConclusionsBased on a literature review, we identify a commonly deleted region and suggest that KAT6B is a critical gene within the 10q21.3q22.2 region. However, a review of the reported overlapping deletions also suggests that there are additional critical genes contributing to the clinical presentation of these patients.

Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders.

The radial spatial positioning of individual gene loci within interphase nuclei has been associated with up- and downregulation of their expression. In cancer, the genome organization may become disturbed due to chromosomal abnormalities, such as translocations or deletions, resulting in the repositioning of genes and alteration of gene expression with oncogenic consequences. In this study, we analyzed the nuclear repositioning of HLXB9 (also called MNX1), mapping at 7q36.3, in patients with hematological disorders carrying interstitial deletions of 7q of various extents, with a distal breakpoint in 7q36. We observed that HLXB9 remains at the nuclear periphery, or is repositioned towards the nuclear interior, depending upon the compositional properties of the chromosomal regions involved in the rearrangement. For instance, a proximal breakpoint leading the guanine-cytosine (GC)-poor band 7q21 near 7q36 would bring HLXB9 to the nuclear periphery, whereas breakpoints that join the GC-rich band 7q22 to 7q36 would bring HLXB9 to the nuclear interior. This nuclear repositioning is associated with transcriptional changes, with HLXB9 in the nuclear interior becoming upregulated. Here we report an in cis rearrangement, involving one single chromosome altering gene behavior. Furthermore, we propose a mechanistic model for chromatin reorganization that affects gene expression via the influences of new chromatin neighborhoods.

SUN-290 Responsiveness of Growth Hormone Therapy in a Patient with Complex Chromosome 4 q Interstitial Deletion

Background Information: Chromosome 4 q interstitial deletion is a rare chromosomal disorder characterized by post natal growth retardation, developmental delay, craniofacial dysmorphism and behavioral problems. Not only are the characteristics of growth failure in these patients ill defined, but their responsiveness to growth hormone (GH) treatment is also lacking in the literature. An index case of a 7 year old male with unique interstitial deletion of chromosome 4 q deletion at q13.3 and q22.12 with a normal segment in between presented with significant growth failure in early infancy and was treated with growth hormone as described below. Case Report: He was born at 36 weeks gestation with a birth weight of 4 pounds 6 ounces (3rd percentile) and a birth length of 19 inches (50th percentile). Pregnancy was complicated by oligohydraminos. Post natal course was complicated by feeding difficulties and jaundice. He grew along the 5th percentile till age 6 months and then started faltering off below the 3rd percentile in both height and weight. He was started on dense caloric formula but his growth parameters continued to decline. His intake was reported good and had no diarrhea or vomiting. A TFT obtained demonstrated a slightly elevated TSH of 9.4 mcIU/ml (reference range 0.4-9.2) and marginally low Free T4 of 0.76 ng/dl (reference range 0.89-1.48). He was started on a small dose of 12.50 mcg thyroxin daily which did not improve his growth (thyroxin was discontinued at age 4 ½ year). His chemistry panel, IGF-1 and IGFBP-3 obtained were all normal. A bone age was concordant with his chronological age. Karyotype was 46 XY. Comparative genomic hybridization (CGH) array revealed a de novo 2.2 Mb deletion at 4q 13.3 and 2.2 Mb deletion at 4q22.1-q22.3. Deletions were separated by 18.3 Mb of normal copy number sequence. Other tests obtained demonstrated a normal pituitary gland on brain MRI and no tethered cord on the spinal MRI. He was started on GH for small for gestational age indication at age 13 month. His height and weight percentile improved significantly from <1% at age 13 month to 5th% by age 2 year and has continued to grow along 10-12 % since age 4 year. His other associated medical problems include improving developmental delay (attends special class with IEP and speech therapy), sleep disturbances (on melatonin and clonidine), mild hypotonia (received OT and PT, now resolved), poor dental enamel (has needed 8 crowns), obstructive sleep apnea with high arched palate (status post turbinate reduction and CPAP), clinodactyly, hyperopia with astigmatism (wears glasses) and sacral dimple. His behavior problems include high anxiety and obsessive/perseveration behavior. Conclusions: Growth failure is a characteristic feature in patients with chromosome 4 q deletion. These patients with growth retardation when treated with GH may respond with improved growth velocity and weight gain and hence should be considered.

Interstitial 14q31.3-q32.13 deletion

Aim: With the exception of ring chromosome 14 or translocations, interstitial deletions of the long arm of chromosome 14 are very rare. All patients with these deletions share common phenotypic characteristics, primarily mild dysmorphia and developmental delay. Molecular karyotyping (array CGH) enabled the precise breakpoint determination and improved the analysis of genotype-phenotype correlations. Case presentation: In a 7-year-old girl, array CGH was performed due to developmental delay. The array CGH study showed 8.3Mb de novo interstitial deletion of the 14q31.3–q32.13 region. Conclusions: Comparison of our patient´s phenotype with previously reported chromosome 14q interstitial deletion cases confirmed the presence of common clinical features and highlights the utility of array CGH as a diagnostic tool in clarifying the developmental delay etiology.

Alleles dropout patterns of Y-short tandem repeats in infertile males with Y chromosome microdeletions

Y chromosomal short tandem repeat (Y-STR) typing is the most commonly used genetic technique in forensic studies. However, there may be a limit to the application of Y-STR in forensic science as Y-STR loci are subject to loss or variation caused by the higher chromosomal structures' spontaneous mutation rate. Located in the long arm of the Y chromosome, azoospermia factor (AZF) have been shown to participate in spermatogenesis and its deletion could cause infertility. However, little is known about the Y-STR dropout pattern in individuals with Y chromosome microdeletions. In this study, 85 infertile males with Y chromosome interstitial deletion were identified and special Y-STR allele dropout patterns were analyzed by employing a Y-STR Commercial Kit and a Y chromosome Deletion Kit. Results demonstrate that AZF a region deletion are related to DYS439-DYS389I-DYS389II alleles dropout, while AZF b region or c region deletions correlate to DYS448 allele dropout. Null DYS385-DYS392-DYS448 alleles were observed in AZF b+c+d region deletion individuals. While null DYS390-Y-GATA-H4-DYS385-DYS392-DYS448 alleles were observed in AZF a+b+c+d large region deletion individuals. Our data suggest that Y chromosome microdeletions may indicate specific Y-STR locus dropout patterns.

IKZF1 Deletions with COBL Breakpoints Are Not Driven by RAG-Mediated Recombination Events in Acute Lymphoblastic Leukemia

IKZF1 deletion (ΔIKZF1) is an important predictor of relapse in both childhood and adult B-cell precursor acute lymphoblastic leukemia (B-ALL). Previously, we revealed that COBL is a hotspot for breakpoints in leukemia and could promote IKZF1 deletions. Through an international collaboration, we provide a detailed genetic and clinical picture of B-ALL with COBL rearrangements (COBL-r). Patients with B-ALL and IKZF1 deletion (n = 133) were included. IKZF1 ∆1-8 were associated with large alterations within chromosome 7: monosomy 7 (18%), isochromosome 7q (10%), 7p loss (19%), and interstitial deletions (53%). The latter included COBL-r, which were found in 12% of the IKZF1 ∆1-8 cohort. Patients with COBL-r are mostly classified as intermediate cytogenetic risk and frequently harbor ETV6, PAX5, CDKN2A/B deletions. Overall, 56% of breakpoints were located within COBL intron 5. Cryptic recombination signal sequence motifs were broadly distributed within the sequence of COBL, and no enrichment for the breakpoint cluster region was found. In summary, a diverse spectrum of alterations characterizes ΔIKZF1 and they also include deletion breakpoints within COBL. We confirmed that COBL is a hotspot associated with ΔIKZF1, but these rearrangements are not driven by RAG-mediated recombination.

Abstract P5-05-08: Molecular cross-talk between retinoic acid and NOTCH1 signaling pathways: Role in triple negative breast cancer

Abstract Triple Negative Breast Cancer (TNBC) represents 10-20% of all breast cancers and it is characterized by poor prognosis and high recurrence rate. The heterogeneity of the disease and the absence of well-defined molecular targets have so far challenged successful therapeutic strategies. NOTCH1 has been found to act as a driver oncogene in a small subset of TNBC characterized by constitutive activation of the protein, acting as a transcription factor. Preclinical studies support an anti-tumor activity of All-Trans Retinoic Acid (ATRA) in specific subsets of breast cancer. By screening a large panel of breast cancer cell lines recapitulating the heterogeneity of TNBC we identify a specific subset sensitive to the anti-proliferative activity of ATRA. These cell lines (N-TNBC cell lines) are characterized by a Notch1 intragenic fusion transcript conferring gain of function activity to the protein. Indeed, sequence analysis reveals that the cell lines harbor an interstitial deletion in the NOTCH1 gene encompassing the negative regulatory region (NRR) domain. These cell lines depend on Notch active signaling for their proliferation since their cell growth is impaired by Notch inhibitors (γ-secretase inhibitors, e.g. DAPT, PF-3084014). Proliferation assays reveal that ATRA and γ-secretase inhibitors act synergistically in inhibiting cancer cell growth in N-TNBC cell lines suggesting the existence of a cross talk between the molecular pathways engaged by retinoic acid and NOTCH1. By using retinoic acid receptors (RARs) agonists and antagonists as well as RAR specific silencing experiments we identify RARα as the retinoic acid receptor responsible of the anti-proliferation activity of ATRA in N-TNBC cell lines. In particular N-TNBC cell lines respond to RARα activation by inducing high amounts of the onco-supressor protein RARβ. This feature is unique in ATRA sensitive TNBC cell lines and does not occur in ATRA sensitive luminal cell lines arguing for the existence of a retinoic acid specific mechanism of action in N-TNBC. Since RARs act as transcription factors inside the cells, to gain insights into the molecular pathway at the basis of the observed ATRA/NOTCH1 cross talk, we performed RNAseq analysis of ATRA and/or DAPT treated N-TNBC cells. Gene set enrichment analysis reveal that ATRA is able to directly affect NOTCH1 transduction pathway by modulating the expression of NOTCH1 target genes. In particular, in two out of three N-TNBC cell lines ATRA directly inhibits the NOTCH1 expression at a transcriptional level and its downregulation is increased by ATRA/DAPT combinations. Pathway analysis has allowed the identification of putative molecular hubs responsible for the synergistic effects observed and therefore likely at the basis of the crosstalk between ATRA/NOTCH pathways. These findings are of clinical interest since both the retinoid and NOTCH signaling display crucial physiologic activities and their pleiotropic effects could impinge on the success of therapeutic options based on their pathway modulation. The newly discovered specificity of ATRA action in the context of NOTCH1 addicted TNBC provides new tools for the identification of patients candidates benefitting from strategies targeting the ATRA/NOTCH axis. Citation Format: Paroni G, Zanetti A, Bolis M, Vallerga A, Troiani M, Fratelli M, Kurosaki M, Terao M, Garattini E. Molecular cross-talk between retinoic acid and NOTCH1 signaling pathways: Role in triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-08.

A Rare Co-occurrence of Intestinal Malrotation and Hirschsprung's Disease in a Neonate with 13q21.31q33.1 Interstitial Deletion Including the EDNRB Gene

We report a rare co-occurrence of intestinal malrotation and Hirschsprung's disease (HSCR) in a male neonate with a large 38.8 Mb interstitial deletion of chromosome 13 extending from q21.31 to q33.1 including the EDNRB gene, who presented with craniofacial dysmorphic features and central nervous system malformations. The loss of EDNRB gene in addition to bilateral hearing loss and HSCR suggested an additional diagnosis of Waardenburg-Shah's syndrome. This case highlights the fact that prior knowledge of this rare association in infants with 13q deletion syndrome would enable early diagnosis and prompt interventions to prevent gastrointestinal complications.

Neonate with 10q Interstitial Deletion within the Long Arm of Chromosome 10- A Case Report and Literature Review

Introduction: Partial deletion of distal chromosome 10q was first reported in 1978 by Lewandowski1. Interstitial deletions within bands 10q25e10q26.3 are rare. Seven such cases were reported so far2. Patient Information: A term AGA male newborn was delivered at our perinatal center with antenatal diagnosis of unbalanced translocation of chromosomes 10 and 12, and fetal cleft lip and cleft palate. Blood was sent for chromosome analysis using GTG banding method. Baby had facial dysmorphism, left cleft lip, bilateral cleft of soft and hard palate, intact nasal septum, normal ears and micrognathus. Abdominal ultrasound showed absence of right testis in inguinal canal and abdomen (anorchia). Hospital course was unremarkable except for feeding problems requiring feeding team, plastic surgery planned at 2- 3 months of age, and taping of the cleft lip. He went home on day 7. Conclusion: Here, we reported an extremely rare case of a male newborn with an interstitial deletion within the long arm of chromosome 10 between bands 10q25.1 and 10q26.1, with dysmorphic features, along with a few unreported associations (atypical Pierre-Robin sequence and bilateral dorsal horn ventriculomegaly). We added a comprehensive review of literature on chromosome 10q deletions to the case report. We also listed clinical implications of 71 RefSeq and OMIM genes noted in that ~13.3Mb 10q deletion in the Appendix. Earlier detection of both common and rare chromosomal- genetic abnormalities might prepare the family and health care team to plan optimal care to the mother, and baby.

An immunohistochemical approach to detect oncogenic CTNNB1 mutations in primary neoplastic tissues

The Wnt/β-catenin signaling pathway is dysregulated in different types of neoplasms including colorectal cancer (CRC). Aberrant activation of this signaling pathway is a key early event in the development of colorectal neoplasms, and is mainly caused by loss of function mutations in Adenomatous Polyposis Coli (APC), and less frequently by β-catenin stabilization mutations via missense or interstitial genomic deletions in CTNNB1. In this study, we have defined an immunohistochemical algorithm to dissect Wnt pathway alterations in formalin-fixed and paraffin-embedded neoplastic tissues. Basically, consecutive sections of tumor specimens were stained by immunohistochemistry with two different monoclonal antibodies against β-catenin: one (anti-active β-catenin antibody) recognizes hypo-phosphorylated β-catenin and the other recognizes the total pool of β-catenin. We validated the strategy in the HCT116 CRC cell line which has an in-frame deletion of β-catenin serine 45, and then studied human tumor microarrays containing colon adenomas, CRCs, solid pseudopapillary neoplasms of the pancreas as well as the whole tissue sections of CRCs, desmoid fibromatosis, and pilomatrixoma of the skin. In some tumors, we found strong β-catenin cytoplasmic and/or nuclear staining with the total β-catenin antibody but no staining with the anti-active β-catenin antibody. This was inferred to be an altered/mutant β-catenin staining pattern. All six colon adenomas of the 126 total adenomas studied for the altered/mutant β-catenin staining pattern had presumptively pathogenic point mutations or deletions in CTNNB1. Four of 10 CRCs with the alterated/mutant β-catenin staining pattern studied in depth, from 181 total CRCs from tissue microarray, had pathogenic CTNNB1 mutations. The frequencies of CTNNB1 alterations in non-colonic tumors with altered/mutant β-catenin staining ranged between 46 and 100%. Our results demonstrate that the immunohistochemical approach described here can detect oncogenic forms of β-catenin in primary tissue samples and can also highlight other tumors with presumptive novel defects activating the Wnt/β-catenin pathway.Wnt/β-catenin signaling pathway activation is frequent event in the development of neoplasms. In this study, the authors defined an immunohistochemical approach to dissect CTNNB1 (β-catenin) mutations in formalin-fixed and paraffin-embedded primary neoplasms. They validated an immunohistochemical mutation detection algorithm in colon adenomas, carcinomas and various non-colonic Wnt pathway activated tumors.

A Novel de Novo Paracentric Inversion [inv(20)(q13.1q13.3)] Accompanied by an 11q14.3-q21 Microdeletion in a Pediatric Patient with an Intellectual Disability.

A novel de novo paracentric inversion of the long arm of chromosome 20 [inv(20)(q13.1q13.3)], detected by conventional karyotyping in a 14-year-old boy with mental retardation is described. Further investigation by array comparative genomic hybridization (aCGH) revealed that the 20q inversion was not accompanied by microdeletions/microduplications containing disease-associated genes near or at the breakpoints. Two deletions at chromosomal regions 11q14.3q21 and 20q12 of 4.5 and 1.97 Mb size, respectively, containing important online Mendelian inheritance in man (OMIM) genes, were detected. The 4.5Mb 11q14.3q21 microdeletion was contained within a region that is involved, in most of the reported cases, with the interstitial 11q deletion and may be related to the mental retardation and developmental delay present in the patient. On the other hand, the published data about the 20q12 microdeletion are very few and it is not possible to correlate this finding with our patient’s phenotype. This case report contributes to the description of a new chromosomal entity, not previously reported, and is therefore important, especially in prenatal diagnosis and management of patients. Array comparative genomic hybridization has proven a useful technique for detecting submicroscopic rearrangements and should be offered prenatally, especially in cases of de novo karyotypically balanced chromosomal inversions or translocations in order to unveil other unbalanced chromosomal abnormalities such as deletions and amplifications.

Rare Case of a Heterozygous Microdeletion 9q21.11-q21.2: Clinical and Genetic Characteristics.

Intellectual disability is affecting 3.0-4.0% of the general population. Copy number variants (CNVs) are a significant cause leading to neurodevelopmental disorders such as intellectual disability, epilepsy, autism spectrum disorders and developmental delay. The use of single nucleotide polymorphism (SNP)-array and array comparative genomic hybridization (aCGH) as diagnostic tools has led to the recognition of new microdeletion/microduplication syndromes associated with neurodevelopmental disorders. It is also useful for further characterization of marker chromosomes. Here, we report a girl with mild intellectual disability and mild facial dysmorphisms. Cytogenetic analysis showed a marker chromosome in some percent of the cells and was followed by SNP-array karyotyping that detected, in addition, a 9655 Mb de novo interstitial deletion at 9q21.1-9q21.2.