Chromosome 22q11 Research Articles

Outcomes of patients with multiple myeloma and 1q gain/amplification receiving autologous hematopoietic stem cell transplant: the MD Anderson cancer center experience

The prognostic impact of additional copies of chromosome 1q (1q + ) on outcomes of newly-diagnosed multiple myeloma (NDMM) patients undergoing autologous transplantation (autoSCT) is unclear. We conducted a retrospective single-center analysis of NDMM patients with 1q21 gain/amplification (3 or ≥4 copies of 1q, respectively) that received autoSCT between 2008–2018. 213 patients were included (79% 1q gain; 21% 1q amplification). The most commonly used induction regimen was bortezomib, lenalidomide, and dexamethasone (41%). At day100 post-autoSCT and at best post-transplant response, 78% and 87% of patients achieved ≥VGPR, and 38% and 50% achieved MRD-negative ≥VGPR, respectively. Median PFS and OS for the entire cohort were 35.5 months and 81.4 months, respectively. On multivariable assessment for PFS, MRD negative ≥VGPR before autoSCT (HR 0.52, p = 0.013) was associated with superior PFS, whereas 1q amplification was associated with inferior PFS (2.03, p = 0.003). On multivariate analysis for OS, achieving MRD negative ≥VGPR at best post-transplant response was associated with superior survival (0.29, p < 0.001), whereas R-ISS III and concomitant del17p or t(4:14) were associated with inferior survival (6.95, p = 0.030, 2.33, p = 0.023 and 3.00, p = 0.047, respectively). In conclusion, patients with 1q+ NDMM, especially 1q amplification, have inferior survival outcomes compared to standard-risk disease after upfront autoSCT, though outcomes are better than other high-risk cytogenetic abnormalities.

Thrombospondin-1 is an endogenous substrate of cereblon responsible for immunomodulatory drug–induced thromboembolism

AbstractImmunomodulatory drugs (IMiDs) are key drugs for treating multiple myeloma and myelodysplastic syndrome with chromosome 5q deletion. IMiDs exert their pleiotropic effects through the interaction between cell-specific substrates and cereblon, a substrate receptor of the E3 ubiquitin ligase complex. Thus, identification of cell-specific substrates is important for understanding the effects of IMiDs. IMiDs increase the risk of thromboembolism, which sometimes results in fatal clinical outcomes. In this study, we sought to clarify the molecular mechanisms underlying IMiDs-induced thrombosis. We investigated cereblon substrates in human megakaryocytes using liquid chromatography–mass spectrometry and found that thrombospondin-1 (THBS-1), which is an inhibitor of a disintegrin-like and metalloproteinase with thrombospondin type 1 motifs 13, functions as an endogenous substrate in human megakaryocytes. IMiDs inhibited the proteasomal degradation of THBS-1 by impairing the recruitment of cereblon to THBS-1, leading to aberrant accumulation of THBS-1. We observed a significant increase in THBS-1 in peripheral blood mononuclear cells as well as larger von Willebrand factor multimers in the plasma of patients with myeloma, who were treated with IMiDs. These results collectively suggest that THBS-1 represents an endogenous substrate of cereblon. This pairing is disrupted by IMiDs, and the aberrant accumulation of THBS-1 plays an important role in the pathogenesis of IMiDs-induced thromboembolism.

A NOVEL NON-CODING RNA-BASED APPROACH TO MODULATE OSTEOCLAST BEHAVIOUR

Osteoclasts (OCs) are multinucleated cells that play a pivotal role in skeletal development and bone remodeling. Abnormal activation of OCs contributes to the development of bone-related diseases, such as osteoporosis, bone metastasis and osteoarthritis. Restoring the normal function of OCs is crucial for bone homeostasis. Recently, RNA therapeutics emerged as a new field of research for osteoarticular diseases.The aim of this study is to use non-coding RNAs (ncRNAs) to molecularly engineer OCs and modulate their function. Specifically, we investigated the role of the microRNAs (namely miR-16) and long ncRNAs (namely DLEU1) in OCs differentiation and fusion.DLEU1/DLEU2 region, located at chromosome 13q14, also encodes miR-15 and miR-16. Our results show that levels of these ncRNA transcripts are differently expressed at distinct stages of the OCs differentiation. Specifically, silencing of DLEU1 by small interfering RNAs (siDLEU1) and overexpression of miR-16 by synthetic miRNA mimics (miR-16-mimics) led to a significant reduction in the number of OCs formed per field (OC/field), both at day 5 and 9 of the differentiation stage. Importantly, time-lapse analysis, used to track OCs behavior, revealed a significant decrease in fusion events after transfection with siDLEU1 or miR-16-mimics and an alteration in the fusion mode and partners. Next, we investigated the migration profile of these OCs, and the results show that only miR-16-mimics-OCs, but not siDLEU-OCs, have a lower percentage of immobile cells and an increase in cells with mobile regime, compared with controls. No differences in cell shape were found. Moreover, mass-spectrometry quantitative proteomic analysis revealed independent effects of siDLEU1 and miR-16-mimics at the protein levels. Importantly, DLEU1 and miR-16 act by distinct processes and pathways.Collectively, our findings support the ncRNAs DLEU1 and miR-16 as therapeutic targets to modulate early stages of OCs differentiation and, consequently, to impair OC fusion, advancing ncRNA-therapeutics for bone-related diseases.Acknowledgements: Authors would like to thank to AO CMF / AO Foundation (AOCMFS-21-23A). SRM and MIA are supported by FCT (SFRH/BD/147229/2019 and BiotechHealth Program; CEECINST/00091/2018/CP1500/CT0011, respectively).

Gain of Chromosome 5q Predicts a Favorable Prognosis in Localized Renal Cell Carcinoma

Approximately 65% of renal cell carcinomas (RCC) are diagnosed at a localized stage. We investigated the chromosome 5q gain impact on disease-free survival (DFS) in RCC patients. Overall, 676 patients with stages 1–2 RCC and having cytogenetic analysis were included. Gain of 5q was observed in 108 patients, more frequently in clear cell (ccRCC) than non-clear cell tumors. Gain of 5q is likely an independent prognostic factor since the concerned patients had a decreased recurrence risk in stages 1–2 RCC, confirmed in multivariable analysis. Detecting 5q gain could enhance recurrence risk assessment, allowing tailored post-surgery surveillance, and reducing unnecessary treatments.

Rudimentary and Incipient-Yolk Sac Tumour- Testis

Yolk sac tumour of testis configures as a germ cell neoplasm comprised of cellular articulations or structures simulating embryonic or foetal yolk sac, allantois and extra-embryonal mesenchyme. Testicular yolk sac tumour is pre-eminently comprised of prepubertal subtype which is non-concordant to germ cell neoplasia in situ, emerges as a ‘pure’ neoplasm and demonstrates multiple gains within chromosome 1q, 20q or 22 and losses within chromosomes 1p, 4 or 6q. Postpubertal subtype is concurrent to germ cell neoplasia in situ (GCNIS), preponderantly configures as a component of ‘mixed tumour’ and occurs due to testicular dysgenesis syndrome, subfertility or as single nucleotide polymorphism (SNP) variants within KITLG, SPRY4 or DMRT1 genes and expounds gain of isochromosome 12p. Upon microscopy, neoplasm may configure distinctive configurations as microcystic or reticular pattern, macrocystic pattern, myxomatous pattern, sarcomatoid or spindle shaped cellular pattern, solid pattern, glandular or alveolar pattern, endodermal sinus or perivascular pattern, hepatoid pattern, papillary pattern, parietal pattern or poly-vesicular vitelline pattern. Yolk sac tumour appears immune reactive to alpha fetoprotein (AFP), glypican 3, SALL4, pancytokeratin, villin or CK7. Neoplastic cells appear immune non-reactive to OCT3/4, CD30, CD117, placental alkaline phosphatase (PLAP), podoplanin (D2-40), inhibin, GATA3 or p63. Testicular yolk sac tumour requires segregation from neoplasms as teratoma, seminoma, embryonal carcinoma, rete testis with hyaline globules and microcystic leydig cell tumour. Tumefaction preponderantly depicts elevated levels of serum alpha fetoprotein (AFP). Testicular yolk sac tumour may be optimally subjected to surgical manoeuvers as orchiectomy.

Huddled and Preternatural- Atypical Lobular Hyperplasia

Atypical lobular hyperplasia manifests as a clonal proliferation of dis-cohesive epithelial cells emerging from terminal duct lobular units. Neoplasm appears reminiscent of lobular carcinoma in situ (LCIS) although cellular quantification is reduced. Characteristically, the incidentally discovered lesion is associated with dysfunction or decimation of E-cadherin. Additionally designated as lobular intraepithelial neoplastic 1 (LIN1), tumefaction exemplifies a female preponderance. Typically, adult subjects are implicated. Tumefaction is commonly encountered within the fifth decade although no age of disease emergence is exempt. Atypical lobular hyperplasia is detected within&lt;1% of core needle biopsies adopted for evaluating BI-RADS 4 lesions [1,2]. Atypical lobular hyperplasia may incriminate bilateral breasts wherein specific lesion localization is absent. Tumefaction exhibits loss of chromosome 16qand deletion of CDH1 genes with loss of function of E-cadherin, a Tran’s membrane cell adhesion molecule. Alternatively, altered function of E-cadherin may occur. Exceptionally, various adhesion proteins are implicated wherein E-cadherin molecule appears stable [1,2]. Characteristically, atypical lobular hyperplasia is a diploid neoplasm. Tumefaction exhibits loss of heterozygosis (LOH) at chromosome 16q. A subset of neoplasms demonstrates methylation of CDH1 gene. Several tumefaction express loss of chromosome 22q and 16p, gain of chromosome 2p11.2, 5q32- 33.1 (CSF1R), 6q, 11q13 or 14q32.33.

Wilson’s disease

Wilson?s disease (WD) is an autosomal recessive inherited disorder of copper metabolism caused by mutations in the ATP7B gene, which is located on chromosome 13q14.3. The global genetic prevalence of WD at birth is approximately 13.9?15.4 per 100,000 population. Although WD is a rare condition associated with treatment efficacy, mortality rates in patients with WD (5?6.1%) are higher than healthy controls. Prevalent features of WD include hepatic, neurologic, and psychiatric syndromes, even though various signs and symptoms of the disease have been depicted to this point. If diagnosed and treated at an early stage, WD patients would likely improve and be often largely asymptomatic for the rest of their lives. Prompt diagnosis and lifelong treatment substantially affect outcome. We aimed to summarize current knowledge about WD epidemiology, genetics, clinical manifestations, diagnostic workup, and current WD management.

Genetic and transcriptional alterations and mutations of RB1 gene in retinoblastoma

Cancer is ninth among the leading causes of mortality for children in India between the ages of five and fourteen. Retinoblastoma (RB), an intraocular childhood cancer that affects 1 in 15,000 live births in India, accounts for 3% of all childhood cancer cases. In India, the majority of patients arrive at a later stage of their illness, leaving them with little alternatives for saving their lives and vision. Numerous lives and visions may be saved if the genetics of the RB were understood. In RB, autosomal dominant inheritance with varying penetrance was noted. Individuals who are heterozygous carriers of a germline mutation and have a favorable family history (6–10%) are more likely to develop melanomas, osteosarcoma, and soft tissue sarcoma in the future. Germline mutations might account for around 15% of unilateral patient’s varied penetrance of RB. RB1 gene, which is 180 kb long and has 27 exons, is the cause of RB. It was originally cloned and discovered to be a tumor suppressor gene in humans and situated on chromosome 13q14. There have been few reports of certain variants having varied penetrance and expressivity, despite the fact that the majority of patients with RB1 mutations have significant penetrance with clinical symptoms. Understanding the carcinogenesis and variability in the illness phenotype requires studying the transcript of RB1 and other tumor-related genes. The genetic and transcriptional research might be enhanced by epigenetic investigations of RB1 and associated genes.

DNA copy number profiles and systems biology connect chromatin remodeling and DNA repair in high-risk neuroblastoma.

Neuroblastoma (NB) is a solid tumor that accounts for 15% of all pediatric oncological deaths, and much is due to the low response to therapy in relapsed tumors. High-risk NB may present deletions in chromosome 11q, which may be associated with other chromosomal alterations and a poor response to therapy, but this association is still poorly understood. Using a systems biology network approach, we studied three patients with high-risk NB with deleted 11q stage 4 to highlight the connections between treatment resistance and copy number alterations in distinct cases. We built different protein-protein interaction networks for each patient based on protein-coding genes mapped at the cytobands pre- and post-chemotherapy from distinct copy number alterations data. In the post-chemotherapy networks, we identified five common regulatory nodes corresponding to the gained region located in ch17q:BIRC5, BRCA1, PRKCA, SUMO2, andGPS1. A crosslink between DNA damage and chromatin remodeling proteins was also found - a connection still poorly understood in NB. We identified a potential connection between XPB gain and chemoresistance of NB. The findings help elucidate the molecular profiles of high-risk NB with 11q deletion in pre- and post-chemotherapy tumor samples, which may reflect unique profiles in poor response to treatment.

Evaluation of an In-House Genetic Testing Method for Confirming Prader-Willi and Angelman Syndromes in Sri Lanka.

Prader-Willi syndrome (PWS, MIM 176,270) and Angelman syndrome (AS, MIM 105,830) are caused by imprinting defects of chromosome 15q11-13, with loss of maternal gene expression causing AS and paternal gene expression causing PWS. The diagnosis, once established in most cases by using a methylation-specific PCR test, enables appropriate therapeutic interventions and avoids the need for further investigations. Genetic testing for PWS/AS is limited in Sri Lanka (and in other low- and middle-income countries), mainly because parents are unable to pay for testing as these are not funded by the health service. Ninety cases (46 female) with clinical features suggesting PWS (n = 37) and AS (n = 53), referred by a pediatric endocrinologist and a pediatric neurologist, were recruited. Clinical information and blood samples were obtained following informed consent. DNA was extracted and methylation-specific PCR (MS-PCR) was performed following bisulfite modification of DNA by using an in-house method and a kit. Results were validated using known positive controls. Parent-child trio DNA samples were used in cases with confirmed PWS and AS to determine if the disease was due to a deletion or uniparental disomy. The cost of the MS-PCR testing of the two modification methods and the microsatellite analysis was determined. Among the suspected PWS cases, 19/37 were positive, while 5/53 of the suspected AS cases were positive. The lower identification rate of AS is probably related to the overlap of clinical features of this condition with other disorders. The kit-based modification method was more reliable, less time-consuming, and cost-effective in our laboratory. The kit-based modification followed by MS-PCR described in this study enables more affordable genetic testing of suspected PWS/AS cases, and this is likely to improve patient care by targeting appropriate therapy for the affected cases. Parental genetic counselling is made possible regarding the low recurrence risk, especially where a deletion or uniparental disomy is confirmed. In MS-PCR, negative cases with a strong clinical suspicion of AS, UBE3A mutation testing is required. In addition, imprinting center mutation/deletion testing may also be needed in strongly clinically suspected, MS-PCR negative PWS and AS cases.

An integrated action plan to fund and support drug development for Dup15q syndrome: a patient organization perspective.

Maternal 15q11.2-13.1 duplication syndrome, or Dup15q syndrome (Dup15q), is a rare neurodevelopmental disorder affecting as many as 1 in 5000 to 1 in 20,000 children worldwide. Autism and seizures are two of the most commonly observed phenotypes in Dup15q, with intellectual disability, hypotonia, gastrointestinal distress, and substantial fine and gross motor deficits also commonly reported. The community that is now known as the Dup15q Alliance started in 1994 as a small group of families raising children with chromosome 15q duplications. Originally named IsoDicentric 15 Exchange, Advocacy and Support (IDEAS), the group received official nonprofit organization status 10 years later and rebranded to its current name, Dup15q Alliance, shortly thereafter. Today, there are over 2200 families affiliated with Dup15q Alliance, with an average intake of 10 new families each month. Historically, Dup15q Alliance has provided the community with access to family and caregiver resources in addition to serving as a repository for basic educational information about Dup15q and research developments. The recent installation of a dedicated director of scientific and clinical initiatives alongside other infrastructural changes has now primed the Dup15q Alliance to expand its scientific footprint by funding cutting-edge research, supporting clinical sites and trials, and investing in novel therapeutics that have the potential to change the reality of a Dup15q syndrome diagnosis. To do this, we have developed the LEARN. TREAT. CURE. program to align initiatives, fast-track progress, and bring hope and reality into coexistence. Briefly, we seek to learn as much as we can about the syndrome through cutting-edge research, natural history studies, and patient registry utilization, identify and develop methods to treat the symptoms of our patient community, with the ultimate goal of developing a cure for the disease-causing symptoms of the syndrome.

Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies

We performed comprehensive proteogenomic characterization of small cell lung cancer (SCLC) using paired tumors and adjacent lung tissues from 112 treatment-naive patients who underwent surgical resection. Integrated multi-omics analysis illustrated cancer biology downstream of genetic aberrations and highlighted oncogenic roles of FAT1 mutation, RB1 deletion, and chromosome 5q loss. Two prognostic biomarkers, HMGB3 and CASP10, were identified. Overexpression of HMGB3 promoted SCLC cell migration via transcriptional regulation of cell junction-related genes. Immune landscape characterization revealed an association between ZFHX3 mutation and high immune infiltration and underscored a potential immunosuppressive role of elevated DNA damage response activity via inhibition of the cGAS-STING pathway. Multi-omics clustering identified four subtypes with subtype-specific therapeutic vulnerabilities. Cell line and patient-derived xenograft-based drug tests validated the specific therapeutic responses predicted by multi-omics subtyping. This study provides a valuable resource as well as insights to better understand SCLC biology and improve clinical practice.

Subglottic stenosis as an early presentation of DiGeorge Syndrome

&lt;b&gt;&lt;br&gt;Introduction:&lt;/b&gt; DiGeorge Syndrome, a microdeletion on chromosome 22q11.2, encompasses a myriad of congenital abnormalities. These often include cardiac malformations, velopharyngeal insufficiency, immune deficiency, parathyroid hypoplasia, and hypocalcemia. Although congenital defects of the larynx are quite well acknowledged in the literature, their presence and prevalence in this syndrome remain unknown.&lt;/br&gt; &lt;b&gt;&lt;br&gt;Aim:&lt;/b&gt; We present a case report describing an infant whose initial presentation and symptoms were not suggestive of DiGeorge Syndrome. We also discuss the prevalence of subglottic stenosis among young patients diagnosed with DiGeorge Syndrome.&lt;/br&gt; &lt;b&gt;&lt;br&gt;Case report:&lt;/b&gt; A two-month-old infant was admitted to the Pediatric Otolaryngology Department after difficulties with intubation and extubation during surgical repair of intestinal malrotation. Laryngoscopic examination revealed stage III subglottic stenosis. Laryngotracheoplasty with anterior costal cartilage graft was performed, followed by a series of balloon dilation procedures due to postoperative adhesions and recurrent subglottic stenosis. A comprehensive postsurgical evaluation of the patient confirmed the diagnosis of DiGeorge Syndrome.&lt;/br&gt; &lt;b&gt;&lt;br&gt;Conclusions:&lt;/b&gt; The presented case underscores the broad clinical presentation of DiGeorge Syndrome and emphasizes the importance of maintaining a high index of suspicion in patients demonstrating an unusual confluence of symptoms. Detailed investigation and early diagnosis can significantly contribute to appropriate management, thereby potentially improving outcomes in this patient population.&lt;/br&gt;

PRAME Expression: A Target for Cancer Immunotherapy and a Prognostic Factor in Uveal Melanoma.

Uveal melanoma (UM) is a rare disease with a high mortality, and new therapeutic options are being investigated. Preferentially Expressed Antigen in Melanoma (PRAME) is a cancer testis antigen, expressed in the testis, but also in cancers, including uveal melanoma. PRAME is considered a target for immune therapy in several cancers, and PRAME-specific T cell clones have been shown to kill UM cells. We studied the literature on PRAME expression in hematological and solid malignancies, including UM, and its role as a target for immunotherapy. The distribution of tumor features was compared between PRAME-high and PRAME-low UM in a 64-patient cohort from the Leiden University Medical Center (LUMC) and in the Cancer Genome Atlas (TCGA) cohort of 80 cases and differential gene expression analysis was performed in the LUMC cohort. PRAME is expressed in many malignancies, it is frequently associated with a negative prognosis, and can be the target of T cell receptor (TCR)-transduced T cells, a promising treatment option with high avidity and safety. In UM, PRAME is expressed in 26% to 45% of cases and is correlated with a worse prognosis. In the LUMC and the TCGA cohorts, high PRAME expression was associated with larger diameter, higher Tumor-Node-Metastasis (TNM) stage, more frequent gain of chromosome 8q, and an inflammatory phenotype. We confirm that PRAME is associated with poor prognosis in UM and has a strong connection with extra copies of 8q. We show that PRAME-specific immunotherapy in an adjuvant setting is promising in treatment of malignancies, including UM.

Clinicopathological and genetic landscape of plasmablastic lymphoma in Taiwan

Plasmablastic lymphoma (PBL) is an aggressive large B-cell lymphoma with a terminal B-cell differentiation phenotype and is frequently associated with immunodeficiency. We aimed to investigate the clinicopathological and immunophenotypic features, genetic alterations, and mutational landscape of PBL in Taiwan. We retrospectively recruited 26 cases. Five (5/18; 28%) patients were HIV-positive and 21 (81%) presented extranodally. There were two morphological groups: one with purely monomorphic large cells (85%) and the other comprising large cells admixed with plasmacytic cells (15%). Phenotypically, the tumors expressed MYC (8/10; 80%), CD138 (20/26; 77%), and MUM1 (20/20; 100%), but not CD20 (n = 26; 0%). Fourteen (54%) cases were positive for EBV by in situ hybridization; the EBV-positive cases were more frequently HIV infected (p = 0.036), with extranodal presentation (p = 0.012) and CD79a expression (p = 0.012), but less frequent light chain restriction (p = 0.029). Using fluorescence in situ hybridization, we identified 13q14 deletion, MYC rearrangement, and CCND1 rearrangement in 74%, 30%, and 5% cases, respectively, without any cases having rearranged BCL6 or IGH::FGFR3 fusion. In the 15 cases with adequate tissue for whole exome sequencing, the most frequent recurrent mutations were STAT3 (40%), NRAS (27%), and KRAS (20%). In conclusion, most PBL cases in Taiwan were HIV-unrelated. Around half of the cases were positive for EBV, with distinct clinicopathological features. Deletion of chromosome 13q14 was frequent. The PBL cases in Taiwan showed recurrent mutations involving JAK-STAT, RAS-MAPK, epigenetic regulation, and NOTCH signaling pathways, findings similar to that from the West.

Angelman syndrome: A genetic challenge for physical and learning disabilities

Angelman syndrome (AS) was first reported in 1965 by Dr. Harry Angelman. It is a condition of neurodevelopment characterized by, a lack of speech, distinctive behavior, seizure, intellectual capacity, and cheerful disposition. The cause of AS is a lack of production by maternal imprinted genes (UBE3A) on the 15q11-q13 chromosome. The complications of AS are strabismus, atrophy of the optical nerve, and blindness, which are rarely reported. There is a possibility of complications in the laboratory diagnostic tests for AS. One method is to evaluate with DNA methylation analysis of AS/Prader-Willi Syndrome (PWS) imprinting center (IC). On cytogenetic analysis, at least 50–60% of patients had a maternally induced de novo mutation of chromosome 15q11-13 with more serious clinical phenotypes such as microcephaly, seizures, language impairment, and motor difficulties. Multiexonic or whole gene deletion is identified by array-comparative genomic hybridisation (CGH) in some cases and laboratory and methodology may vary such deletions. Diagnosis of AS can be suggested by unsteady movements before walking. Based on the patient’s medical history, electroencephalogram (EEG) data, clinical symptoms, and the presence or absence of a chromosome 50 deletion, a diagnosis of AS is made. Incidence estimated for AS is approximately 1 in 12,000–20,000 birth lives, but the epidemiological measures of life expectancy remains unknown. The clinical features of AS phenotype include seizures, sleep disturbance, intellectual disability, and movement disorders such as tremor and ataxia, anxiety, expressive language is limited, behavioral changes, pleasant demeanor, and easily manipulated laughs, EEG abnormalities were discovered in around 100% of the patients. The researcher identified problems with inflammation at the injection site caused by a higher dose of a drug and they monitored proteins in the individual’s blood and cerebrospinal fluid as an additional safety precaution. Genetic counseling for families with one child with AS to address the likelihood of recurrence can be a challenging subject that frequently requires specialist advice.

DELE1 haploinsufficiency causes resistance to mitochondrial stress-induced apoptosis in monosomy 5/del(5q) AML

Monosomy 5 and deletions of the chromosome 5q (−5/del(5q)) are recurrent events in de novo adult acute myeloid leukemia (AML), reaching up to 40% of cases in secondary AML. These chromosome anomalies are associated with TP53 mutations and with very poor prognosis. Using the large Leucegene genomic and transcriptomic dataset composed of 48 −5/del(5q) patient specimens and 367 control AML, we identified DELE1 – located in the common deleted region – as the most consistently downregulated gene in these leukemias. DELE1 encodes a mitochondrial protein recently characterized as the relay of mitochondrial stress to the cytosol through a newly defined OMA1-DELE1-HRI pathway which ultimately leads to the activation of ATF4, the master transcription factor of the integrated stress response. Here, we showed that the partial loss of DELE1 expression observed in −5/del(5q) patients was sufficient to significantly reduce the sensitivity to mitochondrial stress in AML cells. Overall, our results suggest that DELE1 haploinsufficiency could represent a new driver mechanism in −5/del(5q) AML.

Metabolic signature of the pathogenic 22q11.2 deletion identifies carriers and provides insight into systemic dysregulation

Large deletions at chromosome 22q11.2 are known to cause severe clinical conditions collectively known as 22q11.2 deletion syndrome. Notwithstanding the pathogenicity of these deletions, affected individuals are typically diagnosed in late childhood or early adolescence, and little is known of the molecular signaling cascades and biological consequences immediately downstream of the deleted genes. Here, we used targeted metabolomics to compare neonatal dried blood spot samples from 203 individuals clinically identified as carriers of a deletion at chromosome 22q11.2 with 203 unaffected individuals. A total of 173 metabolites were successfully identified and used to inform on systemic dysregulation caused by the genomic lesion and to discriminate carriers from non-carriers. We found 84 metabolites to be differentially abundant between carriers and non-carriers of the 22q11.2 deletion. A predictive model based on all 173 metabolites achieved high Accuracy (89%), Area Under the Curve (93%), F1 (88%), Positive Predictive Value (94%), and Negative Predictive Value (84%) with tyrosine and proline having the highest individual contributions to the model as well as the highest interaction strength. Targeted metabolomics provides insight into the molecular consequences possibly contributing to the pathology underlying the clinical manifestations of the 22q11 deletion and is an easily applicable approach to first-pass screening for carrier status of the 22q11 to prompt subsequent verification of the genomic diagnosis.

Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family

AbstractGenetic susceptibility to familial colorectal cancer (CRC), including for individuals classified as Familial Colorectal Cancer Type X (FCCTX), remains poorly understood. We describe a multi-generation CRC-affected family segregating pathogenic variants in both BRCA1, a gene associated with breast and ovarian cancer and RNF43, a gene associated with Serrated Polyposis Syndrome (SPS). A single family out of 105 families meeting the criteria for FCCTX (Amsterdam I family history criteria with mismatch repair (MMR)-proficient CRCs) recruited to the Australasian Colorectal Cancer Family Registry (ACCFR; 1998–2008) that underwent whole exome sequencing (WES), was selected for further testing. CRC and polyp tissue from four carriers were molecularly characterized including a single CRC that underwent WES to determine tumor mutational signatures and loss of heterozygosity (LOH) events. Ten carriers of a germline pathogenic variant BRCA1:c.2681_2682delAA p.Lys894ThrfsTer8 and eight carriers of a germline pathogenic variant RNF43:c.988 C &gt; T p.Arg330Ter were identified in this family. Seven members carried both variants, four of which developed CRC. A single carrier of the RNF43 variant met the 2019 World Health Organization (WHO2019) criteria for SPS, developing a BRAF p.V600 wildtype CRC. Loss of the wildtype allele for both BRCA1 and RNF43 variants was observed in three CRC tumors while a LOH event across chromosome 17q encompassing both genes was observed in a CRC. Tumor mutational signature analysis identified the homologous recombination deficiency (HRD)-associated COSMIC signatures SBS3 and ID6 in a CRC for a carrier of both variants. Our findings show digenic inheritance of pathogenic variants in BRCA1 and RNF43 segregating with CRC in a FCCTX family. LOH and evidence of BRCA1-associated HRD supports the importance of both these tumor suppressor genes in CRC tumorigenesis.

A novel BRAF::PTPRN2 fusion in meningioma: a case report

Gene fusion events have been linked to oncogenesis in many cancers. However, gene fusions in meningioma are understudied compared to somatic mutations, chromosomal gains/losses, and epigenetic changes. Fusions involving B-raf proto-oncogene, serine/threonine kinase (BRAF) are subtypes of oncogenic BRAF genetic abnormalities that have been reported in certain cases of brain tumors, such as pilocytic astrocytomas. However, BRAF fusions have not been recognized in meningioma. We present the case of an adult female presenting with episodic partial seizures characterized by déjà vu, confusion, and cognitive changes. Brain imaging revealed a cavernous sinus and sphenoid wing mass and she underwent resection. Histopathology revealed a World Health Organization (WHO) grade 1 meningioma. Genetic profiling with next generation sequencing and microarray analysis revealed an in-frame BRAF::PTPRN2 fusion affecting the BRAF kinase domain as well as chromothripsis of chromosome 7q resulting in multiple segmental gains and losses including amplifications of cyclin dependent kinase 6 (CDK6), tyrosine protein-kinase Met (MET), and smoothened (SMO). Elevated pERK staining in tumor cells provided evidence of activated mitogen-activated protein kinase (MAPK) signaling. This report raises the possibility that gene fusion events may be involved in meningioma pathogenesis and warrant further investigation.