Disease Characteristics of AML Patients with Germline DDX41 Variants

Introduction: Germline pathogenic variants in DDX41 represent the most common predisposition to myeloid neoplasms accounting for 1-4% of patients (pts). Myeloid neoplasm with germ line DDX41 mutation is included as a separate entity in the revised 2016 World Health Organization classification of myeloid neoplasms and acute leukemia. The risk to develop any myeloid neoplasm in individuals with pathogenic germline DDX41 variants is modest, estimated to be about 20-30%. The recent inclusion of DDX41 on next generation sequencing panel (NGS) for myeloid neoplasms has led to increase in identification of DDX41 variants. Identification of germline DDX41 variants in MDS/AML pts will inform on donor selection and genetic testing of family members who are potential hematopoietic stem cell transplant (HSCT) donors is critical to eliminate the risk for transmission of a donor derived leukemia. Herein, we describe 10 pts with acute myeloid leukemia who were identified to have a DDX41 variantsince January 2020. Methods Among the pts diagnosed with acute myeloid leukemia in Utah between January 2020 and April 2021, 10 pts were identified to have a DDX41 variant on myeloid NGS panel (peripheral blood or bone marrow) performed at the time of diagnosis (9 pts) or through genetic testing performed on cultured skin fibroblasts (1 pt). When possible, pts with met a genetic counselor and germline genetic testing was performed utilizing DNA obtained from cultured skin fibroblasts through GeneDX Laboratory and Prevention Genetics. DDX41 variants are classified (Table 1) as per the ACMG criteria. Results Of the 10 pts with a DDX41 variant on myeloid NGS panel, 9 (90%) were diagnosed with AML. One pt (10%, Pt 9)) was initially diagnosed as AML and subsequently classified as mixed phenotype T/myeloid leukemia on repeat marrow evaluation after failure of initial induction based on blasts co-expressing cytoplasmic CD3 and MPO. The DDX41 variant was classified as pathogenic and variant of uncertain significance (VUS) in 6 (60%) and 4 (40%) pts, respectively. The variant allele frequency (VAF) of DDX41 variants was above 35% in all pts (Table1). Seven pts had germline testing performed from cultured skin fibroblasts, all were found to have germline DDX41 variants. Three pts did not undergo germline genetic testing, but the VAFs were highly suggestive of germline origin. Baseline demographics and the AML disease characteristics are outlined in Table 1. ELN risk category was unknown in 1 pt (10%), favorable in 1 pt (10%), intermediate in 3 pts (30%) and adverse in 5 pts (50%). Karyotype was normal in6 pts (60%), 20 q deletion in one pt and a complex in 2 pts (20%). Other somatic variants identified on the myeloid NGS panel are outlined in Table 1. First line treatment included intensive chemotherapy in 6 pts (60%) and 4 pts (40%) received hypomethylating agent based (HMA) therapy. Seven pts achieved a complete remission (CR), after first line treatment, of whom 5 received intensive chemo and 2 received HMA based treatment. One pt who received HMA therapy failed to achieve CR or CRi (pt 5), achieved CR after receiving intensive chemo for salvage. One pt failed initial induction with idarubicin and cytarabine (7+3 regimen) and achieved CR after reinduction with cycle 1 A of HyperCVAD. 5 pts relapsed after first line treatment (2 after intensive chemo and 3 after HMA based treatment). At the time of this report, 2 pts received allogeneic stem cell transplant (allo-SCT) both from unrelated donors and 3 pts died. Conclusion: In our experience, AML pts with germline DDX41 variant presented after fifth decade similarly to sporadic AML. Most pts had pathogenic variants in DDX41 (per ACMG), though 3 pts were classified as uncertain variants which represent an area of further knowledge. The majority of the pts had a normal karyotype at diagnosis. A second somatic DDX41 variant was observed in 2 pts. ASXL1 mutations were observed in 3 pts. Inclusion of the DDX41 gene in a myeloid NGS panel is necessary to identify this subset of pts and in addition germline testing should also be considered for all MDS/AML pts with age <40. Multicenter registry-based studies are necessary to further characterize and develop a standardized treatment approach for these individuals and the role of allo-SCT. Figure 1 Figure 1. Disclosures Tashi: PharmaEssentia: Membership on an entity's Board of Directors or advisory committees, Other: Advisory Board. Shami: JSK Therapeutics: Consultancy, Current holder of individual stocks in a privately-held company, Membership on an entity's Board of Directors or advisory committees; Bastion Biologics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Chimerix: Research Funding; Takeda: Consultancy; Gilead: Consultancy; BMS: Consultancy; Chimerix: Research Funding; Amgen: Research Funding; Aptevo: Research Funding. Kovacsovics: Stemline: Honoraria; Novartis: Research Funding; Amgen Inc.: Research Funding; Janssen Pharmaceuticals: Research Funding; AbbVie: Research Funding; Jazz Pharmaceutials: Honoraria. Maese: Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Tantravahi: Karyopharm Therapeutics Inc.: Consultancy, Honoraria, Research Funding; Abbvie Inc.: Research Funding; CTI BioPharma: Research Funding; Novartis: Research Funding; BMS: Research Funding.

Effect of rapamycin on mitochondria and lysosomes in fibroblasts from patients with mtDNA mutations

Maintaining mitochondrial function and dynamics is crucial for cellular health. In muscle, defects in mitochondria result in severe myopathies where accumulation of damaged mitochondria causes deterioration and dysfunction. Importantly, understanding the role of mitochondria in disease is a necessity to determine future therapeutics. One of the most common myopathies is mitochondrial encephalopathy lactic acidosis stroke-like episodes (MELAS), which has no current treatment. Recently, MELAS patients treated with rapamycin exhibited improved clinical outcomes. However, the cellular mechanisms of rapamycin effects in MELAS patients are currently unknown. In this study, we used cultured skin fibroblasts as a window into the mitochondrial dysfunction evident in MELAS cells, as well as to study the mechanisms of rapamycin action, compared to control, healthy individuals. We observed that mitochondria from patients were fragmented, had a 3-fold decline in the average speed of motility, a 2-fold reduced mitochondrial membrane potential and a 1.5-2-fold decline in basal respiration. Despite the reduction in mitochondrial function, mitochondrial import protein Tim23 was elevated in patient cell lines. MELAS fibroblasts exhibited increased MnSOD levels and lysosomal function when compared to healthy controls. Treatment of MELAS fibroblasts with rapamycin for 24 hrs resulted in increased mitochondrial respiration compared to control cells, a higher lysosome content, and a greater localization of mitochondria to lysosomes. Our studies suggest that rapamycin has the potential to improve cellular health even in the presence of mtDNA defects, primarily via an increase in lysosomal content.

Nearly half of TP53 variants are misattributed to Li-Fraumeni syndrome: A clinical evaluation of individuals with TP53 variants detected by hereditary cancer panel assays on blood or saliva.

10501 Background: Multigene panel testing (MGPT) has identified TP53 pathogenic or likely pathogenic (P/LP) variants in patients with diverse phenotypes from no cancer to classic Li-Fraumeni syndrome (LFS). There is increasing recognition of variants at low allelic fraction (VAF) for TP53 in particular, which can be suggestive of post-zygotic mosaicism or aberrant clonal expansion (ACE), comprising clonal hematopoiesis of indeterminate potential (CHIP) or occult hematologic neoplasia. Distinguishing among these categories is essential because of widely different cancer risk and management implications for patients and their relatives. We report an evaluation of TP53 positive probands to determine germline versus somatic status from a cancer genetics clinic. Methods: We reviewed probands with TP53 P/LP variants by MGPT on blood (N = 83) or saliva (N = 1) samples from 2012-2019. Available VAFs were collected from commercial testing laboratories. Probands positive for a known familial variant, who met LFS testing criteria without indication of low VAF, or who carried the Brazil founder p.R337H variant were considered germline. For those with uncertain germline status, data was obtained from ancillary testing of family members, cultured skin fibroblasts, and other somatic benign or tumor tissues. TP53 variants were further categorized based on all available data. Results: Of the 84 probands, 28 (33%) had germline TP53 P/LP variants determined by above initial criteria; 18 (21%) were confirmed germline through ancillary testing. Seven (8%) individuals were classified as having constitutional mosaicism. In eleven (13%) individuals, the TP53 variants were consistent with ACE, in 9 (11%) with CHIP and in 2 (2%) with a hematologic malignancy (1 CLL, 1 NHL). Five (6%) cases could not be categorized despite ancillary testing. Fifteen (18%) probands declined any further workup. Conclusions: A TP53 P/LP variant found on peripheral blood or saliva MGPT does not always originate in the germline. In a clinical cancer genetics cohort, only 54% of patients had TP53 P/LP germline variants; these patients plus those with constitutional mosaicism (8%) require intensified surveillance. Assessment of VAF, family member testing, and analysis of TP53 in cultured fibroblasts or other tissue samples may distinguish germline and constitutional mosaic variants from the ACE spectrum. Expanding use of MGPT will increase this clinical challenge, which may motivate the modification of lab reports to include VAF and possible non-germline explanations. The findings of this study support a framework of multiple strategies to discern true constitutional status of a TP53 P/LP variant.

A ZFYVE19 gene mutation associated with neonatal cholestasis and cilia dysfunction: case report with a novel pathogenic variant

Background ZFYVE19 (Zinc Finger FYVE-Type Containing 19) mutations have most recently been associated to a novel type of high gamma-glutamyl transpeptidase (GGT), non-syndromic, neonatal-onset intrahepatic chronic cholestasis possibly associated to cilia dysfunction. Herein, we report a new case with further studies of whole exome sequencing (WES) and immunofluorescence in primary cilia of her cultured fibroblasts which confirm the observation. Results A now 5-year-old girl born to clinically healthy consanguineous Moroccan parents was assessed at 59 days of life due to severe cholestatic jaundice with increased serum bile acids and GGT, and preserved hepatocellular synthetic function. Despite fibrosis/cirrhosis and biliary ducts proliferation on liver biopsy suggested an extrahepatic biliary obstacle, normal intra-operatory cholangiography excluded biliary atresia. Under choleretic treatment, she maintained a clinically stable anicteric cholestasis but developped hyperlipidemia. After exclusion of the main causes of cholestasis by multiple tests, abnormal concentrations of sterols and WES led to a diagnosis of hereditary sitosterolemia (OMIM #618666), likely unrelated to her cholestasis. Further sequencing investigation revealed a homozygous non-sense mutation (p.Arg223Ter) in ZFYVE19 leading to a 222 aa truncated protein and present in both heterozygous parents. Immunofluorescence analysis of primary cilia on cultured skin fibroblasts showed a ciliary phenotype mainly defined by fragmented cilia and centrioles abnormalities. Conclusions Our findings are consistent with and expands the recent evidence linking ZFYVE19 to a novel, likely non-syndromic, high GGT-PFIC phenotype with neonatal onset. Due to the possible role of ZFYVE19 in cilia function and the unprecedented coexistence of a coincidental hereditary sterol disorder in our case, continuous monitoring will be necessary to substantiate type of liver disease progression and/or possible emergence of a multisystemic involvement. What mentioned above confirms that the application of WES in children with undiagnosed cholestasis may lead to the identification of new causative genes, widening the knowledge on the pathophysiology.

Scale-up of a Composite Cultured Skin using a novel Bioreactor Device in a Porcine Wound Model

Extensive deep burn management with a two-stage strategy can reduce reliance on skin autografts; a biodegradable polyurethane scaffold to actively temporise the wound and an autologous composite cultured skin (CCS) for definitive closure. The materials fulfilling each stage have undergone in vitro and in vivo pre-testing in ‘small’ large animal wounds. For humans, producing multiple, large CCSs requires a specialised bioreactor. This paper reports a system to close large porcine wounds. Three Large White pigs were used, each with two wounds (24.5cm x 12cm) into which biodegradable dermal scaffolds were implanted. A sample from discarded tissue allowed isolation/culture of autologous fibroblasts and keratinocytes. CCS production began by pre-soaking a 1mm-thick biodegradable polyurethane foam in autologous plasma. In the bioreactor cassette, fibroblasts were seeded into the matrix with thrombin until established, followed by keratinocytes. The CCSs were applied onto integrated dermal scaffolds on Day 35, alongside a sheet skin graft (30% of one wound). Serial punch biopsies, trans-epidermal water loss readings (TEWL) and wound measurements indicated epithelialisation. During dermal scaffold integration, negligible wound contraction was observed (average 4.5%). After CCS transplantation, the control skin grafts were ‘taken’ by Day 11 when visible islands of epithelium were clinically observed on 2/3 CCSs. Closure was confirmed histologically, with complete epithelialisation by Day 63 post-CCS transplantation (CCS TEWL ~ normal skin average 11.9g/m 2h). Four of six wounds demonstrated closure with robust, stratified epithelium. Generating large pieces of CCS capable of healing large wounds is thus possible using a specialised designed bioreactor.

A New Controlled Release System for Propolis Polyphenols and Its Biochemical Activity for Skin Applications

Propolis is a resinous substance produced by bees that exhibits antimicrobial, immunostimulatory and antioxidant activity. Its use is common in functional foods, cosmetics and traditional medicine despite the fact that it demonstrates low extraction yields and inconsistency in non-toxic solvents. In this work, a new encapsulation and delivery system consisting of liposomes and cyclodextrins incorporating propolis polyphenols has been developed and characterized. The antioxidant, antimutagenic and antiaging properties of the system under normal and UVB-induced oxidative stress conditions were investigated in cultured skin cells and/or reconstituted skin model. Furthermore, the transcript accumulation for an array of genes involved in many skin-related processes was studied. The system exhibits significant polyphenol encapsulation efficiency, physicochemical stability as well as controlled release rate in appropriate conditions. The delivery system can retain the anti-mutagenic, anti-oxidative and anti-ageing effects of propolis polyphenols to levels similar and comparable to those of propolis methanolic extracts, making the system ideal for applications where non-toxic solvents are required and controlled release of the polyphenol content is desired.

Assessing the Feasibility and Limitations of Cultured Skin Fibroblasts for Germline Genetic Testing in Hematologic Disorders

Introduction Peripheral blood is the standard tissue source for germline genetic testing in most scenarios. In patients with hematologic malignancies, however, peripheral blood frequently contains tumor- or clonal hematopoiesis-related acquired genetic variants, often occurring in genes that can also cause inherited cancer susceptibility if present in the germline. Thus, an alternative tissue source is necessary. Cultured skin fibroblasts have been used as a potentially ideal alternative because they are free from blood contamination and provide ample DNA yields, advantages that other alternatives such as saliva or nail clippings lack. However, optimal culture methods, expected time from biopsy to sufficient DNA yield, culture failure rate, and limitations of this technique, including the possibility of variants being acquired solely due to the culturing process, are not yet known. Methods We conducted a retrospective cohort study of subjects with cytopenias or hematologic malignancies who underwent skin biopsy and fibroblast culture for germline genetic testing from April 2014 to June 2018. Skin biopsy culture technical data, including time from biopsy to culture set-up, shipment from an outside institution, culture failure, and biopsy size, were abstracted from tissue culture logs. Patient demographics, comorbidities, medication history, and hematologic diagnosis and treatment were abstracted from medical records. Next generation sequencing data from targeted capture of 144 inherited cancer and bone marrow failure predisposition genes obtained for clinical genetic testing purposes were analyzed to identify variants at both germline (40-60%) and subclonal (10-40%) variant allele frequencies (VAF). Pathogenicity was interpreted according to ACMG/AMP guidelines. Fisher's exact tests and logistic regression models were used to assess associations with culture failure. T-tests and linear regression models were used to assess factors associated with mean time to confluency. Results In total, we studied 350 samples from unique patients, including 61 (24%) who carried one or more pathogenic or likely pathogenic cancer susceptibility gene variant(s). Overall, 16 of the 350 (5%) biopsies failed to grow in culture. The median time from skin biopsy to sufficient growth to extract DNA for genetic testing was 27 days (IQR 22-29 days). Culture failure was significantly more likely in samples with a delay in culture initiation for 24 hours post biopsy (OR=4.32; p<0.01), and a pathogenic germline variant in a gene associated with telomere maintenance (OR=64.50; p<0.01). Factors associated with an increased mean time to sufficient growth included prior allogeneic stem cell transplant (32.1 days versus 27.2 days; p<0.01) and prior intravenous (IV) steroid exposure (29.9 days versus 26.4 days; p<0.01). Among samples cultured successfully, carriers of any pathogenic germline variant had a significantly decreased mean time to sufficient growth (25.4 days versus 28.6 days; p<0.01). A pathogenic or likely pathogenic subclonal variant was identified in 11 (4%) subjects at a median VAF of 20%. Among eight of these with additional tissue available, the presence of the variant was confirmed in four (50%). In individual cases, we found evidence of loss of a pathogenic variant in the hematopoietic malignancy. In one patient with a pathogenic variant with a 50% VAF in the original skin culture, the variant was not present in a skin culture from a second, fresh skin biopsy done due to discordant phenotype. Conclusions Culturing of skin fibroblasts for germline genetic testing in patients with hematologic disorders has a high success rate, especially when cultures are initiated within 24 hours of collection, and adds on average 27 days to genetic testing turnaround time. From patients with a hereditary syndrome, most skin biopsies will culture with the exception of individuals with a short telomere syndrome. For this subset, a direct skin biopsy without culture may be necessary. Subclonal variants at VAFs relevant to interpretation of a germline test were found in 4% of cases. Half were confirmed in an alternative tissue. Etiology of the subclonal variants, whether acquired during the culturing process or due to mosaicism or sequencing biases was not always clear. Careful assessment of the clinical phenotype in interpreting and applying germline genetic results to patient care will always be warranted. Disclosures Godley: UptoDate, Inc.: Honoraria; Invitae, Inc.: Membership on an entity's Board of Directors or advisory committees. Segal:BMS: Consultancy, Research Funding; AbbVie: Consultancy; Merck: Consultancy; Astra Zeneca: Consultancy. Churpek:UpToDate, Inc: Honoraria.