Short Variant Research Articles

Optical genome mapping identifies structural variants in potentially new cancer predisposition candidate genes in pediatric cancer patients.

Genetic predisposition is one of the major risk factors for pediatric cancer, with ~10% of children being carriers of a predisposing germline alteration. It is likely that this is the tip of the iceberg and many children are underdiagnosed, as most of the analysis focuses on single or short nucleotide variants, not considering the full spectrum of DNA alterations. Hence, we applied optical genome mapping (OGM) to our cohort of 34 pediatric cancer patients to perform an unbiased germline screening and analyze the frequency of structural variants (SVs) and their impact on cancer predisposition. All children were clinically highly suspicious for germline alterations (concomitant conditions or congenital anomalies, positive family cancer history, particular cancer type, synchronous or metachronous tumors), but whole exome sequencing (WES) had failed to detect pathogenic variants in cancer predisposing genes. OGM detected a median of 49 rare SVs (range 27-149) per patient. By analysis of 18 patient-parent trios, we identified three de novo SVs. Moreover, we discovered a likely pathogenic deletion of exon 3 in the known cancer predisposition gene BRCA2, and identified a duplication in RPA1, which might represent a new cancer predisposition gene. We conclude that optical genome mapping is a suitable tool for detecting potentially predisposing SVs in addition to WES in pediatric cancer patients.

Cesin, a short natural variant of nisin, displays potent antimicrobial activity against major pathogens despite lacking two C-terminal macrocycles.

Nisin is a widely used lantibiotic owing to its potent antimicrobial activity and its food-grade status. Its mode of action includes cell wall synthesis inhibition and pore formation, which are attributed to the lipid II binding and pore-forming domains, respectively. We discovered cesin, a short natural variant of nisin, produced by the psychrophilic anaerobe Clostridium estertheticum. Unlike other natural nisin variants, cesin lacks the two terminal macrocycles constituting the pore-forming domain. The current study aimed at heterologous expression and characterization of the antimicrobial activity and physicochemical properties of cesin. Following the successful heterologous expression of cesin in Lactococcus lactis, the lantibiotic demonstrated a broad and potent antimicrobial profile comparable to that of nisin. Determination of its mode of action using lipid II and lipoteichoic acid binding assays linked the potent antimicrobial activity to lipid II binding and electrostatic interactions with teichoic acids. Fluorescence microscopy showed that cesin lacks pore-forming ability in its natural form. Stability tests have shown the lantibiotic is highly stable at different pH values and temperature conditions, but that it can be degraded by trypsin. However, a bioengineered analog, cesin R15G, overcame the trypsin degradation, while keeping full antimicrobial activity. This study shows that cesin is a novel (small) nisin variant that efficiently kills target bacteria by inhibiting cell wall synthesis without pore formation. IMPORTANCE The current increase in antibiotic-resistant pathogens necessitates the discovery and application of novel antimicrobials. In this regard, we recently discovered cesin, which is a short natural variant of nisin produced by the psychrophilic Clostridium estertheticum. However, its suitability as an antimicrobial compound was in doubt due to its structural resemblance to nisin(1-22), a bioengineered short variant of nisin with low antimicrobial activity. Here, we show by heterologous expression, purification, and characterization that the potency of cesin is not only much higher than that of nisin(1-22), but that it is even comparable to the full-length nisin, despite lacking two C-terminal rings that are essential for nisin's activity. We show that cesin is a suitable scaffold for bioengineering to improve its applicability, such as resistance to trypsin. This study demonstrates the suitability of cesin for future application in food and/or for health as a potent and stable antimicrobial compound.

Comprehensive synergy mapping links a BAF- and NSL-containing “supercomplex” to the transcriptional silencing of HIV-1

Host repressors mediate HIV latency, but how they interactively silence the virus remains unclear. Here, we develop "reiterative enrichment and authentication of CRISPRi targets for synergies (REACTS)" to probe the genome for synergies between HIV transcription repressors. Using eight known host repressors as queries, we identify 32 synergies involving eleven repressors, including BCL7C, KANSL2, and SIRT2. Overexpression of these three proteins reduces HIV reactivation in Jurkat Tcells and in CD4 Tcells from people living with HIV on antiretroviral therapy (ART). We show that the BCL7C-containing BAF complex and the KANSL2-containing NSL complex form a "supercomplex" that increases inhibitory histone acetylation of the HIV long-terminalrepeat (LTR) and its occupancy by the short variant of the acetyl-lysine reader Brd4. Collectively, we provide a validated platform for defining gene synergies genome wide, and the BAF-NSL "supercomplex" represents a potential target for overcoming HIV rebound after ART cessation.

GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data.

Copy number variants (CNVs) are major contributors to genetic diversity and disease. While standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short variants, technical challenges have confounded uniform large-scale CNV analyses from whole-exome sequencing (WES) data. Given the profound impact of rare and de novo coding CNVs on genome organization and human disease, we developed GATK-gCNV, a flexible algorithm to discover rare CNVs from sequencing read-depth information, complete with open-source distribution via GATK. We benchmarked GATK-gCNV in 7,962 exomes from individuals in quartet families with matched genome sequencing and microarray data, finding up to 95% recall of rare coding CNVs at a resolution of more than two exons. We used GATK-gCNV to generate a reference catalog of rare coding CNVs in WES data from 197,306 individuals in the UK Biobank, and observed strong correlations between per-gene CNV rates and measures of mutational constraint, as well as rare CNV associations with multiple traits. In summary, GATK-gCNV is a tunable approach for sensitive and specific CNV discovery in WES data, with broad applications.

Piccolino is required for ribbon architecture at cochlear inner hair cell synapses and for hearing.

Cochlear inner hair cells (IHCs) form specialized ribbon synapses with spiral ganglion neurons that tirelessly transmit sound information at high rates over long time periods with extreme temporal precision. This functional specialization is essential for sound encoding and is attributed to a distinct molecular machinery with unique players or splice variants compared to conventional neuronal synapses. Among these is the active zone (AZ) scaffold protein piccolo/aczonin, which is represented by its short splice variant piccolino at cochlear and retinal ribbon synapses. While the function of piccolo at synapses of the central nervous system has been intensively investigated, the role of piccolino at IHC synapses remains unclear. In this study, we characterize the structure and function of IHC synapses in piccolo gene-trap mutant rats (Pclogt/gt ). We find a mild hearing deficit with elevated thresholds and reduced amplitudes of auditory brainstem responses. Ca2+ channel distribution and ribbon morphology are altered in apical IHCs, while their presynaptic function seems to be unchanged. We conclude that piccolino contributes to the AZ organization in IHCs and is essential for normal hearing.

Reconfiguration of cliques in a graph

We study reconfiguration problems for cliques in a graph, which determine whether there exists a sequence of cliques that transforms a given clique into another one in a step-by-step fashion. As one step of a transformation, we consider three different types of rules, which are defined and studied in reconfiguration problems for independent sets. We first prove that all the three rules are equivalent in cliques. We then show that the problems are PSPACE-complete for perfect graphs, while we give polynomial-time algorithms for several classes of graphs, such as even-hole-free graphs and cographs. In particular, the shortest variant, which computes the shortest length of a desired sequence, can be solved in polynomial time for chordal graphs, bipartite graphs, planar graphs, and bounded treewidth graphs.

Lung transplant recipients with telomere-mediated pulmonary fibrosis have increased risk for hematologic complications

Idiopathic pulmonary fibrosis lung transplant recipients (IPF-LTRs) are enriched for short telomere length (TL) and telomere gene rare variants. A subset of patients with nontransplant short-TL are at increased risk for bone marrow (BM) dysfunction. We hypothesized that IPF-LTRs with short-TL and/or rare variants would be at increased risk for posttransplant hematologic complications. Data were extracted from a retrospective cohort of 72 IPF-LTRs and 72 age-matched non-IPF-LTR controls. Genetic assessment was done using whole genome sequencing or targeted sequence panel. TL was measured using flow cytometry and fluorescence in-situ hybridization (FlowFISH) and TelSeq software. The majority of the IPF-LTR cohort had short-TL, and 26% of IPF-LTRs had rare variants. Compared to non-IPF controls, short-TL IPF-LTRs were more likely to have immunosuppression agents discontinued due to cytopenias (P = .0375), and BM dysfunction requiring BM biopsy was more prevalent (29% vs 4%, P = .0003). IPF-LTRs with short-TL and rare variants had increased requirements for transfusion and growth factor support. Multivariable logistic regression demonstrated that short-TL, rare variants, and lower pretransplant platelet counts were associated with BM dysfunction. Pretransplant TL measurement and genetic testing for rare telomere gene variants identified IPF-LTRs at increased risk for hematologic complications. Our findings support stratification for telomere-mediated pulmonary fibrosis in lung transplant candidates.

Myosin Va, a Novel Interaction Partner of STXBP1, Is Required to Transport Syntaxin1A to the Plasma Membrane

Syntaxin-binding protein 1 (STXBP1, also known as Munc18-1) regulates exocytosis as a chaperone protein of Syntaxin1A. The haploinsufficiency of STXBP1 causes early infantile-onset developmental and epileptic encephalopathy, known as STXBP1 encephalopathy. Previously, we reported impaired cellular localization of Syntaxin1A in induced pluripotent stem cell-derived neurons from an STXBP1 encephalopathy patient harboring a nonsense mutation. However, the molecular mechanism of abnormal Syntaxin1A localization in the haploinsufficiency of STXBP1 remains unknown. This study aimed to identify the novel interacting partner of STXBP1 involved in transporting Syntaxin1A to the plasma membrane. Affinity purification coupled with mass spectrometry analysis identified a motor protein Myosin Va as a potential binding partner of STXBP1. Co-immunoprecipitation analysis of the synaptosomal fraction from the mouse and tag-fused recombinant proteins revealed that the STXBP1 short splice variant (STXBP1S) interacted with Myosin Va in addition to Syntaxin1A. These proteins colocalized at the tip of the growth cone and axons in primary cultured hippocampal neurons. Furthermore, RNAi-mediated gene silencing in Neuro2a cells showed that STXBP1 and Myosin Va were required for membrane trafficking of Syntaxin1A. In conclusion, this study proposes a potential role of STXBP1 in the trafficking of the presynaptic protein Syntaxin1A to the plasma membrane in conjunction with Myosin Va.

Gynecologic-cancer analysis of ARID1A alterations detected in tissue and liquid biopsies.

5593 Background: The tumor suppressor gene ARID1A is an emerging target for new cancer treatment strategies including ATR inhibition. This study aimed to describe the landscape of ARID1A alterations ( ARID1Amut) in gynecologic malignancies. Methods: Patients (pts) with a diagnosis of ovarian (OC) or uterine cancer (UC) of different histologies and comprehensive genomic profiling (CGP) by Foundation Medicine Inc. were included in this study. CGP of solid tissue biopsies (Tbx; FoundationOneCDx) included evaluation of genomic loss of heterozygosity (gLOH; gLOH-high as ≥16% as validated in OC), microsatellite instability (MSI), and tumor mutational burden (TMB; high as ≥10 mutations/Megabase). CGP of peripheral whole-blood liquid biopsies (Lbx; FoundationOneLiquidCDx) included evaluation of MSI and tumor fraction (TF), a measure of the relative quantity of circulating tumor DNA (ctDNA). TF was calculated by measures of aneuploidy and allele frequency and binned as TF < 1%, TF 1 to < 10%, or TF ≥10%. Results: Tbx Cohort: 5,778/30,212 (19.1%) cases were ARID1Amut. Pts had a median age of 63 (range 21-89) years. ARID1Amut were observed across many subtypes and most frequently in endometrial endometrioid (n = 3,052, 57.7%) and ovarian clear cell (n = 982, 57.6%) but rarely in serous (OC, n = 12,258, 2.8%; UC, n = 2,682, 8.9%). Pts frequently harbored more than one ARID1Amut (2,360/5,778, 40.8%). Of the 8,484 observed ARID1Amut, 97.6% were short variants (SV), 0.5% were deletions, and 1.9% were inactivating rearrangements. SV were primarily frameshifts (68.5%) and nonsense mutations (27.6%). The most frequent alterations observed were frameshifts at the D1860 codon. SV were predicted to be homozygous in 11.9%, heterozygous in 65.3%, or unknown zygosity in 22.8%. Overall, 16.6% of ARID1Amut cases with SV had at least one homozygous alteration. 6.6% of pts with homozygous ARID1Amut were MSI-high (MSI-H), while 39.4% of pts with only heterozygous or unknown zygosity ARID1Amut were MSI-H (p < 0.0001). Overall, 1,905 (33.0%) of ARID1Amut cases were MSI-H, and 2,183 (37.8%) were TMB high. For ARID1Amut cases with evaluable gLOH (n = 4745), the median gLOH was 2.7%, and 5.9% pts were gLOH-high. The most frequently altered co-occurring genes were PTEN (62.2%), PIK3CA (54.2%), and TP53 (27.6%). 8.7% of ARID1Amut also harbored a BRCA alteration. Lbx Cohort: 59/967 (6.1%) cases were ARID1Amut. 17 (28.8%) were MSI-H. Frequency of ARID1Amut increased as TF increased, with a detected frequency of 1.3%, 6.7%, and 14.0% among Lbx with TF < 1%, TF 1 to < 10%, or TF ≥10% respectively. Conclusions: ARID1Amut are observed across a variety of Gynecologial cancer subtypes but are enriched in clear cell and endometrioid histologies and detected in both tissue and liquid biopsies. ARID1Amut were not associated with elevated gLOH but were often MSI-H and TMB ≥10mut/Mb. Clinical trials targeting ARID1A may wish to consider the context of co-occuring biomarkers.

CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS).

4587 Background: CDH1 mutated bladder cancers are characterized by plasmacytoid histology and are associated with an aggressive clinical course. Methods: Cohort 1: 6,676 clinically advanced UBC patients underwent hybrid capture based comprehensive genomic profiling (CGP) to evaluate all classes of genomic alterations (GA) as well as microsatellite instability (MSI), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH, high ≥16%). Tumor cell PD-L1 expression was determined by immunohistochemistry (Dako 22C3). GAs were compared between CDH1 mutated and wild-type (WT) patients using Chi-square. Cohort 2: 586 UBC patients underwent a RWCOS using the de-identified Flatiron Health-Foundation Medicine urothelial clinicogenomic database. The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care) between January 2011 and April 2022. Differences in real-world progression-free survival (rwPFS) and overall survival (rwOS) were evaluated by Cox proportional hazard models. Results: Cohort 1: 217 UBC patients featured a CDH1 short variant mutation with 65.2% featuring plasmacytoid histology (PLC). The PLC cohort was slightly younger, with a higher proportion of male patients, and MSI-High status. Cell-Cycle regulatory GAs were significantly higher in the non-PLC cohort, specifically CDKN2A (25.5% vs 9.7%, p=0.01) and CDKN2B (23.6% vs 5.8%, p<0.01). CDH1-mutated UBCs featured a higher MSI high frequency (2.7% vs 0.8%; p=.002), mean TMB (14.8 vs 9.9mut/Mb p<.0001), RB1 GA (52.5% vs 20.3%; p<.0001), PTEN GA (9.2% vs 4.3%; p=.006) and PIK3CA GA (29.5% vs 21.8%; p=.02), but lower gLOH (6.8% vs 15.9%; p=.009), CDKN2A loss (12.4% vs 38.3%; p<.0001), MTAP loss (10.1% vs 25.1%; p<.0001), and FGFR3 GA (9.7% vs 18.1%; p=.002). TP53 GAs and PD-L1 expression levels were similar between groups. From cohort 2: 22 (3.7%) patients featured CDH1 mutations. When compared with the CDH1 WT patients, the age, gender, ethnicity and ECOG status were similar. CDH1 mutation was associated with less favorable outcomes for 270 UBC patients treated with immune checkpoint inhibitors (ICPI) including rwPFS (2.8 vs 3.5 months; p=.096) and rwOS (3.3 vs 9.5 months; p=.03). Similar comparisons for 316 UBC patients treated with chemotherapy showed no significant adverse impact of CDH1 mutation status on either rwPFS (7.9 vs 6.2 months; p=.11) and rwOS (13.4 vs 13.4 months; p=0.83). Conclusions: In addition to its classic association with PLC histology, CDH1-mutated UBC features an unique genomic landscape including higher MSI and TMB, activating GAs in the MTOR pathway, but lower frequency of FGFR3 GAs. RWCOS further supports that CDH1 mutation predicts resistance to ICPI-based treatment, but does not systemic chemotherapy. These findings support CGP to guide therapeutic approaches based on the personalized genomic signature of UBC.

Comparison of the genomic profiles of primary and recurrent lesions in patients with advanced bladder carcinomas.

e16575 Background: Bladder carcinomas (BCs) is featured by high incidence of recurrence which remains to be a big clinical challenge. This study aimed to compare the genomic profiles of primary and recurrent BCs in advanced stage. Methods: Primary and recurrent tissues (and control blood) were collected and somatic variants including short variants, copy number variations, gene rearrangements and TMB (Tumor Mutation Burden) were analyzed following the CAP/CLIA-certificated workflows. Chi-Square Test/Fisher Test was applied to compare the difference between two variables. Results: To eliminate the impact of stage, only patients in advanced stages were included (stage III-IV) in this study. 53 patients were investigated, including 43 primary and 10 recurrent (evidence of tumor observed after radical treatment). It should be noted that matched primary and recurrent samples were not obtained from the same patient. Median age of the patients was 64 years old. The proportion of male patients was 86% (n = 37) in the primary cohort and 60% (n = 6) in the recurrent cohort. Among the primary cases, the most frequent alterations were detected in TP53 (58.1%), TERT (51.2%), KMT2D (27.9%), KDM6A (23.3%) and RB1 (23.3%). Among the recurrent cases, the most frequent alternations were showed in TERT (70%), KMT2D (50%), PIK3CA (50%), TP53 (50%) and KDM6A (40%). PIK3CA substitution and KRAS substitution showed significant difference when comparing between the two cohorts. PIK3CA substitution preferentially occurred in recurrent samples (50% recurrent vs 14% primary, p-value = 0.01), mostly occurred in E545K; while KRAS substitution showed 4.7% in primary and 30% in recurrent with p-value = 0.04, all presented as G12V. TMB showed no significant difference between the two cohorts (6.2 vs 6.3 muts/Mb, p-value = 0.72). Conclusions: By NGS, we observed that substitutions in PIK3CA and KRAS showed significant difference between primary and recurrent samples from advanced BCs patients. PIK3CA and KRAS mutations were reported to be associated with local recurrence in CRC, but no association was observed in early stage non-muscle-invasive BCs. Our findings may provide a different insight into the treatment selections for advanced BCs, although the sample size is small.

Bioinformatics pipeline to guide post-GWAS studies in Alzheimer's: A new catalogue of disease candidate short structural variants.

Short structural variants (SSVs), including insertions/deletions (indels), are common in the human genome and impact disease risk. The role of SSVs in late-onset Alzheimer's disease (LOAD) has been understudied. In this study, we developed a bioinformatics pipeline of SSVs within LOAD-genome-wide association study (GWAS) regions to prioritize regulatory SSVs based on the strength of their predicted effect on transcription factor (TF) binding sites. The pipeline utilized publicly available functional genomics data sources including candidate cis-regulatory elements (cCREs) from ENCODE and single-nucleus (sn)RNA-seq data from LOAD patient samples. We catalogued 1581 SSVs in candidate cCREs in LOAD GWAS regions that disrupted 737 TF sites. That included SSVs that disrupted the binding of RUNX3, SPI1, and SMAD3, within the APOE-TOMM40, SPI1, and MS4A6A LOAD regions. The pipeline developed here prioritized non-coding SSVs in cCREs and characterized their putative effects on TF binding. The approach integrates multiomics datasets for validation experiments using disease models.

Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data.

Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.

A Wnt-induced lncRNA-DGCR5 splicing switch drives tumor-promoting inflammation in esophageal squamous cell carcinoma

Alternative splicing (AS) is a critical mechanism for the aberrant biogenesis of long non-coding RNA (lncRNA). Although the role of Wnt signaling in AS has been implicated, it remains unclear how it mediates lncRNA splicing during cancer progression. Herein, we identify that Wnt3a induces a splicing switch of lncRNA-DGCR5 to generate a short variant (DGCR5-S) that correlates with poor prognosis in esophageal squamous cell carcinoma (ESCC). Upon Wnt3a stimulation, active nuclear β-catenin acts as a co-factor of FUS to facilitate the spliceosome assembly and the generation of DGCR5-S. DGCR5-S inhibits TTP's anti-inflammatory activity by protecting it from PP2A-mediated dephosphorylation, thus fostering tumor-promoting inflammation. Importantly, synthetic splice-switching oligonucleotides (SSOs) disrupt the splicing switch of DGCR5 and potently suppress ESCC tumor growth. These findings uncover the mechanism for Wnt signaling in lncRNA splicing and suggest that the DGCR5 splicing switch may be a targetable vulnerability in ESCC.

The cytoplasmic N-terminal tail of Zika virus NS4A protein forms oligomers in the absence of detergent or lipids

The non-structural (NS) NS4A protein in flaviviruses has three predicted transmembrane domains, is critical for virulence and participates in membrane morphogenesis. In Dengue virus (DENV), both hydrophylic N-terminal tail and its first transmembrane domain participate in the formation of oligomers which are important for pathogenicity. However, the relative importance of the N-terminal domain in oligomerization has been under debate. In particular, since in the absence of detergent or lipids, this domain (residues 1–48) in both DENV and Zika virus (ZIKV) NS4A, was found to be disordered. Recently, however, we reported preliminary data that showed that peptide ZIKV NS4A 4–58 adopts a defined secondary structure in aqueous solution and forms oligomers, signaling its importance for full length NS4A oligomerization. Herein we have performed detailed analytical ultracentrifugation experiments to further characterize the oligomerization of this peptide and also a shorter variant (residues 4–44). In both cases, sedimentation velocity produced a single species with concentration-dependent sedimentation coefficient, consistent with a fast equilibrium between at least two species. Combining sedimentation velocity and equilibrium experiments, data is best fitted to a monomer–dimer–trimer equilibrium. Possible models of NS4A oligomers obtained with AlphaFold-2 predict the stabilizing role for residues in this N-terminal domain, such as Arg20, Asn27, Ala44 and Glu50, all at highly conserved positions in flavivirus NS4A proteins. Our results are thus consistent with N-terminal domain interactions acting as one of the driving forces for NS4A homo-oligomerization.

ONT long-read WGS for variant discovery and orthogonal confirmation of short read WGS derived genetic variants in clinical genetic testing.

Technological advances in Next-Generation Sequencing dramatically increased clinical efficiency of genetic testing, allowing detection of a wide variety of variants, from single nucleotide events to large structural aberrations. Whole Genome Sequencing (WGS) has allowed exploration of areas of the genome that might not have been targeted by other approaches, such as intergenic regions. A single technique detecting all genetic variants at once is intended to expedite the diagnostic process while making it more comprehensive and efficient. Nevertheless, there are still several shortcomings that cannot be effectively addressed by short read sequencing, such as determination of the precise size of short tandem repeat (STR) expansions, phasing of potentially compound recessive variants, resolution of some structural variants and exact determination of their boundaries, etc. Therefore, in some cases variants can only be tentatively detected by short reads sequencing and require orthogonal confirmation, particularly for clinical reporting purposes. Moreover, certain regulatory authorities, for example, New York state CLIA, require orthogonal confirmation of every reportable variant. Such orthogonal confirmations often involve numerous different techniques, not necessarily available in the same laboratory and not always performed in an expedited manner, thus negating the advantages of "one-technique-for-all" approach, and making the process lengthy, prone to logistical and analytical faults, and financially inefficient. Fortunately, those weak spots of short read sequencing can be compensated by long read technology that have comparable or better detection of some types of variants while lacking the mentioned above limitations of short read sequencing. At Variantyx we have developed an integrated clinical genetic testing approach, augmenting short read WGS-based variant detection with Oxford Nanopore Technologies (ONT) long read sequencing, providing simultaneous orthogonal confirmation of all types of variants with the additional benefit of improved identification of exact size and position of the detected aberrations. The validation study of this augmented test has demonstrated that Oxford Nanopore Technologies sequencing can efficiently verify multiple types of reportable variants, thus ensuring highly reliable detection and a quick turnaround time for WGS-based clinical genetic testing.

Biosynthesis of polyprenylated xanthones in Hypericum perforatum roots involves 4-prenyltransferase.

Polyprenylated xanthones are natural products with a multitude of biological and pharmacological activities. However, their biosynthetic pathway is not completely understood. In this study, metabolic profiling revealed the presence of 4-prenylated 1,3,5,6-tetrahydroxyxanthone derivatives in St. John's wort (Hypericum perforatum) root extracts. Transcriptomic data mining led to the detection of five variants of xanthone 4-prenyltransferase (HpPT4px) comprising four long variants (HpPT4px-v1 to HpPT4px-v4) and one short variant (HpPT4px-sh). The full-length sequences of all five variants were cloned and heterologously expressed in yeast (Saccharomyces cerevisiae). Microsomes containing HpPT4px-v2, HpPT4px-v4, and HpPT4px-sh catalyzed the addition of a prenyl group at the C-4 position of 1,3,5,6-tetrahydroxyxanthone, 1,3,5-trihydroxyxanthone, and 1,3,7-trihydroxyxanthone, whereas microsomes harboring HpPT4px-v1 and HpPT4px-v3 additionally accepted 1,3,6,7-tetrahydroxyxanthone. HpPT4px-v1 produced in Nicotiana benthamiana displayed the same activity as in yeast, while HpPT4px-sh was inactive. The kinetic parameters of HpPT4px-v1 and HpPT4px-sh chosen as representative variants indicated 1,3,5,6-tetrahydroxyxanthone as the preferred acceptor substrate, rationalizing that HpPT4px catalyzes the first prenylation step in the biosynthesis of polyprenylated xanthones in H. perforatum. Dimethylallyl pyrophosphate was the exclusive prenyl donor. Expression of the HpPT4px transcripts was highest in roots and leaves, raising the question of product translocation. C-terminal yellow fluorescent protein fusion of HpPT4px-v1 localized to the envelope of chloroplasts in N. benthamiana leaves, whereas short, truncated, and masked signal peptides led to the disruption of plastidial localization. These findings pave the way for a better understanding of the prenylation of xanthones in plants and the identification of additional xanthone-specific prenyltransferases.

Overexpression of a Short Sulfonylurea Splice Variant Increases Cardiac Glucose Uptake and Uncouples Mitochondria by Regulating ROMK Activity.

The mitochondrial splice variant of the sulfonylurea receptor (SUR2A-55) is associated with protection from myocardial ischemia-reperfusion (IR) injury, increased mitochondrial ATP sensitive K+ channel activity (mitoKATP) and altered glucose metabolism. While mitoKATP channels composed of CCDC51 and ABCB8 exist, the mitochondrial K+ pore regulated by SUR2A-55 is unknown. We explored whether SUR2A-55 regulates ROMK to form an alternate mitoKATP. We assessed glucose uptake in mice overexpressing SUR2A-55 (TGSUR2A-55) compared with WT mice during IR injury. We then examined the expression level of ROMK and the effect of ROMK modulation on mitochondrial membrane potential (Δψm) in WT and TGSUR2A-55 mice. TGSUR2A-55 had increased glucose uptake compared to WT mice during IR injury. The expression of ROMK was similar in WT compared to TGSUR2A-55 mice. ROMK inhibition hyperpolarized resting cardiomyocyte Δψm from TGSUR2A-55 mice but not from WT mice. In addition, TGSUR2A-55 and ROMK inhibitor treated WT isolated cardiomyocytes had enhanced mitochondrial uncoupling. ROMK inhibition blocked diazoxide induced Δψm depolarization and prevented preservation of Δψm from FCCP perfusion in WT and to a lesser degree TGSUR2A-55 mice. In conclusion, cardio-protection from SUR2A-55 is associated with ROMK regulation, enhanced mitochondrial uncoupling and increased glucose uptake.

Abstract 2120: Exploring the genomic landscape of colorectal cancer for enabling clinical genomics informed and real-world data based clinical development

Abstract Background: Activation of the MAPK-signaling by RAS- (KRAS or NRAS) alterations is an important driver event in colorectal cancer (CRC) tumorigenesis that determines treatment selection (1).Real-world data (RWD) mining is an important tool to inform patient selection and stratification (2,3). Here, RWD genomics data mining was conducted using the Foundation Medicine database to explore RAS and BRAF-alterations in CRC patients and to investigate the general alterations’ landscape - including rare alterations. The prevalence of microsatellite instability (MSI) and tumor mutational burden (TMB) were also explored. Methods: The prevalence of gene alterations and their co-occurrence with RAS/BRAF-alterations in tumor tissue of CRC patients (N=42800) were investigated using the FoundationInsightsTM web platform, which includes harmonized results from the FoundationOneCDx, FoundationOneHeme, and PD-L1 assays from 2012 to March 2022. Data was collected from FMI solid and heme tests from 2012 to March 2022. Alterations that render a particular gene ‘altered’ included single nucleotide variants (SNVs) or insertion-deletion mutations (Indels), collectively referred to as short variants (SVs), rearrangements (RE) and copy number events (CN). TMB (cut-off 10 mut/MB) and MSI status were also characterized. Results: Altogether, 36.9% of CRC samples were RAS/BRAF-WT and 63.1% had a known or likely functional RAS/BRAF-alteration, respectively. Of all KRAS and NRAS alterations (SV, CN and RE regardless of annotation as functional or presence in a hotspot), SVs in exons 2, 3 and 4 constituted 96.1% and 94.2% of all alterations, respectively. Relative to all samples the potentially targetable KRAS p.G12C, p.G12D and p.G12V mutations were present in 3.6%, 15.1% and 10.2% of samples, respectively. The p.G12E variant was present in less than ten samples. The five most frequently altered potentially targetable genes were PIK3CA (19.6%), PTEN (8.7%), ERBB2 (4.7%), EGFR (2.5%) and FGFR1 (2.0%). NTRK-alterations (NTRK1/2/3) were present in 0.9%, ROS1-alterations in 0.4%, RET-alterations in 0.6% and ALK-alterations in 0.5% of samples, respectively. The prevalence of immuno-oncology biomarkers was also explored; overall, 9.6% of samples were TMB-high, 6.1% MSI-high and 0.6% POLE-altered. MSI-high or TMB-high samples were significantly more abundant in the RAS/BRAF-altered subset. In the RAS/BRAF-WT subset 4.6% were MSI-high and 7.9% TMB-high, whereas in the RAS/BRAF-altered subset 7.1% were MSI-high and 10.6% TMB-high. Conclusion: RWD based clinical genomic profiling confirms that the vast majority of RAS-alterations in CRC are SVs in exons 2, 3 and 4. Both TMB-high and MSI-high samples are significantly more abundant in the RAS/BRAF-altered cohort. RWD confirms that PI3K-, ERBB- and FGFR-signaling pathways are frequently altered in CRC. RWD based clinical genomic profiling has the potential to support comprehensive clinical study design as well as patient selection/stratification. Citation Format: Markus Schulze, XiaoZhe (Janet) Wang, Jawad Hamad, Julia F. Hopkins, Julia F. Hopkins, Jürgen Scheuenpflug, Zheng Feng. Exploring the genomic landscape of colorectal cancer for enabling clinical genomics informed and real-world data based clinical development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2120.

Abstract 6694: Evaluation of a multi-omics approach to molecular residual disease detection

Abstract Introduction: Advancements in DNA sequence detection technology and assay design have enabled molecular residual disease (MRD) assays to detect cancer earlier and with greater sensitivity. In Tumor-Informed (TI) strategies, mutations from the tumor are used to define a set of patient-specific markers that are tracked in the blood as circulating tumor DNA (ctDNA). Whereas tumor-naïve (TN) approaches do not require prior genomic information from the tumor and instead employ a fixed panel of marker(s). Methylated DNA Markers (MDMs) can be used to distinguish cancer from non-cancer and can be found in plasma. We have developed a proprietary TN MRD platform for colorectal cancer (CRC) capable of measuring as few as 1-5 strands of MDM target. Additionally, we are actively developing a TI MRD assay platform. Here we describe the evaluation of both TI and TN approaches for the detection of circulating tumor DNA (ctDNA) in blood across all stages of colorectal cancer and explore the complementarity of these two approaches in the context of MRD monitoring. Procedures: A 20-sample cohort of paired tumor/normal and pre-surgery plasma specimens from stage I (6/20), stage II (7/20), stage III (6/20), and stage IV (1/20) CRC patients and 20 demographically matched non-cancer controls were acquired for our study. All cancer plasma samples were collected prior to tumor resection. Neat and diluted plasma samples were tested for the presence of ctDNA containing short variants specifically derived from the corresponding primary tumor and for a pre-defined set of MDMs and protein cancer biomarkers. Tumor-specific short variants were characterized by whole exome sequencing of the primary tumors. MDMs were detected from bisulfite converted cfDNA by Target Enrichment Long probe Quantitative Amplified Signal (TELQAS) for 35 MDMs. A cancer detection classifier for the TN assay was trained and validated using a separate cohort of non-cancer and CRC plasma samples and employed for this study. Protein was detected by high throughput ELISA.Results: Tumor sequencing of the 20 CRC samples identified between 122 and 7146 (median = 230) somatic mutations per tumor sample. The combination of features from TI and TN assays achieved 95% accuracy, demonstrating an improvement over either assay in isolation. Indeed, 5 “positive” calls were made for cancer samples for which only one of the two methods met pre-defined RUO thresholds for ctDNA detection. Comparison of median variant allele fraction from the TI assay with median percent methylation of CRC markers for these CRC samples had a Pearson’s correlation of 0.967. Conclusion: TI and TN assays show high concordance in cancer detection, but also complement each other. Additionally, ctDNA quantifications produced from TI and TN assays are linearly correlated. The combination of data from both assays can be used to further differentiate cancer samples from non-cancer samples. Citation Format: Alanna Chan, Martin You, Oliver Limbo, Billyana Tsevtanova, Gerald Dodson, Brenda Curiel, Karma Farhat, Samantha Scott, Archana Ramesh, Jacquelyn Hennek, Viacheslav Katerov, Michael Kaiser, Hatim Allawi, Brady P. Culver, Michael Reshatoff, Jorge Garces, Gina Costa. Evaluation of a multi-omics approach to molecular residual disease detection. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6694.