Short Variant Research Articles

Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies.

Haemoglobinopathies are the commonest monogenic diseases worldwide and are caused by variants in the globin gene clusters. With over 2400 variants detected to date, their interpretation using the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines is challenging and computational evidence can provide valuable input about their functional annotation. While many in silico predictors have already been developed, their performance varies for different genes and diseases. In this study, we evaluate 31 in silico predictors using a dataset of 1627 variants in HBA1, HBA2, and HBB. By varying the decision threshold for each tool, we analyse their performance (a) as binary classifiers of pathogenicity and (b) by using different non-overlapping pathogenic and benign thresholds for their optimal use in the ACMG/AMP framework. Our results show that CADD, Eigen-PC, and REVEL are the overall top performers, with the former reaching moderate strength level for pathogenic prediction. Eigen-PC and REVEL achieve the highest accuracies for missense variants, while CADD is also a reliable predictor of non-missense variants. Moreover, SpliceAI is the top performing splicing predictor, reaching strong level of evidence, while GERP++ and phyloP are the most accurate conservation tools. This study provides evidence about the optimal use of computational tools in globin gene clusters under the ACMG/AMP framework.

Pan-tumor landscape of fibroblast growth factor receptor 1-4 genomic alterations

Selective tyrosine kinase inhibitors targeting fibroblast growth factor receptor (FGFR) 1-4 genomic alterations are in development or have been approved for FGFR-altered cancers (e.g. bladder cancer and advanced intrahepatic cholangiocarcinoma). Understanding FGFR inhibitor-resistance mechanisms is increasingly relevant; we surveyed the pan-tumor landscape of FGFR1-4 genomic alterations [short variants (SVs), gene rearrangements (REs), and copy number alterations (CNAs)], including their association with tumor mutational burden (TMB) and the genomic comutational landscape. Comprehensive genomic profiling of 355 813 solid tumor clinical cases was performed using the FoundationOne and FoundationOne CDx assays (Foundation Medicine, Inc.) to identify genomic alterations in >300 cancer-associated genes and TMB (determined on ≤1.1 megabases of sequenced DNA). FGFR1-4 SVs and REs occurred in 9603/355 813 (2.7%), and CNAs in 15 078/355 813 (4.2%) samples. Mostcommon FGFR alterations for bladder cancer, intrahepatic cholangiocarcinoma, and glioma were FGFR3 SVs (1051/7739, 13.6%), FGFR2 REs (618/6641, 9.3%), and FGFR1 SVs (239/11 550, 2.1%), respectively. We found several, potentially clinically relevant, tumor-specific associations between FGFR1-4 genomic alterations and other genomic markers. FGFR3 SV-altered bladder cancers and FGFR1 SV-altered gliomas were significantly less likely to be TMB-high versus unaltered samples. FGFR3 SVs in bladder cancer significantly co-occurred with TERT and CDKN2A/B alterations; TP53 and RB1 alterations were mutually exclusive. In intrahepatic cholangiocarcinoma, FGFR2 REs significantly co-occurred with BAP1 alterations, whereas KRAS, TP53, IDH1, and ARID1A alterations were mutually exclusive. FGFR1 SVs in gliomas significantly co-occurred with H3-3A and PTPN11 alterations, but were mutually exclusive with TERT, EGFR, TP53, and CDKN2A/B alterations. Overall, our hypothesis-generating findings may help to stratify patients in clinical trials and guide optimal targeted therapy in those with FGFR alterations.

Functional analysis of the short splicing variant encoded by CHI3L1/YKL-40 in glioblastoma.

The glycoprotein YKL-40 has been well studied as a serum biomarker of prognosis and disease status in glioblastoma. YKL-40 is a chitinase-like protein with defective chitinase activity that plays an important role in promoting cell proliferation, migration, and metastasis in glioblastoma multiforme (GBM). The short variant (SV) of YKL-40, generated by an alternative splicing event that splices out exon 8, was reported in the early developing human musculoskeletal system, although its role in GBM is still unknown. Our results showed that individual glioblastoma cell lines displayed increased expression of the short variant of YKL-40 after low serum treatment. In addition, unlike the full-length (FL) version, which was localized to all cell compartments, the short isoform could not be secreted and was localized only to the cytoplasm. Functionally, FL YKL-40 promoted cell proliferation and migration, whereas SV YKL-40 suppressed them. Transcriptome analysis revealed that these opposing roles of the two isoforms may be modulated by differentially regulating several oncogenic-related pathways, including p53, the G2/M checkpoint, and MYC-related signaling. This study may provide new ideas for the development of targeted anti-YKL-40 therapy in GBM treatment.

Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease

Background and aimsSingle nucleotide polymorphism rs6903956 has been identified as one of the genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1. We aim to interrogate the molecular basis of 6p24.1 containing rs6903956 risk alleles in endothelial disease biology. Methods and ResultsWe generated induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and non-CAD subjects (GG non-risk genotype at rs6903956). CRISPR-Cas9-based deletions (Δ63-89bp) on 6p24.1, including both rs6903956 and a short tandem repeat variant rs140361069 in linkage disequilibrium, were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells, with removal of ‘A’ risk alleles, exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. A CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/AG were also found to have 10 folds higher CXCL12 transcript copies/cell than those with non-risk genotype GG. ConclusionsOur study reveals the trans-acting impact of 6p24.1 with another CAD locus on 10q11.21 and is associated with intensified endothelial injury.

Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features.

Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA methylation groups with distinct biological drivers, clinical outcomes, and therapeutic vulnerabilities. Alternative meningioma grouping schemes using copy number variants, gene expression profiles, somatic short variants, or integrated molecular models have been proposed. These data suggest meningioma DNA methylation groups may harbor subgroups unifying contrasting theories of meningioma biology. A total of 565 meningioma DNA methylation profiles from patients with comprehensive clinical follow-up at independent discovery (n = 200) or validation (n = 365) institutions were reanalyzed and classified into Merlin-intact, Immune-enriched, or Hypermitotic DNA methylation groups. RNA sequencing from the discovery (n = 200) or validation (n = 302) cohort were analyzed in the context of DNA methylation groups to identify subgroups. Biological features and clinical outcomes were analyzed across meningioma grouping schemes. RNA sequencing revealed differential enrichment of FOXM1 target genes across two subgroups of Hypermitotic meningiomas. Differential expression and ontology analyses showed the subgroup of Hypermitotic meningiomas without FOXM1 target gene enrichment was distinguished by gene expression programs driving macromolecular metabolism. Analysis of genetic, epigenetic, gene expression, or cellular features revealed Hypermitotic meningioma subgroups were concordant with Proliferative or Hypermetabolic meningiomas, which were previously reported alongside Merlin-intact and Immune-enriched tumors using an integrated molecular model. The addition of DNA methylation subgroups to clinical models refined the prediction of postoperative outcomes compared to the addition of DNA methylation groups. Meningiomas can be separated into three DNA methylation groups and Hypermitotic meningiomas can be subdivided into Proliferative and Hypermetabolic subgroups, each with distinct biological and clinical features.

Sobre el origen de la escansión larga de la sílaba reduplicada de ἵημι

Abstract The reduplicated present ἵημι exhibits an alternating scansion of the reduplication syllable. The iota tends to be long in Attic but short in Homer and in other dialects. Martin Peters explained the long iota as the result of a compensatory lengthening after the loss of laryngeals, i.e. *Hi-Hi̯eh₁- > hīēmi. The short variant would have appeared by analogy with other reduplicated presents such as δίδωμι, ἵστημι, and τίθημι. This implies that the Attic long scansion is an archaism. The purpose of this paper is to show that Peters’ scenario is highly improbable and that the long iota is more likely due to levelling after the conflation of another present *ϝῑ́εμαι with ἵημι’s middle forms.

Genomic landscape of lung cancer in the young.

BackgroundLung cancer in the young is a rare entity of great interest due to the high frequency of targetable mutations. In this study, we explored the genomic landscape of non-small cell lung cancer (NSCLC) in young patients and compared it with genetic alterations in older patients.MethodsComparative study of the genomic profile of NSCLC young (≤40 years old) vs older patients (>40 years old) from Instituto Nacional de Enfermedades Neoplásicas (INEN) in Lima, Peru. Archival paraffin-embedded tumor samples were profiled with FoundationOne CDx assay to identify short variants alterations (insertions and deletions), copy number variations (CNV), tumor mutational burden and microsatellite instability in 324 driver genes and rearrangements in 28 commonly rearranged genes. A targetable alteration was defined as any alteration in a driver oncogene for which an FDA approved therapy existed at the time of study enrollment.ResultsOverall, 62 tumors were profiled, 32 from young and 30 from older patients. All clinicopathological features (smoking status, clinical stage, and histology) were similar between groups, except for gender (65.6% of females in the younger group vs 40% in the older group, P=0.043). At least one actionable mutation was present in 84.4% and 83.3% in younger and older patients, respectively. Alteration rates in the main genes were: BRAF, 3.1%(n=1) vs 0%; EGFR, 46.9% (n=15) vs 43.3% (n=13); ERBB2, 12.5% (n=4) vs 16.7% (n=5); KRAS, 15.6% (n=5) vs 16.7% (n=5); ALK, 6.3% (n=2) vs 3.3% (n=1); RET, 0.0% vs 3.3% (n=1); ROS1, 3.1% (n=1) vs 3.3% (n=1); NTRK1, 0.0% vs 3.3% (n=1) and MET, 3.1% (n=1) vs 13.3% (n=4). Mean TMB was 4.04 Mut/Mb (SD ± 3.98) for young vs 8.06 Mut/Mb (SD ± 9.84) for older patients (P=0.016). There were not significant differences in CNV, frequency of gene rearrangements, or microsatellites instability.ConclusionNSCLC in the young in our cohort was characterized by a high frequency of actionable genetic aberrations and a low TMB, which was also true for our older patients. The enrichment of actionable mutations in young patients described in other reports might be attributed to differences in the etiology and clinicopathological characteristics between younger and older patients and therefore not be applicable to all populations.

Mannan-binding lectin serine protease-2 (MASP-2) in human kidney and its relevance for proteolytic activation of the epithelial sodium channel

Proteolytic activation of the renal epithelial sodium channel (ENaC) is increased by aldosterone. The aldosterone-sensitive protease remains unidentified. In humans, elevated circulating aldosterone is associated with increased urinary extracellular vesicle (uEVs) excretion of mannan-binding lectin associated serine protease-2 (MASP-2). We hypothesized that MASP-2 is a physiologically relevant ENaC-activating protease. It was confirmed that MASP2 mRNA is abundantly present in liver but not in human and mouse kidneys. Aldosterone-stimulation of murine cortical colleting duct (mCCD) cells did not induce MASP-2 mRNA. In human kidney collecting duct, MASP-2 protein was detected in AQP2-negative/ATP6VB1-positive intercalated cells suggestive of MASP2 protein uptake. Plasma concentration of full-length MASP-2 and the short splice variant MAp19 were not changed in a cross-over intervention study in healthy humans with low (70 mmol/day) versus high (250 mmol/day) Na+ intake despite changes in aldosterone. The ratio of MAp19/MASP-2 in plasma was significantly increased with a high Na+ diet and the ratio correlated with changes in aldosterone and fractional Na+ excretion. MASP-2 was not detected in crude urine or in uEVs. MASP2 activated an amiloride-sensitive current when co-expressed with ENaC in Xenopus oocytes, but not when added to the bath solution. In monolayers of collecting duct M1 cells, MASP2 expression did not increase amiloride-sensitive current and in HEK293 cells, MASP-2 did not affect γENaC cleavage. MASP-2 is neither expressed nor co-localized and co-regulated with ENaC in the human kidney or in urine after low Na+ intake. MASP-2 does not mediate physiological ENaC cleavage in low salt/high aldosterone settings.

Genetic aetiologies for childhood speech disorder: novel pathways co-expressed during brain development

Childhood apraxia of speech (CAS), the prototypic severe childhood speech disorder, is characterized by motor programming and planning deficits. Genetic factors make substantive contributions to CAS aetiology, with a monogenic pathogenic variant identified in a third of cases, implicating around 20 single genes to date. Here we aimed to identify molecular causation in 70 unrelated probands ascertained with CAS. We performed trio genome sequencing. Our bioinformatic analysis examined single nucleotide, indel, copy number, structural and short tandem repeat variants. We prioritised appropriate variants arising de novo or inherited that were expected to be damaging based on in silico predictions. We identified high confidence variants in 18/70 (26%) probands, almost doubling the current number of candidate genes for CAS. Three of the 18 variants affected SETBP1, SETD1A and DDX3X, thus confirming their roles in CAS, while the remaining 15 occurred in genes not previously associated with this disorder. Fifteen variants arose de novo and three were inherited. We provide further novel insights into the biology of child speech disorder, highlighting the roles of chromatin organization and gene regulation in CAS, and confirm that genes involved in CAS are co-expressed during brain development. Our findings confirm a diagnostic yield comparable to, or even higher, than other neurodevelopmental disorders with substantial de novo variant burden. Data also support the increasingly recognised overlaps between genes conferring risk for a range of neurodevelopmental disorders. Understanding the aetiological basis of CAS is critical to end the diagnostic odyssey and ensure affected individuals are poised for precision medicine trials.

Structural organization and sequence diversity of the complete nucleotide sequence encoding the Plasmodium malariae merozoite surface protein-1

The merozoite surface protein-1 (MSP1) is a prime candidate for an asexual blood stage vaccine against malaria. However, polymorphism in this antigen could compromise the vaccine’s efficacy. Although the extent of sequence variation in MSP1 has been analyzed from various Plasmodium species, little is known about structural organization and diversity of this locus in Plasmodium malariae (PmMSP1). Herein, we have shown that PmMSP1 contained five conserved and four variable blocks based on analysis of the complete coding sequences. Variable blocks were characterized by short insertion and deletion variants (block II), polymorphic nonrepeat sequences (block IV), complex repeat structure with size variation (block VI) and degenerate octapeptide repeats (block VIII). Like other malarial MSP1s, evidences of intragenic recombination have been found in PmMSP1. The rate of nonsynonymous nucleotide substitutions significantly exceeded that of synonymous nucleotide substitutions in block IV, suggesting positive selection in this region. Codon-based analysis of deviation from neutrality has identified a codon under purifying selection located in close proximity to the homologous region of the 38 kDa/42 kDa cleavage site of P. falciparum MSP1. A number of predicted linear B-cell epitopes were identified across both conserved and variable blocks of the protein. However, polymorphism in repeat-containing blocks resulted in alteration of the predicted linear B-cell epitope scores across variants. Although a number of predicted HLA-class II-binding peptides were identified in PmMSP1, all variants of block IV seemed not to be recognized by common HLA-class II alleles among Thai population, suggesting that diversity in this positive selection region could probably affect host immune recognition. The data on structural diversity in PmMSP1 could be useful for further studies such as vaccine development and strain characterization of this neglected malaria parasite.

THE STATE OF HYPOCORISTIC NAMES IN ONOMASTIC SUBSYSTEM OF LANGUAGE

Introduction. One of the tasks of modern linguistics is to build a dynamic modelof the human language through the analysis of functionally motivated linguistic units, which,in particular, include hypocoristic names – a non-unofficial (short) variants of a personalname, used mainly for communication purposes. The analysis of the formal and semanticstructure of hypocoristic names, studying their functional features in comparison with those ofthe official (full) names will make it possible to get closer to the understanding of the lingualstatus of the proper name. The purpose of the paper is to examine hypocoristic names inthe languages of the same and different structure in order to clarify the common features anddiscuss the obtained results to confirm or deny the hypothesis of their own place in onomasticsubsystem of language. Methods. Typological method is used in the paper. Results: hypocoristicnames are frequently used in English, French, German, Spanish, Russian, Ukrainian, Japanese, andPersian languages in three main models: monosyllabic, disyllabic and reduplicative. Thereare vivid commonalities among the languages under analysis which could be due to thecommunicative function of hypocoristics in vocatives. Vocative discourse is where hypocoristicswork their way to the language structure. A vivid example of the process is the Russiantruncated vocative which broadens the scope of its function from originally short names tofull names and positions outside vocative discourse. Hypocoristics whose zone of productionis vocative discourse are neutral to morphological-syntactic indices. However, the mindprocesses short forms of the name in accordance with the general processes that are at theheart of the linguistic organization and human communication. The main of such processes isiconism – the motivation of a linguistic form. The main way of handling hypocoristics is aniconic diagram – a systematic organization of signs, which are not necessarily similar to theirreferents, but whose interconnection reflects their relation to the referents. Conclusion. Thehypothesis was confirmed but further investigation is to be continued.

1368P TALAPRO-1: Talazoparib monotherapy in metastatic castration-resistant prostate cancer (mCRPC) with DNA damage response alterations (DDRm) – Exploration of tumor genetics associated with prolonged benefit

TALAPRO-1 enrolled men with progressive mCRPC, measurable soft-tissue disease, and tumor DDRm involved directly or indirectly in homologous recombination repair (11-gene panel). Enrolled men had received 1–2 taxane-based chemotherapy regimens and progressed on ≥1 novel hormonal therapy. Confirmed objective response rate (primary endpoint; per RECIST 1.1; blinded independent central review [BICR]) was 29.8%. The molecular bases of prolonged clinical benefit with poly(ADP-ribose) polymerase inhibitors are incompletely understood, although limited evidence suggests that patients exhibiting large deletions in BRCA genes may experience extended benefit. Exploratory post hoc biomarker analyses assessed tumor genetics associated with prolonged antitumor benefit in TALAPRO-1. Tumor alterations were assessed using FoundationOne®CDx. Zygosity of tumor alterations was predicted using somatic-germline-zygosity. Prolonged benefit was assessed as radiographic progression-free survival ([rPFS]; RECIST 1.1/PCWG3; BICR) time to event or censoring. Data cutoff was Sept 4, 2020 (primary completion date). Of 104 men in the efficacy population, 16 had rPFS of ≥12 months. Of their 16 tumors, 15 (94%) had BRCA2 alterations, including 10 large structural variants (9 copy number loss, 1 rearrangement) and 5 short variants (SV; 4 homozygous). In contrast, only 6/27 (22%) men with rPFS <2.0 months exhibited BRCA2 alterations (1 rearrangement, 1 non-defined, and 4 SV with 2 homozygous). Of 61 men with rPFS <12 months but ≥2 months, 36 (59%) had BRCA2 alterations (9 copy number loss, 1 rearrangement, 21 SV [11 homozygous], 2 multiple alterations [1 homozygous], and 3 not defined). Conversely, TP53 alterations were less common for men with rPFS ≥12 months vs <2 months (2/16 vs 14/27; P=0.02 Fisher’s exact test, 2-tails), potentially reflecting negative prognosis or a subgroup less sensitive to PARP inhibition. Based on these retrospective, exploratory analyses of TALAPRO-1, men exhibiting prolonged benefit typically exhibited BRCA2 copy number loss or homozygous alterations, and lacked TP53 alterations.

Intronic NEFH variant is associated with reduced risk for sporadic ALS and later age of disease onset

Neurofilament heavy (NEFH) is one of the critical proteins required for the formation of the neuronal cytoskeleton and polymorphisms in NEFH are reported as a rare cause of sporadic ALS (sALS). In the current study, a candidate tetranucleotide (TTTA) repeat variant in NEFH was selected using an in-silico short structural variant (SSV) evaluation algorithm and investigated in two cohorts of North American sALS patients, both separately and combined (Duke cohort n = 138, Coriell cohort n = 333; combined cohort n = 471), compared to a group of healthy controls from the Coriell Institute biobank (n = 496). Stratification according to site of disease onset revealed that the 9 TTTA allele was associated with reduced disease risk, specifically confined to spinal-onset sALS patients in the Duke cohort (p = 0.001). Furthermore, carriage of the 10 TTTA allele was associated with a 2.7 year later age of disease onset in the larger combined sALS cohort (p = 0.02). These results suggest that the 9 and 10 TTTA motif length may have a protective advantage for potentially lowering the risk of sALS and delaying the age of disease onset, however, these results need to be replicated in larger multicenter and multi-ethnic cohorts.

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples

Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short reads from 262 whole-exome sequencing samples of Bos Taurus were mapped to the Bos Taurus ARS-UCD1.2 reference genome. The GATK best practice workflow was applied for variant calling. Comprehensive annotation of all recorded variants was done using the Ensembl Variant Effect Predictor (VEP). An in-depth analysis of the population structure revealed the breeds comprising the database. The Exomes Aggregate of Bovine- ExAgBov is a comprehensively annotated dataset of more than 20 million short variants, of which ~2% are located within open reading frames, splice regions, and UTRs, and more than 60,000 variants are predicted to be deleterious.

Landscape of Genomic Alterations and Biomarkers in Endometrial Cancer (EC) Identified by Comprehensive Genomic Profiling (CGP) of Peripheral Blood Biopsies (181)

<b>Objectives:</b> Circulating tumor DNA (ctDNA) extracted from peripheral blood presents an alternative to tumor tissue for molecular testing when the latter is unavailable. We explored the landscape of genomic alterations (GA) from liquid biopsies of patients with advanced/recurrent EC to determine utility to inform prognosis, treatment selection, and clinical trial eligibility. <b>Methods:</b> Comprehensive genomic profiling (CGP) by hybrid capture sequencing on peripheral blood-derived cell-free DNA (cfDNA) from 193 patients with EC (b-EC cohort) interrogated 324 genes (including 75 with enhanced sensitivity and 21 with introns; F1LCDx) and assessed microsatellite instability-high status (MSI-H; detected/not detected) and blood tumor mutational burden (bTMB; muts/Mb). The proportion of cfDNA predicted to be tumor-derived (ctDNA) was calculated as tumor fraction (TF). Additionally, 7148 tissue samples from patients with advanced EC (t-EC cohort) were analyzed by a 324-gene CGP assay (F1CDx) for comparison to the b-EC cohort. <b>Results:</b> Sixty-seven of 193 b-EC were submitted with specified histologic diagnosis (25 endometrioid [13%], 21 serous [11%], 12 carcinosarcomas [6%], seven clear cells, and two of mixed histology), while the remaining 126 b-EC (65%) were not further specified. Patients had a median age of 69 years (range: 36 -87 years), 182 (94%) had detectable ctDNA, and 18% had a TF >10%. Among b-EC with detectable ctDNA, the median bTMB was 2.5mut/Mb. Eleven b-EC had MSI-H status detected, and among them, the median bTMB was 29 mut/Mb (range: 14 - 109). At least one GA in a potentially targetable pathway was identified in 48% of b-EC, including PI3K/mTOR, MEK, HRR, and receptor tyrosine kinases (Table 1). In cases with TF>10%, alteration frequencies for these genes were generally higher and more similar to rates detected in t-EC. Six b-EC with <i>ERBB2</i> alterations (three amplifications and three activating short variants) and two b-EC with an activating <i>ESR1</i> mutation (Y537S; commonly seen in endocrine-resistant breast cancer) were detected. Sixteen patients had <i>BRCA1/2</i> alterations, of which six had variant allele frequencies suggesting possible germline origin. Other potentially targetable alterations were detected in <i>EGFR</i> (six short variants) and <i>ALK</i> rearrangements (two cases). The most frequently altered gene was <i>TP53</i>, seen in 58% b-EC and 74% of TF>10 b-EC (vs 63% t-EC; p=0.28). Since clonal hematopoiesis (CH) can contribute to alterations in cfDNA, significantly more b-EC samples had one or more alterations in potential CH genes (<i>DNMT3a</i>, <i>TET2, ASXL1</i>) compared to t-EC (53% vs 11%; p<0.0001). <b>Conclusions:</b> A total of 94% of patients with b-EC had detectable ctDNA, and 48% had a potentially targetable alteration or biomarker, confirming liquid biopsy as a viable alternative in EC when appropriate tumor tissue is lacking and could increase access to clinical trials. MSI-H status, high-bTMB, and alterations detected in ctDNA could also suggest an EC subtype with associated prognostic implications and/or molecular mechanism of treatment resistance. Since sensitivity depends on ctDNA shed, negative liquid biopsy results must be confirmed with tumor tissue testing if clinically appropriate.

Conditional knockout of oestrogen receptor alpha in CD11c+ cells impacts female survival and inflammatory cytokine profile in murine lupus.

Oestrogen and oestrogen receptor alpha (ERα) have been implicated in systemic lupus erythematosus pathogenesis. ERα signalling influences dendritic cell (DC) development and function, as well as inflammation and downstream immune responses. We previously reported that ERα modulates multiple Toll-like receptor-stimulated pathways in both conventional and plasmacytoid DCs in lupus-prone mice. For example, CD11chi MHCII+ cell numbers are reduced in mice with global ERα deficiency or when expressing a short variant of ERα. Herein, RNA-seq analysis of CD11chi cells from bone marrow of NZM2410 mice expressing WT ERα versus ERα short versus ERα null revealed differentially expressed complement genes, interferon-related genes and cytokine signalling (e.g., IL-17 and Th17 pathways). To better understand the role of ERα in CD11c+ cells, lupus prone NZM2410 mice with selective deletion of the Esr1 gene in CD11c+ cells were generated. Phenotype and survival of these mice were similar with the exception of Cre positive (CrePos) female mice. CrePos females, but not males, all died unexpectedly prior to 35 weeks. DC subsets were not significantly different between groups. Since ERα is necessary for robust development of DCs, this result suggests that DC fate was determined prior to CD11c expression and subsequent ERα deletion (i.e., proximally in DC ontogeny). Overall, findings point to a clear functional role for ERα in regulating cytokine signalling and inflammation, suggesting that further study into ERα-mediated regulatory mechanisms in DCs and other immune cell types is warranted.

HOTAIR interacts with PRC2 complex regulating the regional preadipocyte transcriptome and human fat distribution.

Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.

Genomic landscape of non-small-cell lung cancer with methylthioadenosine phosphorylase (MTAP) deficiency.

New treatment strategies for advanced non-small-cell lung carcinoma (NSCLC) include synthetic lethality targets focused on protein arginine methyl transferases such as PRMT5 that exploit the impact of genomic loss of methylthioadenosine phosphorylase (MTAP). Twenty nine thousand three hundred seventy nine advanced NSCLC cases underwent hybrid-capture based comprehensive genomic profiling between June 1, 2018 and May 31, 2020. PD-L1 expression was determined by immunohistochemistry (Dako 22C3 PharmDx assay). 13.4% (3928/29,379) NSCLC cases exhibited MTAP loss distributed in adenocarcinoma (59%), squamous cell carcinoma (22%), NSCLC not otherwise specified (16%), and 1% each for large-cell neuroendocrine, sarcomatoid, and adenosquamous carcinoma. Statistically significant differences in mitogenic driver alterations included more KRAS G12C mutations in MTAP-intact versus MTAP-lost (12% vs. 10%, p=0.0003) and fewer EGFR short variant mutations in MTAP-intact versus MTAP-lost NSCLC (10% vs. 13%, p < 0.0001). Statistically significant differences in currently untargetable genomic alterations included higher frequencies of TP53 (70% vs. 63%, p < 0.0001) and RB1 inactivation (10% vs. 2%, p < 0.0001) in MTAP-intact compared to MTAP-lost NSCLC. SMARCA4 inactivation (7% vs. 10%, p < 0.0001) was less frequent in MTAP-intact versus MTAP-lost NSCLC. Alterations in ERBB2, MET, ALK, ROS1, and NTRK1 did not significantly differ between the two groups. Predictors of immunotherapy efficacy were higher in MTAP-intact versus MTAP-lost NSCLC including tumor mutational burden (9.4 vs. 8.6 mut/Mb, p=0.001) and low (30% vs. 28%, p=0.01) and high PD-L1 (32% vs. 30%, p=0.01) expression. Alterations in biomarkers potentially predictive of immune checkpoint inhibitor resistance (STK11, KEAP1, and MDM2) were similar in the two groups. MTAP loss occurs in 13% of NSCLC, supporting the development of targeted therapies to exploit PRMT5 hyper-dependence. MTAP loss is accompanied by small differences in targeted and immunotherapy options which may impact future combination strategies.

Abstract 753: Comprehensive genomic profiling (CGP) reveals site-specific enrichment of immunotherapy biomarkers and targetable alterations in non-small cell lung cancer (NSCLC) metastasis

Abstract Introduction NSCLCs are frequently identified at a later stage, with 30-40% of cases presenting with metastasis at the time of diagnosis. Metastatic progression is a major cause of cancer death, thereby making it critical to understand the genomic differences across metastatic sites and their associated treatment implications. Methods CGP was performed on 64,062 NSCLCs for all classes of alterations in at least 324 genes (Foundation Medicine, Inc.). The cohort comprised 59% lung (LB), 25% metastatic site (MB) and 17% regional/distant lymph node (LN) biopsies. A subset of 386 patients with matched LB/MB samples were examined. Tumor mutational burden (TMB) was determined on 0.8-1.1 Mb and PD-L1 IHC (DAKO 22C3) was evaluated in a subset of cases. Results MB NSCLCs comprised liver (23%), brain (23%), bone (15%), soft tissue (14%), adrenal gland (8%) and other rare sites (e.g., spine, head&amp;neck, kidney). MB NSCLCs had elevated TMB compared to LB NSCLCs (median 7.8 v 6.3 mut/Mb; P &amp;lt; 10-4), most notably in brain (11.3 mut/Mb), adrenal gland (10.4 mut/Mb) and kidney (9.2 mut/Mb) MB, whereas TMB in liver MB was similar to LB (6.3 mut/Mb). Heterogeneity in PD-L1 expression (≥50%) was also observed, with higher rates in head&amp;neck (42%), adrenal gland (40%), LN (39%), and soft tissue (35%) compared to LB (30%; all P &amp;lt; 0.05). Clinically informative alterations and known NSCLC drivers exhibited site-specific patterns. EGFR alterations differed by sites with the highest rates in omentum (40% v 15% LB), bone (20%) and liver (18%). Fusions in ALK, RET and ROS1 were more common in MB NSCLCs relative to LB, while MET exon 14 skipping alterations were rarer in MB NSCLCs. Liver MB had fewer KRAS alterations (21% v 31% LB, P&amp;lt;10-4), while brain MB had elevated rates of KRAS, KEAP and STK11 alterations (37% v 31%, 16% v 9%, 23% v 15%, respectively, P&amp;lt;10-4). A repertoire of genes with potential role in metastatic spread (e.g., SMARCA4, RICTOR, PIK3CG), were identified to be enriched in specific MB NSCLCs. Of note, MB NSCLCs also presented with significantly higher rates of aneuploidy across the genome. 386 patients with longitudinal LB/MB samples were available (median collection time difference = 474 days). Concordance, defined by percent positive agreement (PPA) of alterations with LB, varied by site and was highest in bone and brain MB. While truncal, driver events were often shared, short variants in PIK3CA, ARID1A and copy number alterations in MYC, RICTOR, MET and CDKN2A/2B were frequently acquired in MB. TMB was elevated in MB compared to LB in 204 cases, though only 39 patients transitioned from TMB &amp;lt;10 to TMB ≥10 mut/Mb status. Conclusions NSCLC metastases exhibit heterogeneity in clinically actionable alterations and immunotherapy biomarkers (PD-L1, TMB). Site-specific alterations may have clinical implications and inform the biology of metastatic progression. Citation Format: Benjamin G. Kaplan, Richard S. Huang, Lucas Dennis, Lee A. Albacker, Garrett M. Frampton, Ethan S. Sokol, Smruthy Sivakumar. Comprehensive genomic profiling (CGP) reveals site-specific enrichment of immunotherapy biomarkers and targetable alterations in non-small cell lung cancer (NSCLC) metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 753.

Associations Between Personality Traits, Perceived Stress and Depressive Symptoms in Gynecological Cancer Patients Characterized by the Short and Long Allele Variant of the 5-HTTLPR Genotype: Preliminary Results.

ObjectiveThe study explored associations between personality traits, perceived stress and symptoms of depression in oncological patients characterized by the two variants of the serotonin transporter (5-HTTLPR) polymorphisms.MethodThe sample was composed of 41 gynecological cancer patients who completed self-reported questionnaires including the NEO Five-Factor Inventory, the dimension of depression-dejection (D/D) of the Profile of Moods State and the Perceived Stress Scale (PSS). The polymerase chain reaction was also employed to identify genotypes in the serotonin (5HTT) polymorphism.ResultsThe one-way ANOVA test, across the 5-HTTLPR genotype groups, showed significant effects of the short variants on neuroticism (p=0.009) and of the long variant on agreeableness (p=0.022), as well as a tendency to a statistical significance of the l/l variant on consciousness (p=0.074). Bivariate correlations showed positive correlations of neuroticism with both psychopathological symptoms (D/D r=0.522; PSS r=0.586) in the combined group S, negative association of agreeableness with depression (D/D r=-0.613) and of consciousness with depression (D/D r=-0.750) and perceived stress (PSS r=-0.702) in the group of the long variant of 5-HT-TLPR genotype.ConclusionsPersonalized medicine should consider the interaction between genotype and phenotype in reducing levels of clinical psychological distress, highlighting how psychotherapeutic processes should improve patients' quality of life.