Exome Sequencing Of DNA Research Articles

Identification of Novel Genetic Risk Variants Associated with Hidradenitis Suppurativa in an Exome Sequencing Cohort of 92,455 Individuals

Introduction: Hidradenitis suppurativa (HS) is a prevalent and persistent inflammatory skin disorder, lacking a known cure or effective biomarkers for early diagnosis at present. The genetic determinants of HS have not been fully documented, but it is believed to result from a combination of genetic and environmental factors. Methods: To identify relevant HS gene variants in sporadic HS patients, this study utilized longitudinal electronic health records (EHRs) and whole-exome sequencing. DNA exome sequencing data from 92,455 participant samples in the MyCode biobank, linked to Geisinger’s EHR, were analyzed. This cohort included 1,092 HS cases and 91,363 healthy controls. The MyCode EHR has a median longitudinal follow-up of 15 years per participant, with an average of 87 clinical encounters, 687 laboratory tests, and 7 procedures. Results: There were 1,092 (901 females and 191 males) participants aged 14–89 years (median 47 years) with HS (L73.2), indicating a 1.18% prevalence and accounting for a 4.7:1 female-to-male ratio among the individuals presenting for clinical care. γ-secretase complex, syndromic, and autoinflammatory gene variants were assessed. Potential pathogenic variants were identified among 66 individuals in the HS genes studied. Molecularly, the estimated HS variant prevalence was 1:1,400 in the cohort, 12.3% of variant carriers had HS diagnosis in EHR. Conclusions: Using longitudinal EHR data, genomic screening identified HS-associated gene variants in a defined group of sporadic HS patients to augment the clinical diagnosis, particularly in cases of ambiguity. Based on this study, the field of skin disorders can benefit from a personalized approach to HS diagnosis using large-scale sequencing.

Loss of STK11 Suppresses Lipid Metabolism and Attenuates KRAS-Induced Immunogenicity in Patients with Non-Small Cell Lung Cancer.

In patients with lung cancer, we demonstrate that KRAS mutations increase tumor immunogenicity; however, KRAS/STK11 co-mutated patients display an immune-excluded phenotype. KRAS/STK11 co-mutated patients also demonstrated significant downregulation of several key lipid metabolism genes, many of which were associated with increased immunogenicity and improved overall survival in KRAS-mutated patients. Hence, alteration to lipid metabolism warrants further study as a potential biomarker and target for therapy in patients with KRAS-mutated lung cancer.

Successful treatment of Darier's disease with apremilast and review of reported cases.

Darier's disease (DD) is a rare autosomal dominant genetic disorder caused by a mutation in ATP2A2, which encodes calcium (Ca2+) ATPase pumps in the endoplasmic reticulum. In this report, we present the first documented case in Japan successfully treated with apremilast. An 18-year-old female presented with red or brown hyperkeratotic papules and plaques on her head, neck, and chest. Histopathological examination revealed a hyperkeratotic, acanthotic epidermis, along with suprabasal acantholysis characterized by corps ronds and grains. Exome sequencing of DNA from peripheral blood mononuclear cells identified a missense mutation in ATP2A2. Based on the above results, we diagnosed her with DD despite the absence of a family history. Given the effectiveness of apremilast, a phosphodiesterase 4 inhibitor, in treating Hailey-Hailey disease (HHD), a genetically related disorder involving ATPases in epidermal calcium channels, we opted for apremilast therapy. Eight weeks post-initiation, significant improvement was observed in the patient's skin lesions on the head, neck, and chest. In this paper, we discuss the successful treatment of DD and HHD cases with apremilast, providing insights into its therapeutic potential, and offer a comprehensive review.

Congenital anomalies of the kidney and urinary tract.

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) refer to a range of conditions that affect the kidney and urinary tract. These anomalies can be severe, such as kidney agenesis, or milder, such as vesicoureteral reflux. CAKUT affects over 1% of live births and accounts for 40-50% of cases of chronic kidney failure in children. The pathogenesis of CAKUT is caused by various environmental, genetic, and epigenetic factors that disrupt normal nephrogenesis. Environmental factors that can lead to CAKUT include maternal diabetes, obesity, malnutrition, alcohol consumption, or medications affecting kidneys development. Genetic factors can cause an imbalance in the metanephros and the ureteric bud interaction. Defects in specific genes such as PAX2, TBX18, NRIP1, REX, SIX2, BMP4, and chromosome 17 cause CAKUT. Over 50 genes have been identified as the root cause of this condition, with monogenetic variants causing up to 20% of all cases. CAKUTs can be diagnosed through fetal ultrasonography, but some anomalies may remain undetected. GWASs, Next Generation Sequencing for targeted and whole exome DNA sequencing may provide additional diagnostic methods. This review article highlights some the leading factors that cause CAKUT, which adversely affects kidney development and urinary tract function.

LGG-44. CLINICAL AND MOLECULAR TUMOR CHARACTERISTICS OF ‘HIGHER RISK’ PEDIATRIC LOW-GRADE GLIOMAS

Abstract BACKGROUND CNS WHO grade 1 pediatric low-grade gliomas (pLGGs) have an overall excellent survival. A small but relevant proportion of these patients, however, suffer from severe disease burden reflected in recurrent progression, metastasis or even death. To unravel clinicomolecular tumor characteristics that identify these ‘pLGG-higher risk’ patients we retrospectively analyzed clinical and molecular data of 223 patients from our center. METHODS All tumors were classified using histology, DNA methylation profiling and whole transcriptome analysis (RNA sequencing), with whole exome or panel DNA sequencing in a subset of cases, revealing a driver alteration in 100% of cases. Progression of disease was defined as continuous tumor growth upon treatment or need for multiple treatments. The effect of clinical and molecular variables on progression free survival was analyzed with the univariate and multivariate cox proportional hazard model. RESULTS The median follow-up of the entire cohort was 3,4 years. In univariate analyses the risk of progression significantly decreased with age (in years) at diagnosis (HR 0.92,p<0.001). For tumor location using hemispheric tumors as reference, chiasm/suprasellar LGGs showed a significantly higher risk of progression (HR 2.96,p<0.001). Type of molecular driver and sex was not associated with progression. In a multivariable model including age, location and driver, there was no longer a significant effect on progression for age but the effect of chiasm/suprasellar location remained intact. Furthermore, NF1 (HR 0.37,p0.02), and posterior fossa LGG (HR 0.24,p0.03) were both significantly associated with a lower risk of progression. CONCLUSIONS Our multivariate results show that the ‘pLGG-higher risk’ patients were characterized by a tumor in the chiasm/suprasellar location, while molecular driver (at least so far) did not affect risk of progression. Future work will focus on extending the cohort and integrating other multiomic data enabling to compose a prediction model for higher risk pLGG.

TRLS-04. EARLY INSIGHTS FROM PNOC027: PERSONALIZED TREATMENT APPROACHES BASED ON REAL-TIME DRUG SCREENING AND GENOMIC TESTING IN PEDIATRIC AND ADOLESCENT PATIENTS WITH RECURRENT MEDULLOBLASTOMA

Abstract BACKGROUND PNOC027, a clinical trial conducted by the Pediatric Neuro-Oncology Consortium (PNOC), explores a precision medicine strategy with up to four FDA-approved agents integrating real-time drug screening with whole exome DNA and RNA sequencing to guide personalized treatment approaches for children and young adults with relapsed medulloblastoma. METHODS Freshly isolated tumor cells from patients undergo high-throughput drug screening, evaluating responses to 232 clinically available compounds over 72 hours. In vitro drug responses are integrated with tumor genomic and transcriptomic data to predict drug combinations for each patient. Drugs are prioritized based on blood-brain barrier permeability, patient age, prior treatments, and other co-morbidities. Correlative studies include the collection of blood to assess circulating tumor DNA (ctDNA) before surgery and during treatment. Health-related quality of life (HRQOL) assessments will also be collected during therapy. RESULTS To date, nine patients have been enrolled. Eight of these have successfully completed real time drug screening with a median turnaround of 7 days from sample receipt. One patient was excluded due to ineligible (non-medulloblastoma) pathology after enrollment. Seven of these had whole exome sequencing, and six had RNA sequencing. Tumor board recommendations were rendered within 21 business days from the date of surgery. Among the diverse drug classes evaluated, histone deacetylase (HDAC) inhibitors, proteasome inhibitors, anthracyclines, DNA crosslinkers, and kinase inhibitors showed the most robust in vitro responses. Six patients received the recommended regimens, experiencing tolerable (grade 1/2) toxicities. Two patients succumbed to disease prior to therapy initiation, three exhibited disease progression while on therapy, and three remain on therapy. CONCLUSION PNOC027 demonstrates preliminary feasibility of real-time drug screening combined with DNA/RNA sequencing to inform targeted therapy selection in clinically relevant timeframes and with potential for disease response.

Individualized neoantigen therapy mRNA-4157 (V940) plus pembrolizumab in resected melanoma: 3-year update from the mRNA-4157-P201 (KEYNOTE-942) trial.

LBA9512 Background: mRNA-4157 is a novel, mRNA-based individualized neoantigen therapy designed to increase endogenous antitumor T-cell responses by targeting unique patient (pt) tumor mutations. In the primary analysis of the Ph 2 mRNA-4157-P201 (KEYNOTE-942) trial (median planned follow-up, 23 mo), pts with completely resected high-risk stage IIIB–IV cutaneous melanoma receiving mRNA-4157 + pembrolizumab (pembro; combo) had prolonged recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) vs pembro alone (Weber JS, et al. Lancet. 2024). Methods: Pts were assigned 2:1 to mRNA-4157 (1 mg IM, max 9 doses) + pembro (200 mg IV, max 18 cycles) or pembro alone. The primary endpoint was investigator-assessed RFS; secondary endpoints were DMFS and safety. This planned supportive analysis was triggered when the last randomized pt had ≥2 y follow-up. Translational subgroup analyses were also reported. HLA genotypes were analyzed by exome sequencing of DNA from PBMC. RFS and DMFS were not formally tested; nominal 2-sided p-values are descriptive. Results: With an additional year follow-up (data cutoff, 03 Nov 2023; median [range], 34.9 [25.1–51.0] mo) after primary analysis, minimal new events occurred. RFS benefit in the combo vs pembro arm was maintained with 49% risk reduction in recurrence and/or death (HR [95% CI], 0.510 [0.288–0.906]; 2-sided nominal p-value 0.019). The 2.5-yr RFS rate of combo treatment (tx) vs pembro alone was 74.8% vs 55.6%. Combo tx also produced clinically meaningful, sustained improvement in DMFS vs pembro alone (HR [95% CI], 0.384 [0.172–0.858], 2-sided nominal p-value 0.0154). OS favored combo vs pembro alone; 2.5-y OS rate was 96.0% vs 90.2% (HR [95% CI], 0.425 [0.114–1.584]). RFS benefit of combo vs pembro was maintained in TMB high (HR [95% CI], 0.564 [0.253–1.258]), TMB non-high (0.571 [0.245–1.331]), PD-L1 positive (0.471 [0.226–0.979]), PD-L1 negative (0.147 [0.034–0.630]), and ctDNA negative (0.207 [0.091–0.470]) subgroups; ctDNA positive HR was not estimable. No significant associations between individual HLA alleles and RFS were observed in either tx arm. Maximal heterozygosity at HLA class I genotype loci (A, B, C) improved RFS vs homozygosity for ≥1 locus in the pembro arm (HR [95% CI], 0.425 [0.179–1.01]) but not combo arm (1.252 [0.498–3.146]). mRNA-4157 was well tolerated and combo tx had a safety profile consistent with previous analysis with no potentiation of immune-related AEs. Conclusions: The current analysis with ∼3 y median follow-up showed durable and meaningful long-term RFS and DMFS benefit with mRNA-4157 + pembro vs pembro alone. A trend for improved OS with combo tx was also observed. HLA and translational subgroup results suggest mRNA-4157 + pembro may benefit a broader pt population vs pembro alone. Clinical trial information: NCT03897881 .

Abstract PO3-23-11: Multiomics analysis of ER+ breast cancer with matched primaries, lymph node metastases and recurrent cancers on adjuvant endocrine therapy

Abstract Background: 80% of all breast cancers (BCs) are ER-positive (ER+). A significant number develop endocrine therapy resistance (ETR) . Clones develop in lymph nodes (LNs) which differ from the primary and these are implicated in ETR. A multiomics analysis of primary ER+ breast cancers, matched LN metastasis (LN+), if present, and matched recurrences (primary, nodal or distant) has been performed. Patients and Methods: The patients included are: Cohort A: 95 patients with matched primary and recurrent ER+ BC on different endocrine therapies. 35% had involved LNs at diagnosis. Recurrences: local in 59/95, concurrent local and nodal in 33/95, LN-only in 3/95. Median time to recurrence 4.5 years. Cohort B: 18 patients with ER+ LN+ BC who developed multiple recurrences (local and/or nodal, >3 consecutive recurrences/patient) on different lines of sequential endocrine therapy. Cohort C: 7 patients with ER+ breast cancer with multiple involved LNs treated with 3-6 months of neoadjuvant ET before surgery. Biopsies of primary and matched LNs performed at diagnosis and throughout treatment (3-4 timepoints/patient). Clinical response by serial ultrasound. Primary and LN samples (mean 12 samples/patient) were analysed together with normal DNA. Targeted RNAseq and DNA exome sequencing and whole-genome expression analysis was performed. Somatic mutations and copy number alterations (CNA) were determined, and differential gene expression analysis was performed. Validation of pathways implicated in ETR was by spatial NanoString GeoMx. All patients have long term follow-up. Results: Cohort A: A mean of 6 potential driver mutations identified by DNA sequencing in each primary BC (range 1-16). Most commonly mutated genes were PIK3CA, TP53, ERBB4, MAP3K1 and ERBB3. Multiple aberrations and a highly diverse mutational landscape were observed in all recurrences. In the majority of recurrences significant changes in variant allele frequency (VAF) were identified across several ETR-implicated genes and in over 50% new gains/losses were identified. Most frequently, losses were seen in ERBB3, ARID1A, HRAS and FOXA1 with gains in CDH1, NF1, PIK3CA, ESR1, TBX3 and GATA3 in recurrences vs primaries. Transcriptomic analysis revealed differentially expressed pathways including ER, HER2, GATA3, AKT, RAS and p63 signalling. Integrated analysis revealed several driver mutations with corresponding changes in upstream pathway activity. 33 patients had concurrent local and nodal recurrences and 52% had similar somatic mutation profiles in both with only minor variance in VAF. In 48%, 1 or more new potential driver mutations was identified in axillary nodes compared to recurrent primary cancers with losses in AKT1, CDH1 and TP53 being most common. Multiomics profiling of Cohorts B and C is complete and analysis underway. Discussion: This multiomics study is the largest cohort to-date of matched early and recurrent ER+/HER2- cancers. It sheds new light on the complex somatic and transcriptomic changes in local and nodal recurrent disease. The mechanisms of ETR are diverse and underlying mechanisms and clinically meaningful biomarkers including potentially actionable mutations and targets have been identified. Cohort C will uniquely capture and compare clonal evolution of breast cancer in primary and multiple matched lymph during neoadjuvant ET. Citation Format: Carlos Martinez-Perez, Charlene Kay, Rebecca Swan, Lorna Renshaw, J Michael Dixon, Arran K Turnbull. Multiomics analysis of ER+ breast cancer with matched primaries, lymph node metastases and recurrent cancers on adjuvant endocrine therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-23-11.

НАСЛЕДСТВЕННАЯ ТУБУЛОПАТИЯ: ФОСФАТ-ДИАБЕТ (Два клинических наблюдения)

Introduction. Phosphate diabetes is a representative of a group of diseases known as tubulopathies. It is more often of a hereditary nature. The disease manifests at an early age with symptoms similar to alimentary rickets, which creates problems for diagnosing and prescribing an adequate therapy. In this case, the current situation leads to the development of bone deformities and disability, delayed physical development, and the need for surgical treatment, which reduces the quality of life of the patients for a long time. Aim: To consider two clinical cases of phosphate diabetes with typical symptoms, demonstrate the diagnosing challenges, and analyze the treatment effects. Materials and Methods. Two clinical cases of phosphate diabetes are presented. The first patient: 16 years old, observed from the age of 2, and takes vitamin D and inorganic phosphates from the diagnosis date. The geneticist found the autosomal dominant of the pathology. The girl underwent two surgeries for her leg deformity. The second patient, 10 years old, was diagnosed at the age of 4 years. DNA diagnostics detected a mutation in the COL9A3 gene. They refused the complete DNA exome sequencing. From the diagnosis date, the patient is treated with the active vitamin D metabolite and inorganic phosphates. Results and Discussion. Clinician-observed: Patient 1 had leg deformities, painful legs, and disharmonious physical development caused by her growth retardation. Blood concentrations of calcium and phosphorus are within normal, there is hypocalciuria typical of phosphate diabetes in the urine, while phosphates are within normal. The patient’s kidney function is not impaired. Clinician-observed: Patient 2 is physically retarded, there are varus foot deformities and pes planovalgus feet. Kidney function is not impaired, the level of alkaline phosphatase is increased, the total blood calcium levels are decreased with phosphorus indicating normal values, and the urine phosphaturia and hypocalciuria are within normal ranges. Due to the COL9A3 mutation detected, Stickler syndrome was excluded. Orthopedic surgeon recommended surgical treatment of her leg deformities. Conclusions. The examination showed that the therapy allows keeping phosphate diabetes under control and avoiding the side effects of taking vitamin D.

Not Only RET but NF1 and Chromosomal Instability Are Seen in Young Patients with Sporadic Medullary Thyroid Carcinoma.

Genetic analysis of sporadic medullary thyroid carcinoma (MTC) has revealed somatic variants in RET, RAS, and occasionally other genes. However, around 20% of patients with sporadic MTC lack a known genetic driver. To uncover potential new somatic or germline drivers, we analyze a distinct cohort of patients with sporadic, very early-onset, and aggressive MTC. Germline and somatic DNA exome sequencing was performed in 19 patients, previously tested negative for germline RET variants. Exome sequencing of 19 germline samples confirmed the absence of RET and identified an NF1 pathogenic variant in 1 patient. Somatic sequencing was successful in 15 tumors revealing RET variants in 80%, predominantly p.Met918Thr, which was associated with disease aggressiveness. In RET-negative tumors, pathogenic variants were found in HRAS and NF1. The NF1 germline and somatic variants were observed in a patient without a prior clinical diagnosis of neurofibromatosis type 1, demonstrating that the loss of heterozygosity of NF1 functions as a potential MTC driver. Somatic copy number alterations analysis revealed chromosomal alterations in 53.3% of tumors, predominantly in RET-positive cases, with losses in chromosomes 9 and 22 being the most prevalent. This study reveals that within a cohort of early-onset nonhereditary MTC, RET remains the major driver gene. In RET-negative tumors, NF1 and RAS are drivers of sporadic MTC. In addition, in young patients without a RET germline mutation, a careful clinical evaluation with a consideration of germline NF1 gene analysis is ideal to exclude Neurofibromatosis type 1 (NF1).

Abstract 7366: Loss of STK11 suppresses lipid metabolism to attenuate KRAS-induced immunogenicity in patients with non-small cell lung cancer

Abstract Background: Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death in the United States. Though NSCLC is genetically heterogeneous, as many as 30% of NSCLC patients harbor gain-of-function mutations in the KRAS oncogene. Recent studies have demonstrated that KRAS mutations lead to extensive remodeling of the tumor immune microenvironment. However, though the effect of co-mutations in genes such as TP53 and STK11 are known to have prognostic relevance in KRAS-mutated patients, their mechanistic effect on tumor immunogenicity is largely unknown. Methods: In the present single-center study, we enrolled a total of 189 NSCLC patients. Paraffin specimens from each underwent a standardized analysis including immunohistochemistry for PD-L1 expression, whole exome DNA sequencing, and whole transcriptome RNA sequencing. Results: Patients with activating KRAS mutations demonstrated a significant increase in PD-L1 expression as well as in CD8+ T-cell infiltration, both of which were enhanced by co-occurring TP53 mutation. Interestingly, in patients with loss-of-function STK11 mutations, there was no association between KRAS mutation status and either PD-L1 expression or CD8+ T-cell infiltration. Subsequent genomic analysis demonstrated that KRAS/TP53 co-mutated tumors had a significant decrease in the expression of glycolysis-associated genes, and increase in several genes involved in lipid metabolism, notably Lipoprotein Lipase (LPL), Low Density Lipoprotein Receptor (LDLR), and LDLRAD4. Conversely, in the immune-excluded KRAS/STK11 co-mutated group, we observed diminished lipid metabolism and no change in anaerobic glycolysis. Interestingly, in patients with low expression of LPL, LDLR, or LDLRAD4, gain-of-function KRAS mutations had no effect on tumor immunogenicity. However, in patients with robust expression of these genes, KRAS mutations were strongly associated with increased immunogenicity and associated with improved overall survival. Conclusions: These data suggest that gain-of-function KRAS mutations are associated with an increase in immunogenicity, though this appears to be dependent on a corresponding increase in lipid metabolism. Our data further suggest that the loss of STK11 may function as a metabolic switch to suppress lipid metabolism in favor of glycolysis, thereby negating KRAS-induced immunogenicity. Hence, this concept warrants continued exploration, both as a predictive biomarker and potential target for therapy in patients receiving ICI-based immunotherapy. Citation Format: Daniel Principe, Mary Pasquinelli, Ryan Nguyen, Lawrence Feldman, Alexandre Aissa, Frank D. Weinberg. Loss of STK11 suppresses lipid metabolism to attenuate KRAS-induced immunogenicity in patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7366.

Abstract 3910: The Atlas of Blood Cancer Genomes: A resource for therapeutic and biomarker development

Abstract Developing a novel cancer therapy is an expensive, time-consuming, high-risk endeavor that involves identifying a molecular target as well as target indications. This process could be accelerated by a comprehensive interrogation of driver variants and gene expression profiles across cancer types. The Atlas of Blood Cancer Genomes (ABCG) project was initiated to elucidate the molecular basis of all leukemias and lymphomas, building on advances in genomic technologies, our capabilities for data analysis, and economies of scale. The ABCG project includes collaborators from 25 institutions worldwide who contributed samples from 10,512 patients comprising every type of blood cancer in the World Health Organization classifications. All cases were de-identified and their associated pathology and clinical information entered into a purpose-built web-based system. All cases underwent pathology and clinical data review by experienced hematopathologists and oncologists. Samples were subjected to whole exome DNA and RNA sequencing. We examined three classes of therapeutic targets with selected examples of application: 1. Surface markers: Surface markers are targets of many approved and experimental therapies in blood cancers (CAR-T cells, monoclonal and bispecific antibodies). We found that CD22, which has been evaluated as a target in diffuse large B-cell lymphoma (DLBCL), is also highly expressed in follicular lymphoma, adult ALL, mantle cell lymphoma, and high-grade B cell lymphoma, all areas of clinical need. We can evaluate the expression of virtually any marker or combination of markers across all blood cancers while noting areas of greatest clinical need within and across diseases, providing the basis to reclassify diseases by therapeutic target. 2. Genetic targets: Our work assesses the entire spectrum of genetic alterations including mutations and fusions. We found targetable alterations including BCR-ABL1 fusions, EZH2 Y641, IDH2 R140Q and BRAF V600E mutations in multiple cancers, albeit at low frequency, pointing to potential new indications for existing drugs in subsets of rare diseases. 3. Complex targets (immune or expression signatures or combinations of gene variants): Past work defined DLBCL immune and other signatures associated with response to avadomide, a novel cereblon inhibitor. We found that these signatures are also highly expressed in large subsets of peripheral T-cell lymphomas and acute myeloid leukemia, both areas of major unmet clinical need. Thus, we can interrogate immune and other signatures across the spectrum of cancers to uncover potential biomarkers of response. The ABCG project will enable the comprehensive study of genomic and clinicopathological features of all blood cancers. We anticipate that our data, approaches and results will provide a lasting resource for molecular classification and therapeutic development in all leukemias and lymphomas. Citation Format: Jennifer Shingleton, Raju Pillai, Sarah Ondrejka, Govind Bhagat, Amy Chadburn, Matthew McKinney, Jean Koff, Dina Soliman, Magdalena Czader, Abner Louissaint, Shaoying Li, Choon Kiat Ong, Amir Behdad, Andrew Evens, Yaso Natkunam, Mette Pedersen, Sirpa Leppa, Eric Tse, Jennifer Chapman, Catalina Amador-Ortiz, Yuri Fedoriw, Andrew Evans, Jiong Yan, Mina Xu, Kikkeri Naresh, Clay Parker, David Hsu, Sandeep Dave. The Atlas of Blood Cancer Genomes: A resource for therapeutic and biomarker development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3910.

Clinical and genomic characterization of chemoradiation-resistant HPV-positive oropharyngeal squamous cell carcinoma.

Most patients with HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) have an excellent response to chemoradiation, and trials are now investigating de-escalated treatment. However, up to 25% of patients with HPV-positive OPSCC will experience recurrence, and up to 5% will even progress through primary treatment. Currently, there are no molecular markers to identify patients with poor prognosis who would be harmed by de-escalation. Herein we report the clinical and genomic characteristics of persistent HPV-positive OPSCC after definitive platinum-based chemoradiation therapy. Patients with HPV-positive OPSCC treated with curative intent platinum-based chemoradiation between 2007 and 2017 at two institutions and with a persistent locoregional disease were included. We evaluated clinical characteristics, including smoking status, age, stage, treatment, and overall survival. A subset of five patients had tissue available for targeted exome DNA sequencing and RNA sequencing. Genomic analysis was compared to a previously published cohort of 47 treatment-responsive HPV+ OPSCC tumors after batch correction. Mutational landscape, pathway activation, and OncoGPS tumor states were employed to characterize these tumors. Ten patients met the inclusion criteria. The tumor and nodal stages ranged from T1 to T4 and N1 to N2 by AJCC 8th edition staging. All patients were p16-positive by immunohistochemistry, and eight with available in situ hybridization were confirmed to be HPV-positive. The 1-year overall survival from the time of diagnosis was 57%, and the 2-year overall survival was 17%. TP53 mutations were present in three of five (60%) persistent tumors compared to 2% (one of 47) of treatment-responsive HPV-positive tumors (p = 0.008). Other genes with recurrent mutations in persistent HPV-positive OPSCC tumors were NF1, KMT2D, PIK3C2B, and TFGBR2. Compared to treatment-responsive HPV-positive tumors, persistent tumors demonstrated activation of DNA Repair and p53, EMT, MYC, SRC, and TGF-beta signaling pathways, with post-treatment samples demonstrating significant activation of the PI3K-EMT-Stem pathways compared to pretreatment samples. Chemoradiation-resistant HPV-positive OPSCC occurs infrequently but portends a poor prognosis. These tumors demonstrate higher rates of p53 mutation and activation of MYC, SRC, and TGF-beta pathways. A comparison of tumors before and after treatment demonstrates PI3K-EMT-Stem pathways post-treatment in HPV-positive tumors with persistent disease after platinum-based chemoradiation.

Variants in the ZNF469 gene in families with Brittle cornea syndrome and keratoconus

BackgroundBrittle cornea syndrome 1 (BCS1) is a rare autosomal recessive disorder characterized by corneal and sclera thinning and fragility that is caused by zinc finger protein 469 (ZNF469) gene mutation. Keratoconus is another disease related to corneal thinning. Several reports have linked ZNF469 variants and keratoconus. We recruited a four-generation BCS1 family and two keratoconus families to explore pathogenic ZNF469 variants. MethodsThis study included 11 members from a family with BCS1, 2 families with keratoconus, 368 sporadic keratoconus patients and 325 unrelated healthy controls. Whole exome sequencing of DNA from peripheral blood and cross species conservation analysis was used to investigate and verify ZNF469 variants. ResultsA new homozygous frameshift mutation c. 6727del (p.Asp2243Thr fs*8) in ZNF469 was detected in the BSC1 family. Two ZNF469 heterozygous variants g.88494671G > A (c.793G > A, p.G265S, rs754776767) were detected in keratoconus family 1 and a heterozygous missense variant g.88498262G > A (c.4384G > A, p.D1462 N, rs577890057) was found in keratoconus family 2. Based on the American College of Medical Genetics and Genomics guidelines, rs577890057 and rs754776767 were predicted to be variants of uncertain significance. c. 6727del (p. Asp2243Thr fs*8) in ZNF469 was identified to be pathogenic. ConclusionsWe identified a new homozygous frameshift mutation and two heterozygous missense variations in ZNF469 in the three families. Our findings extend the spectrum of ZNF469 variants associated with keratoconus.

Efficacy of Combined Drug Pre-transplant Conditioning Regimens in Multiple Myeloma Patients with Single Autologous Hematopoietic Stem Cell Transplantation

Aim. To conduct an interim outcome analysis of conditioning regimens with carfilzomib or thiotepa compared to standard melphalan 200 mg/m2 regimen in multiple myeloma (MM) patients with single autologous hematopoietic stem cell transplantation (auto-HSCT).
 Materials & Methods. The retrospective analysis focused on outcomes of 67 single auto-HSCTs performed from 2017 to 2021. Responses as well as progression-free (PFS) and overall survival (OS) rates were compared in MM patients per IWMG criteria in pre- and post-transplant periods. Three conditioning regimens were assigned: melphalan 200 mg/m2 (Mel200), melphalan/carfilzomib combination (Mel/Karfil), and melphalan/thiotepa combination (Mel/Thio). In an additional cohort of 12 MM patients, next-generation sequencing assay was used to detect inherited and somatic mutations associated with proteasome inhibitor efficacy. For this purpose, DNA of peripheral blood lymphocytes and bone marrow plasma cells were examined.
 Results. PFS medians were comparable in MM patients treated with Mel200 (n = 40) and Mel/Karfil (n = 10) conditioning regimens, they were 32 and 23 months, respectively (p = 0.241). In these cohorts, OS median was not reached, and the curves showed no significant differences (p = 0.050). Out of 10 MM patients treated with Mel/Karfil, six received melphalan 140 mg/m2, the remaining 4 patients received 200 mg/m2. Complete response (CR) rate in the Mel200 and Mel/Karfil groups increased two-fold after auto-HSCT: from 35.5 % to 74.2 % and from 25.0 % to 50.0 %, respectively. The worst PFS and OS medians were in the Mel/Thio group, i.e., 12 and 17 months, respectively, and CR rate after auto-HSCT remained unchanged. The best PFS was associated with CR rather than very good partial or partial response after auto-HSCT, they were 48, 21, and 23 months, respectively (p = 0.001). Exome sequencing of DNA of peripheral blood lymphocytes and bone marrow plasma cells revealed polymorphic variants in the genes associated with chemotherapy response.
 Conclusion. The outcomes of Mel/Karfil, the regimen containing the reduced dose of melphalan 140 mg/m2, and the statistical comparability with the Mel200 regimen suggest that this combination can be effective in the treatment of MM patients with impaired renal function, which still needs to be further confirmed. No advantage of the combined conditioning regimen over the standard one can be accounted for by the loss of plasma cell sensitivity to proteasome inhibitors. The obtained data provide ground for modifying the study protocol with a particular focus on evaluating the efficacy and safety of conditioning regimen Mel/Karfil with melphalan 200 mg/m2 depending on biologic phenotype of plasma cell.

Genomic characterization of vulvar squamous cell carcinoma reveals differential gene expression based on clinical outcome

ObjectiveThe greatest challenge in the management of vulvar squamous cell carcinoma (VSCC) is treatment of recurrent disease where options for surgery and radiation have been exhausted, or treatment of disease where distant metastasis is present. Identification of mutations differentially expressed between tumor from patients who died of aggressive disease and tumor from patients with an indolent course could reveal novel prognostic indicators and guide development of therapeutic drugs. MethodsFrom 202 consecutive patients with VSCC, patients who recurred and died of disease (group A) were identified and matched by age, tumor size, depth of invasion and nodal status with those whose disease did not recur (group B). Tumors from 21 patients were subjected to whole exome sequencing of DNA and RNA, immunohistochemistry (IHC) antibodies of PD-L1 and P16, and in-situ hybridization (ISH) for high-risk HPV. ResultsAnalysis of DNA and RNA revealed six genes that were strongly differentially expressed between group A and B: TGM3, ACVR2A, ROS1, NFEL2, CCND1 and BCL6. Clinically relevant DNA mutations were significantly greater in group A versus B: 7 vs 2.3 mutations per patient. The most common genomic alterations were mutations in TP53 and the promoter region of TERT. Other common genomic events include alterations of FAT1, CDKN2A, PIK3CA, CCND1, and LRP1B. All samples were MSI stable and tumor mutational burden (TMB) was similar in groups A and B. Most VSCC specimens (81%) were positive for PD-L1. ConclusionsACVR2A and TGM3 are significantly under-expressed in tumors with poor outcome, suggesting they may play a role in tumor suppression. Clinical outcome of VSCC appears independent of MSI, TMB, or PD-L1 status.

Indicators of Response to the Wee1 Inhibitor Adavosertib in Acute Myeloid Leukemia

Wee1 is a nuclear kinase that regulates cell cycle progression by inhibiting Cdk1, which is essential for G2 to M phase transition. Inhibition of Wee1 leads to high Cdk1 activity, causing cells to bypass proper DNA repair at the G2/M checkpoint, resulting in mitotic catastrophe and cell death, plus increased Cdk2 activity, causing abnormal DNA replication and DNA double-stranded breaks. Inhibitors of Wee1 are being investigated for the treatment of a variety of cancers including AML. In this study, we aimed to identify biomarkers for Wee1 inhibitor (Wee1i) response in AML using ex vivo drug sensitivity data, bulk RNA sequence, exome sequence, and associated clinical data for a large set of primary AML samples tested against the Wee1i adavosertib. Mononuclear cells from bone marrow aspirates (n=136) or peripheral blood samples (n=11) were collected from AML patients using approved protocols and after informed consent. 101 samples were collected at the time of diagnosis and 35 samples were from relapsed/refractory (R/R) patients. For ex vivo drug-sensitivity testing, freshly isolated cells were tested against a library of up to 634 oncology drugs (215 approved drugs) including adavosertib. The drugs were pre-plated in 5 concentrations in a 10,000-fold concentration range and incubated with cells for 72h. Cell viability was assessed using the CellTiter Glo (CTG) assay, and a drug sensitivity score (DSS) calculated based on the area under the dose response curve. Somatic alterations of the drug tested samples were identified via exome sequencing of DNA from the AML samples and matched skin biopsy controls. Gene expression data were obtained from bulk RNA sequence data of the AML samples. Out of 136 samples analyzed, the median DSS for adavosertib was 8.45. We found positive and significant correlations between sensitivity to adavosertib and two factors: 1) malignant cell percentage (R= 0.31, p-value= 0.0097), and 2) final relative viability percentage (R=0.58, p-value= 4.3e-13). Correlation analysis between the DSS of adavosertib and 633 other drugs revealed several strong positive and significant correlations. These included drugs with specific mechanisms of actions including HSP90 inhibitors (n=5), JAK2 inhibitors (n=4), topoisomerase II inhibitors (n=4), CDK4/6 inhibitors (n=3), mitotic inhibitors, vinca alkaloid microtubule depolymerizers (n=3), and PLK1 inhibitors (n=3). Since adavosertib also targets PLK1 in addition to Wee1, the correlation with PLK1 inhibitor activity confirms the similar target profiles. Based on the specific adavosertib DSS thresholds, the samples were separated in two groups. Samples sensitive to adavosertib (n=35) had DSS between 21.3 (max) and 11.9 (3rd quartile). Samples resistant to adavosertib (n=34) had DSS between 0.0 (min) and 5.65 (1st quartile). Differential gene expression analysis between the sensitive vs resistant samples showed that multiple isoforms of the PCDH and HOXB genes were upregulated in adavosertib sensitive samples. The GLI2, PI15, and SKIDA1 genes were also upregulated in the sensitive samples (Figure A). In contrast, genes such DNTT, PF4V1, TRH, CD1B, S100A16, and CD34 were overexpressed in resistant samples (Figure B). Gene set enrichment analysis revealed positive enrichment of pathways related to MYC targets v2 in the sensitive samples. On the other hand, hallmark pathways associated with cell cycle, apoptosis, RAS signaling, and p53 showed significant negative enrichment scores in the sensitive samples. No statistically significant associations were observed between drug response and frequently occuring somatic mutations in our dataset. However, genetic abberations related MLLT4-MLL/MLL-fusions were only observed in sensitive samples. Collectively, our current findings show that there may be specific gene expression signatures associated with Wee1i sensitivity such high expression of PCDH and HOXB. Also, the positive enrichment of the MYC target v2 pathway in adavosertib sensitive samples suggests that highly proliferating tumor cells might be more sensitive to Wee1i. In addition, high CD34 expression in resistant samples suggests that immature stem and progenitor cells may be less susceptible to Wee1i. In summary, targeting of Wee1 in AML - as studied in NCT05682170 azenosertib study - may be effective for a molecularly defined subset of patients.

Clonal Hematopoiesis Is Associated with Cardiovascular Disease Risk and Worse Survival after Autologous Hematopoietic Cell Transplantation for Lymphoma

Introduction: Autologous hematopoietic cell transplantation (HCT) is an effective treatment for patients with relapsed or refractory lymphoma, and use of HCT has contributed to a growing number of survivors. Despite these improvements in outcomes, long-term survivors of lymphoma are at high risk of developing clinically significant cardiovascular disease (CVD) which, to date, has largely been attributed to pre-HCT cardiotoxic therapeutic exposures (e.g. anthracyclines, radiation) and modifiable risk factors (e.g. hypertension, diabetes, dyslipidemia) after HCT. In the general population, clonal hematopoiesis of indeterminate potential (CHIP), which refers to clonal expansion of hematopoietic stem cells with somatic mutations, has been associated with aging-related health conditions including CVD. Accumulating data suggests CHIP is more prevalent in cancer patients compared to age-matched controls, due in part to clonal selection after genotoxic stressors. There is a paucity of information about the association between CHIP and CVD after HCT, including its interaction with modifiable risk factors and subsequent impact on survival after HCT. Methods: This was a retrospective cohort study of 861 consecutive patients who underwent autologous HCT for lymphoma between 2010 and 2016, with available pre-HCT DNA obtained from peripheral blood stem cells. We performed targeted exome sequencing of DNA (92 pre-defined gene panel with 1000x sequencing depth) to determine the presence of CHIP (variant allele frequency ≥2%). CVD outcomes of interest included de novo heart failure, coronary artery disease and stroke after HCT. Five-year cumulative incidence of CVD was calculated taking into consideration competing risk of death. Fine-Gray multivariable regression was used to evaluate the association between CHIP and CVD, adjusting for demographic, clinical and therapeutic factors. The Kaplan-Meier method was used to examine the effect of CHIP on overall survival after HCT. Results: Median age at HCT was 55.7 years (range 18.4-78.1 years); 63.3% were male; race/ethnicity: non-Hispanic White (56.9%), Hispanic (26.1%), Asian (10.8%), Black (5.1%); 78.0% had non-Hodgkin lymphoma; comorbidities at HCT: hypertension (32.1%), dyslipidemia (16.4%), diabetes (10.1%), high (≥3) HCT-comorbidity index (CI) score (46.1%). Nearly all patients (94.3%) had received anthracycline-based chemotherapy prior to HCT, and 63.3% were treated with cumulative dose ≥300mg/m 2; 6% had chest radiotherapy. Overall, 186 patients (21.7% of the cohort) had at least one CHIP variant and 57 (6.6%) had ≥2 variants. DNMT3A, PPM1D, TET2 and TP53 were the most frequently mutated genes. In total, 74 patients developed CVD within five years from HCT. The 5-year cumulative incidence of CVD was significantly higher in patients with CHIP (20.9% vs 9.1%, p<0.001), compared to those without CHIP, and there was a graded relationship between number of CHIP variants and incidence of CVD. In the adjusted (age, cancer diagnosis, HCT-CI, modifiable cardiovascular risk factors) multivariable model, CHIP was significantly and independently associated with a nearly two-fold (HR: 1.8, 95% CI=1.1-3.1; P=0.020) risk of CVD, as well as the individual outcome of heart failure (HR: 2.3, 95%CI=1.3-4.3; P=0.008). Patients who had both CHIP and hypertension had a 3-fold (HR: 3.0, 95%CI=1.4-6.5, p=0.006) risk of CVD (reference: no CHIP, no hypertension). Overall 5-year survival after HCT was significantly worse in patients with CHIP, compared to those without CHIP (47.2% vs 68.2%, p<0.001; adjusted HR: 1.9, 95%CI=1.4-2.6), attributed to the higher burden of non-relapse mortality in patients with CHIP. Conclusions: In this well-characterized and demographically diverse cohort of lymphoma patients undergoing HCT, CHIP was highly prevalent and associated with a significantly higher risk of CVD after HCT, with the highest risk among those with CHIP and hypertension. We confirmed the poor overall survival rate in patients with CHIP, independent of patient and disease-related risk factors. These findings highlight the potential role of CHIP as a novel biomarker to better define CVD risk in patients with lymphoma prior to HCT, setting the stage for better screening and implementation of interventions (e.g., aggressive management of modifiable risk factors) to reduce the risk of CVD and to ultimately improve long-term health outcomes after HCT.

Predictive modelling of response to neoadjuvant therapy in HER2+ breast cancer

HER2-positive (HER2+) breast cancer accounts for 20–25% of all breast cancers. Predictive biomarkers of neoadjuvant therapy response are needed to better identify patients with early stage disease who may benefit from tailored treatments in the adjuvant setting. As part of the TCHL phase-II clinical trial (ICORG10–05/NCT01485926) whole exome DNA sequencing was carried out on normal-tumour pairs collected from 22 patients. Here we report predictive modelling of neoadjuvant therapy response using clinicopathological and genomic features of pre-treatment tumour biopsies identified age, estrogen receptor (ER) status and level of immune cell infiltration may together be important for predicting response. Clonal evolution analysis of longitudinally collected tumour samples show subclonal diversity and dynamics are evident with potential therapy resistant subclones detected. The sources of greater pre-treatment immunogenicity associated with a pathological complete response is largely unexplored in HER2+ tumours. However, here we point to the possibility of APOBEC associated mutagenesis, specifically in the ER-neg/HER2+ subtype as a potential mediator of this immunogenic phenotype.

Molecular predictors and immunomodulatory role of dual checkpoint inhibitor blockade using ipilimumab/nivolumab in patients with extensive stage small cell lung cancer.

8597 Background: Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma with poor prognosis. In extensive stage patients, frontline treatment with chemoimmunotherapy shows modest clinical benefit. However, the biological impact of immunotherapy in SCLC is poorly understood with no clear predictive biomarkers to guide patient selection in this setting. Methods: We collected paired baseline (pre-treatment), on-treatment (week 4), and progression biopsies from patients with relapsed advanced-stage SCLC treated with combination nivolumab (nivo) and ipilimumab (ipi) in a single-arm, phase 2 clinical trial (NCT03670056). Nivo 1 mg/kg and ipi 3 mg/kg were administered every 3 weeks for 4 cycles, followed by nivo maintenance until progressive disease (PD) by RECIST 1.1 or treatment-limiting toxicity. Paired pre/on-treatment samples were available from 16/22 patients, as well as 3 biopsies at progression. The tumor samples were studied using whole exome DNA sequencing (including germline DNA) and RNA-sequencing coupled to Ocean Genomics TxomeAI data analysis pipeline. Results: 6/11 evaluable patients had PD; 5 patients showed clinical activity of treatment (3 with stable disease, 2 with partial response). The frequency of deleterious mutations in TP53 and RB1 was 91% and 64%, respectively. Mutations in HLA-A were more common in baseline samples from patients with PD than those with clinical activity. New TP53 and PLEC mutations were found 4 of 6 patients with PD in week 4 samples vs baseline. The baseline tumor mutational burden was not associated with treatment sensitivity and prominently increased in week 4 biopsies of PD patients. All four molecular SCLC transcriptomic subtypes based on the expression of ASCL1, NEUROD1, and POU2F3 were present in the trial with SCLC-A being the most common (9/16 cases). All patients with clinical activity to ipi/nivo were of SCLC-A subtype. 2/16 of cases showed a different molecular subtype after 4 weeks of treatment: one case with SCLC-N switched to SCLC-A and another case converted from SCLC-A to SCLC-N. Comparison of baseline and on-treatment samples showed upregulation of transcripts associated with T-cell activation and PD-1 signaling. In the 3 biopsies at progression, transcriptomic changes included reduction of neutrophil degranulation, type 1/2 interferon and signatures, as well as down-regulation of β-2 microglobulin, while cell cycle and mitotic prophase pathways were overexpressed. Conclusions: Dual checkpoint blockade using nivo/ipi has a prominent immunomodulatory role in extensive stage SCLC characterized by increased local adaptive immune responses, reduced HLA class-I antigen presentation and change in the molecular subtype in a subset of cases. We identified genomic features associated with treatment sensitivity/resistance. Clinical trial information: NCT03670056 .