Somatic Mutations In Patients Research Articles

Cancer patients with clonal hematopoiesis die from primary malignancy or comorbidities despite higher rates of transformation to myeloid neoplasms.

The occurrence of somatic mutations in patients with no evidence of hematological disorders is called clonal hematopoiesis (CH). CH, whose subtypes include CH of indeterminate potential and clonal cytopenia of undetermined significance, has been associated with both hematologic cancers and systemic comorbidities. However, CH's effect on patients, especially those with concomitant malignancies, is not fully understood. We performed a retrospective evaluation of all patients with CH at a tertiary cancer center. Patient characteristics, mutational data, and outcomes were collected and analyzed. Of 78 individuals included, 59 (76%) had a history of cancer and 60 (77%) had moderate to severe comorbidity burdens. DNMT3A, TET2, TP53, and ASXL1 were the most common mutations. For the entire cohort, the 2-year overall survival rate was 79% (95% CI: 70, 90), while the median survival was not reached. Of 20 observed deaths, most were related to primary malignancies (n = 7, 35%), comorbidities (n = 4, 20%), or myeloid neoplasms (n = 4, 20%). Twelve patients (15%) experienced transformation to a myeloid neoplasm. According to the clonal hematopoiesis risk score, the 3-year transformation rate was 0% in low-risk, 15% in intermediate-risk (p = 0.098), and 28% in high-risk (p = 0.05) patients. By multivariate analysis, transformation was associated with variant allele frequency ≥0.2 and hemoglobin <10 g/dL. In a population including mostly cancer patients, CH was associated with comorbidities and myeloid transformation in patients with higher mutational burdens and anemia. Nevertheless, such patients were less likely to die of their myeloid neoplasm than of primary malignancy or comorbidities.

Dynamic monitoring of UBA1 somatic mutations in patients with relapsing polychondritis

BackgroundCommonly clinically diagnosed with relapsing polychondritis (RP), vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic syndrome (VEXAS) is a recently identified autoinflammatory disease caused by UBA1 somatic mutations. The low frequency and dynamic changes challenge the accurate detection of somatic mutations. The present study monitored these mutations in Chinese patients with RP. We included 44 patients with RP. Sanger sequencing of UBA1 was performed using genomic DNA from peripheral blood. Droplet digital polymerase chain reaction (ddPCR) was performed to screen low-prevalence somatic variants.ResultsMultiple ddPCR detections were performed using available blood samples collected at different follow-up time points. Three male patients were UBA1 somatic mutation carriers. Sanger sequencing detected the somatic UBA1 variant c.122T > C (p.Met41Thr) in two male patients. Initial ddPCR confirmed the variant in the two patients, with allele fractions of 73.75% and 88.46%, respectively, while yielding negative results in other patients. Subsequent ddPCR detected the somatic variant (c.122T > C) with low prevalence (1.02%) in another male patient from blood samples collected at a different time point, and confirmed dynamically fractional abundance in one patient with VEXAS, with allele fractions of 73.75%, 61.28%, 65.01%, and 73.75%. Nine patients assessed by ddPCR at different time points remained negative.ConclusionWe report UBA1 variants in patients with RP in the Chinese population for the first time. Multiple ddPCR detections from samples collected at different time points can enhance sensitivity and should be considered for patients with initial negative ddPCR results.

Outcomes and effect of somatic mutations after erythropoiesis stimulating agents in patients with lower-risk myelodysplastic syndromes.

Erythropoiesis stimulating agents (ESAs) are the first-line therapy in patients with lower-risk myelodysplastic syndromes (LR-MDS). Some predictive factors for ESAs response have been identified. Type and number of somatic mutations have been associated with prognosis and response to therapies in MDS patients. The objective was to evaluate the outcomes after ESAs in patients with LR-MDS and to address the potential predictive value of somatic mutations in ESAs-treated patients. Multi-center retrospective study of a cohort of 722 patients with LR-MDS included in the SPRESAS (Spanish Registry of Erythropoietic Stimulating Agents Study) study. Retrospective analysis of 65 patients with next generation sequencing (NGS) data from diagnosis. ESAs' efficacy and safety were evaluated in patients receiving ESAs and best supportive care (BSC). To assess the potential prognostic value of somatic mutations in erythroid response (ER) rate and outcome, NGS was performed in responders and non-responders. ER rate for ESAs-treated patients was 65%. Serum erythropoietin (EPO) level <200 U/l was the only variable significantly associated with a higher ER rate (odds ratio, 2.45; p = 0.036). Median overall survival (OS) in patients treated with ESAs was 6.7 versus 3.1 years in patients receiving BSC (p < 0.001). From 65 patients with NGS data, 57 (87.7%) have at least one mutation. We observed a trend to a higher frequency of ER among patients with a lower number of mutated genes (40.4% in <3 mutated genes versus 22.2% in ⩾3; p = 0.170). The presence of ⩾3 mutated genes was also significantly associated with worse OS (hazard ratio, 2.8; p = 0.015), even in responders. A higher cumulative incidence of acute myeloid leukemia progression at 5 years was also observed in patients with ⩾3 mutated genes versus <3 (33.3% and 10.7%, respectively; p < 0.001). This large study confirms the beneficial effect of ESAs and the adverse effect of somatic mutations in patients with LR-MDS.

Correlation between Peripheral Blood and Bone Marrow Somatic Mutations Among Patients with Suspected or Established Myelodysplastic Syndromes from the National MDS Study

INTRODUCTION: Myelodysplastic Syndromes (MDS) are caused by progressive clonal dominance of mutated hematopoietic stem cells. While assessment of mutations in peripheral blood (PB) is an established standard for monitoring patients with some diseases such as chronic myeloid leukemia, the sensitivity and precision of PB screening and monitoring for somatic mutations in patients with MDS and related conditions such as clonal cytopenias of undetermined significance (CCUS) is less certain. Multiple published guidelines require bone marrow (BM) evaluations for the above, an invasive procedure not often performed outside of clinical trials. We compared somatic mutations and variant allele frequencies (VAFs) in paired PB and BM samples to assess the utility of PB results as a surrogate for diagnosis and monitoring. METHODS: The National MDS Natural History Study (National MDS Study) is an observational longitudinal cohort study of cytopenic patients suspected of having a diagnosis of MDS. All patients have PB and BM sampled when entering the study, prior to formal diagnosis. For this study, paired PB and BM baseline DNA samples from 36 patients were assessed for somatic mutations. Only subjects with minimum of one variant detected in their BM were included in this study. DNA was extracted from PB using an automated FlexSTAR (AutoGen) and from BM cell pellets using a QIAamp DNA Mini Kit (QIAGEN). Targeted exon sequencing of 96 genes was performed using a NovaSeq 6000 at a mean coverage of &amp;gt;1,200X and a mean breadth (bases covered at ≥100X) of &amp;gt;99.9%. Reads were aligned against a patched version of the build GRCh38 using BWA-MEM. VarScan2 was used to detect single nucleotide variants and short insertions/deletions with a minimum VAF of 2% and 5%, respectively. Resulting variants from 53 genes were manually reviewed to retain likely disease-causing variants. Correlation analysis between PB and BM VAFs was performed using Pearson correlation and linear regression. To confirm paired samples were sourced from the same subject, the Somalier software using a set of highly polymorphic SNPs across different ancestries was utilized to ensure a high level of relatedness. RESULTS: The 36 patients included 10 (28%) with MDS, 2 (6%) with MDS/MPN, 1 (3%) with AML (&amp;lt;30% blasts), and 23 (64%) with CCUS. The median age was 73 years (Table 1). Five of 36 patients had circulating PB blasts. Among the 191 mutations identified, the most common were TET2 (27%), SRSF2 (13%), DNMT3A (9%), SF3B1 (8%), and ASXL1 (8%). Correlation analysis of mutations (n=180) shared between paired PB and BM samples indicated a linear relationship between VAFs detected in PB and BM (Pearson correlation r=0.95, Figure 1), with a slight increase in variance observed with increasing VAFs. The deviation from the perfect (grey line) to the observed (yellow line) linear fit indicated that PB VAFs underestimated VAFs in BM by approximately 23% overall (Figure 1). For example, a BM VAF of 0.20 translated to a mean PB VAF of 0.16 based on the regression fit. The lower sensitivity was confirmed when looking at the number of total missed variants (present in BM, absent in PB): 9 of 101 (9%). Two mutations were detected in PB, but not BM. These mutations and diagnoses were 1) ETNK1 (VAF 0.026) in a patient with MDS-EB-1; and 2) CBL (VAF 0.021) in a patient with MDS with isolated del5q. Next, we assessed the relationship between percent of detected mutations and minimum VAF that was detected using linear regression and found that the higher the minimum VAF, the lower the percent of missed mutations. For example, for a 0.1, 0.2, and 0.3 minimum VAF, 11%, 9%, and 8% of BM mutations were missed, respectively. There was no difference in concordance between MDS and CCUS. SUMMARY &amp; CONCLUSIONS: PB can be used to reliably identify somatic mutations in patients with suspected or established MDS and related conditions. Linear correlation between PB and BM VAFs showed, unsurprisingly, that BM mutations with higher VAFs are more likely to be detected. If PB is positive, this method of variant detection may be used potentially to diagnose and monitor. However, if negative (or if VAF is less than 0.10), bone marrow genomics are still necessary to exclude detectable clonal mutations. For quantitative predictive tools that use VAFs, PB VAFs would need to be corrected to improve predictive results; our estimated linear regression equation could be used to guide this in a larger prospective study.

P11.76.A SPECTRUM OF TP53 SOMATIC MUTATIONS IN A PROSPECTIVE STUDY OF PATIENTS WITH GLIOMA

Abstract BACKGROUND TP53 mutations occur frequently in gliomas, being most common in IDH-wild-type (WT) glioblastomas (GB) and in IDH-mutant (MUT) oligodendrogliomas (OD). Our aim was to describe the mutation spectrum of TP53 somatic mutations in patients (pts) with glioma. MATERIAL AND METHODS This was a prospective multicenter study of patients with glioma diagnosed at four different institutions in Spain. Next-generation sequencing (NGS) of formalin-fixed paraffin-embedded (FFPE) or fresh tumor samples were used for sequencing the TP53 gene in an Illumina Miseq instrument (Illumina, Inc.). Only TP53 pathogenic mutations were considered as valid and are reported here. RESULTS Between February 2017 and March 2020, 61 glioma patients (pts) were enrolled among which 17 different pathogenic mutations in TP53 were detected. Mutant allele frequency (MAF) was &amp;gt; 4% in all cases. TP53 pathogenic mutations occurred at the following loci: L145P, R158H, R175H, H193R, G199V, R202C, R213X, H214R, Y234C, R248Q, I255S, E271Vfs*36, R273C, P278T, G278T, G279E, R280K. Additional clinical characteristics and survival results will be presented at the meeting. CONCLUSION TP53 occur frequently in glioma but widely distributed across the whole exome. The contribution of each specific pathogenic TP53 mutation in gliomas should be further studied.

СОМАТИЧЕСКИЕ МУТАЦИИ ПРИ ЛЕЙКОПЛАКИИ СЛИЗИСТОЙ ОБОЛОЧКИ РОТОВОЙ ПОЛОСТИ

Introduction. Genetic basis for the development of leukoplakia of the oral mucosa is not well understood. Early prediction of oral mucosa cancer development is an important public health problem, which results in the importance of studying the pathogenesis of precancerous diseases. Malignant neoplasms of oral mucosa are mainly the cases of squamous cell carcinoma which commonly develops as the outcome of previous potentially malignant diseases, the leading of which is oral mucosa leukoplakia. Aim. The goal of study is to determine pathogenic somatic mutations in patients with oral mucosa leukoplakia and grade 1 epithelial dysplasia. Material and methods. We have studied 24 samples of altered epithelium of patients with oral mucosa leukoplakia. The QIAamp DNA FFPE Tissue Kit (Qiagen, Germany) was used to isolate deoxyribonucleic acid from the samples. Sequencing was performed with Illumina NextSeq 550 sequencer and TruSight™ Oncology 500 DNA Kit (Illumina, USA). All operations for deoxyribonucleic acid extraction, sampling and sequencing were performed step by step in strict accordance with the instructions supplied with the reagent kits. Bioinformatic analysis was performed using Illumina BaseSpace and Galaxy Project software in accordance with current guidelines. Results and discussion. Pathogenic and probably pathogenic somatic mutations identified during this study in TP53, KRAS, APC, NRAS and BRAF genes, both singly and in combination, are reliably (risk ratios 3000-11000) associated with the development of leukoplakia of the oral mucosa with epithelial dysplasia of 1st degree. The multiplicity of genetic variants associated with epithelial dysplasia, as well as the fact that a number of variants do not occur in all patients simultaneously, suggests that the same histotype of oral mucosa dysplasia may develop under the influence of various mutations. Conclusion. Pathogenic and probably pathogenic variants of TP53, KRAS, APC, NRAS and BRAF genes, both singly and in combinations, are reliably associated with the development of leukoplakia of the oral mucosa with epithelial dysplasia of 1st degree (risk ratios 3000-11000).

Clinical implications of myeloid malignancy‑related somatic mutations in aplastic anemia

Aplastic anemia (AA) is a potentially fatal bone marrow failure syndrome characterized by a paucity of hematopoietic stem cells and progenitor cells with varying degrees of cytopenia and fatty infiltration of the bone marrow space. Recent advances in genomics have uncovered a link between somatic mutations and myeloid cancer in AA patients. At present, the impact of these mutations on AA patients remains uncertain. We retrospectively investigated 279 AA patients and 174 patients with myelodysplastic syndromes (MDS) and performed targeted sequencing of 22 genes on their bone marrow cells using next-generation sequencing (NGS). Associations of somatic mutations with prognostic relevance and response to treatment were analyzed. Of 279 AA patients, 25 (9.0%) patients had somatic mutations, and 20 (7.2%) patients had one mutation. The most frequently mutated genes were ASXL1(3.2% of the patients), DNMT3A (1.8%) and TET2 (1.8%). In the MDS group, somatic mutations were detected in 120 of 174 (69.0%) patients, and 81 patients (46.6%) had more than one mutation. The most frequently mutated genes were U2AF1 (24.7% of the patients), ASXL1 (18.4%) and TP53 (13.2%). Compared with MDS patients, AA patients had a significantly lower frequency of somatic mutations and mostly one mutation. Similarly, the median variant allele frequency was lower in AA patients than in MDS patients (6.9% vs. 28.4%). The overall response of 3 and 6 months in the somatic mutation (SM) group was 37.5% and 66.7%, respectively. Moreover, there was no significant difference compared with the no somatic mutation (N-SM) group. During the 2-years follow-up period, four (20%) deaths occurred in the SM group and 40 (18.1%) in the N-SM group, with no significant difference in overall survival and event-free survival between the two groups. Our data indicated that myeloid tumor-associated somatic mutations in AA patients were detected in only a minority of patients by NGS. AA and MDS patients had different gene mutation patterns. The somatic mutations in patients with AA were characterized by lower mutation frequency, mostly one mutation, and lower median allelic burden of mutations than MDS. Somatic mutations were a common finding in the elderly, and the frequency of mutations increases with age. The platelet count affected the treatment response at 3 months, and ferritin level affected the outcome at 6 months, while somatic mutations were not associated with treatment response or long-term survival. However, our cohort of patients with the mutation was small; this result needs to be further confirmed with large patient sample.

Targeting the Sequences of Circulating Tumor DNA of Cholangiocarcinomas and Its Applications and Limitations in Clinical Practice.

Cholangiocarcinoma is a malignant epithelial tumor arising from bile ducts that is frequently fatal. Diagnosis is difficult due to tumor location in the biliary tract. Earlier diagnosis requires less invasive methods of identifying effective biomarkers for cholangiocarcinoma. The present study investigated the genomic profiles of cell-free DNA (cfDNA) and DNA from corresponding primary cholangiocarcinomas using a targeted sequencing panel. Somatic mutations in primary tumor DNA and circulating tumor DNA (ctDNA) were compared and clinical applications of ctDNA validated in patients with cholangiocarcinoma. A comparison of primary tumor DNA and ctDNA identified somatic mutations in patients with early cholangiocarcinomas that showed clinical feasibility for early screening. The predictive value of single-nucleotide variants (SNVs) of preoperative plasma cfDNA positive for somatic mutations of the primary tumor was 42%. The sensitivity and specificity of postoperative plasma SNVs in detecting clinical recurrence were 44% and 45%, respectively. Targetable fibroblast growth factor receptor 2 (FGFR2) and Kirsten rat sarcoma virus (KRAS) mutations were detected in 5% of ctDNA samples from patients with cholangiocarcinoma. These findings showed that genomic profiling of cfDNA was useful in clinical evaluation, although ctDNA had limited ability to detect mutations in cholangiocarcinoma patients. Serial monitoring of ctDNA is important clinically and in assessing real-time molecular aberrations in cholangiocarcinoma patients.

Analysis of somatic mutations in the &lt;i&gt;JAK2&lt;/i&gt;, &lt;i&gt;CALR&lt;/i&gt;, &lt;i&gt;MPL&lt;/i&gt; and &lt;i&gt;ASXL1&lt;/i&gt; genes and evaluation of their impact on the survival of patients with myelofibrosis

Background. The development of myelofibrosis (MF) is driven by complex molecular genetic events that include driver somatic mutations responsible for the constitutive activation of the JAK/STAT signaling pathway (JAK2, CALR, and MPL), additional mutations affecting epigenetic regulators (TET2, ASXL1, IDH1/2, etc.) and RNA splicing (SRSF2, U2AF1, SF3B1, etc.), as well as genetic aberrations that contribute to genomic instability and disease progression.Aim. To analyze driver (JAK2, CALR, MPL) and prognostic (ASXL1) somatic mutations in patients with MF and evaluate their impact on survival.Materials and methods. The study included 29 patients diagnosed with MF, selected by hematologists from the City Clinical Hospital No. 7 and Regional Clinical Hospital (Krasnoyarsk).Results. 26 (89.6 %) out of 29 examined patients had some driver mutations in JAK2, CALR, MPL genes. The p.V617F mutation in the JAK2 gene was found in 20 (68.9 %) patients. Mutations in the CALR gene were detected in 4 (13.8 %) patients, mutations in the MPL gene were found in 3 patients (10.3 %). In 1 of 26 patients, 2 driver mutations were present simultaneously. 3 (10.3 %) patients were triple negative. Mutations in the ASXL1 gene were detected in 12 (41.4 %) out of 29 examined patients. Conducted targeted NGS (next generation sequencing) for 13 out of 29 patients revealed additional genetic variants that contribute to the understanding of the development mechanism and disease course. When evaluating the overall survival in the groups of patients diagnosed with MF examined by us, depending on the combination of driver (JAK2, CALR, MPL) and prognostic (ASXL1) mutations, no statistically significant differences were found (p = 0.12). This appears to be due to the small sample size. At the same time, assessment of patient survival depending on ASXL1 status showed that in the presence of mutations in the ASXL1 gene, the median survival was 45 months (range 7–120 months), while in the absence of mutations it was 48 months (range 21–359 months) (p = 0.03).Conclusion. The results obtained allow us to assume that the presence of mutations in the ASXL1 gene is an unfavorable factor in the course of the disease.

Cardiovascular and metabolic characters of KCNJ5 somatic mutations in primary aldosteronism.

Primary aldosteronism (PA) is the leading cause of curable endocrine hypertension, which is associated with a higher risk of cardiovascular and metabolic insults compared to essential hypertension. Aldosterone-producing adenoma (APA) is a major cause of PA, which can be treated with adrenalectomy. Somatic mutations are the main pathogenesis of aldosterone overproduction in APA, of which KCNJ5 somatic mutations are most common, especially in Asian countries. This article aimed to review the literature on the impacts of KCNJ5 somatic mutations on systemic organ damage. PubMed literature research using keywords combination, including "aldosterone-producing adenoma," "somatic mutations," "KCNJ5," "organ damage," "cardiovascular," "diastolic function," "metabolic syndrome," "autonomous cortisol secretion," etc. APA patients with KCNJ5 somatic mutations are generally younger, female, have higher aldosterone levels, lower potassium levels, larger tumor size, and higher hypertension cure rate after adrenalectomy. This review focuses on the cardiovascular and metabolic aspects of KCNJ5 somatic mutations in APA patients, including left ventricular remodeling and diastolic function, abdominal aortic thickness and calcification, arterial stiffness, metabolic syndrome, abdominal adipose tissue, and correlation with autonomous cortisol secretion. Furthermore, we discuss modalities to differentiate the types of mutations before surgery. KCNJ5 somatic mutations in patients with APA had higher left ventricular mass (LVM), more impaired diastolic function, thicker aortic wall, lower incidence of metabolic syndrome, and possibly a lower incidence of concurrent autonomous cortisol secretion, but better improvement in LVM, diastolic function, arterial stiffness, and aortic wall thickness after adrenalectomy compared to patients without KCNJ5 mutations.

Germline Cancer Gene Expression Quantitative Trait Loci Are Associated with Local and Global Tumor Mutations.

Analysis of associations between the germline genetic background and somatic mutations in patients with cancer suggests that germline variants can influence local and global tumor mutations by altering expression of cancer-related genes. See related commentary by Kar, p. 1165.

Metastatic Breast Cancer to the Spine: Incidence of Somatic Gene Alterations and Association of Targeted Therapies With Overall Survival.

The increase in use of targeted systemic therapies in cancer treatments has catalyzed the importance of identifying patient- and tumor-specific somatic mutations, especially regarding metastatic disease. Mutations found to be most prevalent in patients with metastatic breast cancer include TP53, PI3K, and CDH1. To determine the incidence of somatic mutations in patients with metastatic breast cancer to the spine (MBCS). To determine if a difference exists in overall survival (OS), progression-free survival, and progression of motor symptoms between patients who do or do not undergo targeted systemic therapy after treatment for MBCS. This is a retrospective study of patients with MBCS. Review of gene sequencing reports was conducted to calculate the prevalence of various somatic gene mutations within this population. Those patients who then underwent treatment (surgery/radiation) for their diagnosis of MBCS between 2010 and 2020 were subcategorized. The use of targeted systemic therapy in the post-treatment period was identified, and post-treatment OS, progression-free survival, and progression of motor deficits were calculated for this subpopulation. A total of 131 patients were included in the final analysis with 56% of patients found to have a PI3K mutation. Patients who received targeted systemic therapies were found to have a significantly longer OS compared with those who did not receive targeted systemic therapies. The results of this study demonstrate that there is an increased prevalence of PI3K mutations in patients with MBCS and there are a significant survival benefit and delay in progression of motor symptoms associated with using targeted systemic therapies for adjuvant treatment.

Long-Term Evolution of Somatic Mutations in Patients with Del(5q) MDS Early Treated with Lenalidomide in the Sintra-Rev Clinical Trial: Safe and Effecitive Approach?

INTRODUCTION Lenalidomide (LEN) is the election treatment in del(5q) MDS, approved only in case of RBC transfusion dependency (TD). Only scarce retrospective data exploring LEN in non-TD setting are available, suggesting a benefit. SintraRev is the first randomized clinical trial evaluating LEN in del(5q) MDS with anemia but without TD. While efficacy has been confirmed in this trial, safety regarding clonal evolution and disease progression has not been addressed in this early treatment context. METHODOLOGY SintraRev is a phase III multicenter clinical trial in low-risk del(5q) MDS patients with anemia without TD. Patients were randomized (2:1) in a double-blind design to LEN (5mg/day continuously) vs placebo (PCB) for 2 years of treatment and 2 years of follow-up (FU). In addition to clinical results, we aimed to study the role of molecular profiling in this early therapeutic approach (LEN use prior to TD) in both arms during FU (baseline, week 12 and the last available FU). Next-generation sequencing (NGS) was performed in available samples. Sequential samples were collected before treatment initiation and then every 6 months until last FU. A capture-based NGS panel targeting 65 myeloid genes was used. Libraries were prepared following manufacturer's instructions (Twist BioScience) and run on Illumina sequencers. Mutations were considered at coverage of 2000x and >5% variant allele frequency (VAF). RESULTS Sixty-one patients were included in SintraRev with a median FU of 60.6 (32.3-73.9) months. A total of 47 patients (29 LEN, 18 PCB) had NGS data. At baseline, 32%, 36% and 32% of patients had 0, 1 and ≥2 mutations, respectively. More frequently mutated genes were SF3B1 (25.5% of patients) and TP53 (21%). No differences were observed regarding SF3B1 (p=0.74), TP53 (p=0.48) and DAT (DNMT3A, ASXL1 and TET2, p=1.0) mutations between groups. Furthermore, no differences in neither median number of mutations per patient (1: 0-4) nor VAF were found between LEN and PCB initially (p>0.05). At week 12, median VAF of mutations was significantly lower in the LEN group as compared to baseline (1.84% vs 9%, respectively p<0.01, n=21), but remaining stable in the PCB arm (18% w12 vs 17% baseline, p=0.594). Interestingly, in the long-term FU (median 22.4 months - 3.03 to 68.77) an increase in median VAF (from 17% to 29%, p<0.001, n=13) was observed in PCB arm (Fig 1). Clonal evolution among LEN & PCB patients during treatment was different, with a reduction in predominating clones in LEN arm, while remaining stable in the PCB group (Fig 2). In the long-term FU, both PCB & LEN showed acquisition of additional mutations (20% PCB & 22.7% LEN, p=1.0). Nevertheless, all these new mutations in the LEN group were acquired several months after loss of response to treatment or LEN discontinuation. Interestingly, dynamics of mutations under LEN treatment did not affect DAT mutations, which remained stable when cytogenetic response (CyR) was achieved. In this way, 87,5% of DAT mutations showed an independent behavior from the clone with 5q deletion. However, most SF3B1 (62,5%) and TP53 mutations (100%) were affected by LEN treatment in parallel with the disappearance of the del(5q) clone at the time of CyR. In this regard, responses were not affected by the persistence of DAT mutations (>80% of erythroid response, ER, and CyR) and interestingly, SF3B1mut patients achieved 100% of ER and CyR. In contrast, only 20% of TP53mut patients achieved ER and 60% CyR. AML evolution occurred in 13.8% and 22.2% patients in LEN & PCB arms, respectively (p=0.43). In patients transforming to AML, 50% had TP53mut in LEN while no TP53 mutations were found in PCB AML progression. No differences were found regarding median time to AML between the two groups (25.87 months, p=0.2). CONCLUSIONS MDS patients showing 5q deletion and without TD early treated with LEN did not showed more clonal evolution than the same set of patients in PCB arm. In fact, the acquisition of additional mutations in LEN patients was observed after loss of response or LEN discontinuation. Interestingly, molecular responses were confirmed in LEN patients by reduction of mutation's median VAF at week 12. Dynamic evolution of DAT alterations was not affected by LEN treatment, suggesting a role as CHIP-associated mutations. In contrast, most SF3B1 and TP53 mutations were modified in parallel with the del(5q) clone at the time of CyR. The maintenance of CHIP-related mutations did not affect either ER or CyR. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

LINC02126 is a potential diagnostic, prognostic and immunotherapeutic target for lung adenocarcinoma

BackgroundAdenocarcinoma has long been an independent histological class of lung cancer, which leads to high morbidity and mortality. We aimed to investigate the contribution of LINC02126 in lung adenocarcinoma.MethodsRNA sequencing data and clinical information were downloaded. Diagnostic efficiency and survival analysis of LINC02126 were performed, followed by functional analysis of genes co-expressed with LINC02126 and differentially expressed genes (DEGs) in different LINC02126 expression groups. Tumor immune microenvironment (TIME) cell infiltration and correlation analysis of tumor mutation burden were performed in different LINC02126 expression groups.ResultsIn lung adenocarcinoma, the expression level of LINC02126 was significantly decreased. Significant expression differences of LINC02126 were found in some clinical variables, including T staging, M staging, sex, stage, and EGFR mutation. LINC02126 had potential diagnostic and prognostic value for patients. In the low LINC02126 expression group, the infiltration degree of most immune cells was significantly lower than that in the high LINC02126 expression group. Tumor mutation burden level and frequency of somatic mutation in patients with low LINC02126 expression group were significantly higher than in patients with high LINC02126 expression group.ConclusionsLINC02126 could be considered as a diagnostic, prognostic and immunotherapeutic target for lung adenocarcinoma.

Next generation sequencing targeted detection of somatic mutations in patients with mucinous adenocarcinoma of the appendix

The aim of this study was to investigate the mutations in mucinous adenocarcinoma of the appendix (MAA). SNV was detected in 15 patients with MAA, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and reactome pathway analyses were performed. Tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), microsatellite instability (MSI) was analysis. Finally, the human leukocyte antigen (HLA) typing of the samples was detected. The results showed that TP53 (27 %) and KRAS (20 %) were the highest mutation frequency in the sample, mainly occur in p53 pathway and RTK-RAS pathway. GO analysis reveals mutated genes are closely related to the regulation of GTPase activity, regulation of small GTPase mediated signal transduction and other BP, related to the CC and MF. Analysis of KEGG pathways indicated that the top canonical pathways associated with SNV was Wnt signaling pathway. Reactome pathway analysis further revealed that the mutant genes were closely related to muscle contraction. Only one patient had moderate TMB level and one patient with high MSI. In conclusion, the most common mutated genes and the signaling pathways closely related to MAA development were detected in this study, which will contribute to the development of immunotherapy for patients with MAA.

Periocular Pigmented Basal Cell Carcinomas: Clinicopathologic Features and Mutational Profile.

Pigmented basal cell carcinomas (PBCC) is an uncommon variant of basal cell carcinoma of the periocular region with limited information in the literature. We highlight the clinicopathological profile and somatic mutations in periocular PBCC. The clinicopathological features and somatic mutations in patients with periocular PBCC were examined and compared with periocular non-PBCC reported in the literature. Next-generation sequencing panel analysis for the excised tumors identified somatic mutations. In a total of 31 patients, PBCC was common in females (54%; p = 0.03); as a unilateral lower eyelid (n = 22; 71%), solitary mass (n = 30; 98%). Pathologic subtypes were variable. Most were nodular or mixed variants (n = 23; 74%). During the follow up (2.5-4.5 years), 1 patient (3.5%) had a recurrence. The clinical and pathologic features of PBCC were similar to those reported in nonperiocular locations. Somatic mutations detected in 25/31 tumors. Variants in 50/161 genes in the panel were noted. PTCH1 (14/31), TERT (12/31), and SMO (7/31) variants were common. Fifteen patients had novel drivers, including POLE, FANCD2, and CREBBP. SMO mutations were significantly more common in females (7/7), lower eyelid (5/7), and TERT mutations were more common in nodular subtype (10/12). In this large cohort of a relatively uncommon variant of BCC, the clinicopathological features and tumor behavior of PBCC was similar to periocular non-PBCC. The somatic mutation spectrum of PBCC resembles that reported in nonperiocular cutaneous BCC with novel drivers identified. We identified several potential actionable mutations that could be targeted with molecular therapy.

Frequency of JAK2V617F and CALR somatic mutations in Egyptian patients with thrombocytosis: relation with clinical and hematological phenotype

Background Thrombocytosis has a multitude of potential etiologies: spurious, reactive, and clonal. Clonal thrombocytosis carries a greater risk of thrombosis than reactive causes. Therefore, careful distinction between the causes of thrombocytosis is important and challenging as it carries implications for evaluation, prognosis, and treatment strategies. Aim of the work To determine the frequency of JAK2V617F and calreticulin (CALR) somatic mutations in patients with thrombocytsis and their relation with clinical and hematological phenotype. Patients and methods A total of 50 BCR-ABL-negative patients with persistent thrombocytosis were tested for both JAK2V617F mutation by real-time polymerase-chain reaction (RT-PCR) and CALR exon-9 mutation by high-resolution melting PCR. Results JAK2V615F mutation was detected in 17 (34%), whereas CALR exon-9 mutation was detected in 10 (20%) out of the 50 studied patients with thrombocytosis. One patient with essential thrombocythemia was heterozygous for both mutations. The incidence of JAK2V615F mutation was significantly higher in males (P=0.007), with higher mean age (P=0.001), higher incidence of thrombosis (0.034), and leukocytosis (0.035) compared with CALR and dual-negative mutations. Meanwhile, anemia (P=0.001), platelets (P=0.009), and lactate dehydrogenase (P=0.009) were significantly higher in CALR-mutated patients. Conclusion Both JAK2 and CALR somatic mutations were detected in 52% of patients with thrombocytosis. CALR-mutated cases show clinical and hematological phenotype different from JAKV617F-positive ones and might be considered as a distinct disease entity with more indolent course.

Abstract IA-07: Genetic ancestry and lung cancer somatic mutations in patients of Latin American descent: Etiology and treatment implications

Abstract Inherited lung cancer risk, particularly in nonsmokers, is poorly understood. In particular, the frequency of somatic EGFR and KRAS mutations in lung cancer varies by ethnicity. Somatic EGFR mutation rates are higher in lung cancers from patients with East Asian ancestry and lower in patients with European or African ancestry. Somatic KRAS mutation rates show the opposite pattern. In patients from Latin America, somatic lung cancer EGFR mutation rates vary by country, highest in countries with more Native American ancestry. To ask whether the somatic genome in lung cancer is affected by ethnicity related germline risk, we studied genomes from 1,153 lung cancers from Mexico and Colombia. This study revealed striking associations between ancestry and somatic lung cancer alterations, including tumor mutational burden, and specific driver mutations in EGFR, KRAS, and STK11. A local ancestry score was more strongly correlated with EGFR mutation frequency compared with global ancestry correlation, suggesting that germline genetics (rather than environmental exposure) underlie these disparities. Our study suggests that the variation in EGFR and KRAS mutation frequency in lung cancer is associated with genetic ancestry in patients from Latin America, and suggests further studies to identify germline alleles that underpin this association. If we find a germline locus, this might help in improving lung cancer prevention and screening for populations of Latin American origin and others. Furthermore, multiple studies now highlight the special importance of EGFR mutation screening and EGFR-directed targeted therapy for lung cancer patients in Latin America and with origins in Latin America. Citation Format: Jian Carrot-Zhang, Giovanny Soca-Chafre, Nick Patterson, Aaron Thorner, Anwesha Nag, Jacqueline Watson, Giulio Genovese, July Rodriguez, Maya Gelbard, Luis Corrales-Rodriguez, Yoichiro Mitsuishi, Gavin Ha, Joshua Campbell, Geoffrey Oxnard, Oscar Arrieta, Andres Cardona, Alexander Gusev, Matthew Meyerson. Genetic ancestry and lung cancer somatic mutations in patients of Latin American descent: Etiology and treatment implications [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA-07.

Mutation of Hashimoto's Thyroiditis and Papillary Thyroid Carcinoma Related Genes and the Screening of Candidate Genes.

Clinical studies have shown similarities in the genetic background and biological functional characteristics between Hashimoto’s thyroiditis (HT) and papillary thyroid carcinoma (PTC), and that HT may increase risks of PTC. Here, we set to determine the gene expression specificity of HT and PTC by screening related genes or co-expressed genes and exploring their genetic correlation. Referencing the Oncomine database, HT-related genes were discovered to be expressed in many different types of thyroid cancer, such as TSHR that is highly expressed in thyroid cancer. An in-depth genetic analysis and verification of 35 cancer and paracancerous tissue pairs from patients with thyroid cancer, and 35 tissues and blood cells pairs from patients with Hashimoto’s thyroiditis was conducted. Gene chip technology research showed that TSHR, BACH2, FOXE1, RNASET2, CTLA4, PTPN22, IL2RA and other HT-related genes were all expressed in PTC, in which TSHR was significantly over-expressed in PTC patients sensitive to radioactive iodine therapy, while BACH2 was significantly under-expressed in these patients. The biologically significant candidate Tag SNP highlighted from HT-related genes was screened by the high-throughput detection method. Somatic mutations in patients with HT and PTC were detected by target region capture technique, and 75 mutations were found in patients with HT and PTC. The upstream regulatory factors of the different genes shared by HT and PTC were analyzed based on Ingenuity Pathway Analysis (IPA), and it was found that HIF-1α and PD-L1 could be used as important upstream regulatory signal molecules. These results provide a basis for screening key diagnostic genes of PTC by highlighting the relationship between some HT-related genes and their polymorphisms in the pathogenesis of PTC.

CD8+ cell somatic mutations in multiple sclerosis patients and controls-Enrichment of mutations in STAT3 and other genes implicated in hematological malignancies.

Somatic mutations have a central role in cancer but their role in other diseases such as common autoimmune disorders is not clear. Previously we and others have demonstrated that especially CD8+ T cells in blood can harbor persistent somatic mutations in some patients with multiple sclerosis (MS) and rheumatoid arthritis. Here we concentrated on CD8+ cells in more detail and tested (i) how commonly somatic mutations are detectable, (ii) does the overall mutation load differ between MS patients and controls, and (iii) do the somatic mutations accumulate non-randomly in certain genes? We separated peripheral blood CD8+ cells from newly diagnosed relapsing MS patients (n = 21) as well as matched controls (n = 21) and performed next-generation sequencing of the CD8+ cells’ DNA, limiting our search to a custom panel of 2524 immunity and cancer related genes, which enabled us to obtain a median sequencing depth of over 2000x. We discovered nonsynonymous somatic mutations in all MS patients’ and controls’ CD8+ cell DNA samples, with no significant difference in number between the groups (p = 0.60), at a median allelic fraction of 0.5% (range 0.2–8.6%). The mutations showed statistically significant clustering especially to the STAT3 gene, and also enrichment to the SMARCA2, DNMT3A, SOCS1 and PPP3CA genes. Known activating STAT3 mutations were found both in MS patients and controls and overall 1/5 of the mutations were previously described cancer mutations. The detected clustering suggests a selection advantage of the mutated CD8+ clones and calls for further research on possible phenotypic effects.