Impact Of Genetic Heterogeneity Research Articles

Hematological relevance of JAK2 V617F and calreticulin mutations in Tunisian patients with essential thrombocythemia

BackgroundThe genetic investigation of essential thrombocythemia(ET) has highlighted the presence of driver mutations in ET. Janus kinase JAK2V617F and calreticulin(CALR) mutations are the most frequent driver mutations and have significantly improved the molecular diagnosis of ET. The impact of genetic heterogeneity on clinical features has not been fully elucidated.This is the first study which aimed to determine the frequency of JAK2V617F and CALR exon9 mutations in Tunisian ET patients and to establish the correlation between hematological characteristics and mutational status.MethodsThis study included Tunisian patients suspected with ET and was conducted between September 2017 and March 2021. Genomic DNA of patients was isolated from peripheral blood samples. JAK2V617F was detected by AS‐PCR and CALR mutations were detected by PCR/direct sequencing. Clinical and hematological characteristics were also analyzed.ResultsTwo hundred and fifty ET patients were enrolled in this study. JAK2V617F mutation was found in 166/250 (66.4%) of patients, whereas CALR mutations were detected in 27/84 (32.1%) patients without JAK2V617F. Compared with JAK2V617F‐positive patients, those with CALR mutations showed lower hemoglobin level and lower leucocytes count (p = 0.007 and p = 0.004,respectively). CALR type 2 was the most frequent mutation of CALR detected in 55.55% of CALR mutated. Six of seven patients with thrombotic events harbored JAK2V617F mutation.ConclusionThe prevalence of driver mutations JAK2V617F or CALR mutations was 77.2% in Tunisian ET patients. Moreover, patients with JAK2 V617F mutation had a higher risk of thrombosis. The mutational status is necessary to improve the diagnosis and contribute to the therapeutic decisions.

Individualized Medicine in Africa: Bringing the Practice Into the Realms of Population Heterogeneity.

The declared aim of “personalized”, “stratified” or “precision” approaches is to place individual variation, as ascertained through genomic and various other biomarkers, at the heart of Scientific Medicine using it to predict risk of disease or response to therapy and to tailor interventions and target therapies so as to maximize benefit and minimize risk for individual patients and efficiency for the health care system overall. It is often contrasted to current practices for which the scientific base is rooted in concepts of a “universal biology” and a “typical” or “average patient” and in which variation is ignored. Yet both approaches equally overlook the hierarchical nature of human variation and the critical importance of differences between populations. Impact of genetic heterogeneity has to be seen within that context to be meaningful and subsequently useful. In Africa such complexity is compounded by the high effective size of its populations, their diverse histories and the diversity of the environmental terrains they occupy, rendering analysis of gene environment interactions including the establishment of phenotype genotype correlations even more cumbersome. Henceforth “Individualized” methods and approaches can only magnify the shortcomings of universal approaches if adopted without due regard to these complexities. In the current perspective we review examples of potential hurdles that may confront biomedical scientists and analysts in genomic medicine in clinical and public health genomics in Africa citing specific examples from the current SARS-COV2 pandemic and the challenges of establishing reference biobanks and pharmacogenomics reference values.

Modeling the impact of genetic heterogeneity on immunotherapy

A panel of genetically engineered mouse models recapitulates genotype-driven responses to immunotherapy and uncovers a driver of immunotherapy resistance in ovarian cancer.

PI3Kδ Inhibition Enhances Sensitivity of Primary High-Risk Childhood B-Cell Acute Lymphoblastic Leukemia Cells to Glucocorticoid Chemotherapy

Introduction: Despite excellent 5-year survival for most patients with B-cell acute lymphoblastic leukemia (B-ALL), those with high-risk (HR) B-ALL continue to have inferior outcomes. The prognosis is even worse for patients who respond poorly to chemotherapy, and improvements to current therapy approaches are needed. Glucocorticoids (GCs) are a key component of chemotherapy regimens. Rapid response to GC monotherapy is a well-documented predictor of favorable outcomes, while slow response to GCs correlates with poor outcomes. We hypothesized that enhancing specific GC toxicity to B-ALL cells can improve clinical outcomes for high-risk patients without increasing systemic toxicity. PI3Kδ is a promising target for this purpose. PI3Kδ is a critical component of the B-cell receptor cell-survival pathway; it restrains GC signaling, while GCs repress its expression. PI3Kδ expression is restricted to lymphoid cells, making it an appealing precision target to enhance GC toxicity in lymphoid cells while minimizing risk of increased systemic GC-associated toxicity. We previously demonstrated synergy between dexamethasone (dex) and the FDA-approved isoform-selective PI3Kδ inhibitor idelalisib (idela) in B-ALL cell lines, patient specimens, and patient-derived xenograft models (Kruth et al Blood 2017). In clinical practice, both dex and prednisone (pred) are essential components of childhood ALL chemotherapy. In this study, we sought to elucidate the extent to which idela in combination with dex or pred could induce synergistic killing of HR B-ALL specimens with various genetic backgrounds. Methods: Peripheral blood or bone marrow from patients ages 1-31 years with newly-diagnosed NCI HR or standard-risk (SR) B-ALL at the University of Iowa Stead Family Children's Hospital was obtained after informed consent on an Institutional Review Board-approved research study. Mononuclear cells were isolated from the specimens via Ficoll gradients and cultured in vitro in 384-well plates. Immediately after isolation, cells were treated with serial dilutions of the GCs dex or pred and idela in RPMI1640+10% FBS medium. Cell viability was measured with PrestoBlue (Invitrogen) after 72 hours of treatment. Survival curves were plotted to determine the LD50 of each drug using GraphPad. Dose effects around the LD50 for each drug were analyzed using Compusyn to determine if the drug combination was synergistic (combination index, CI <1), additive (CI=1), or antagonistic (CI >1). Results: As of August 1, 2019, 5 HR B-ALL patient specimens of various genetic alterations have been tested. Two patients were high-risk at diagnosis due to steroid pre-treatment (MAP011) or by NCI risk criteria (age >10 years and/or WBC count >50K/mm3; MAP014). Three patients with initially SR B-ALL were upstaged due to minimal residual disease (MRD) >1% at day 8 in peripheral blood (MAP012) or marrow MRD ≥0.01% at end of induction (MAP009, MAP010). In our in vitro studies, only one sample (MAP014) showed reduced viability with GC alone, while 4 specimens (all except MAP012) responded to idela alone. Most specimens showed a synergistic response to dex or pred in combination with idela with greater reduction in cell viability compared to GC monotherapies. Surprisingly, one specimen (MAP010) had an antagonistic response with pred and idela combination. This near-haploid B-ALL specimen had reduced viability with idela monotherapy, but an antagonistic response with single-agent pred, raising the question of whether GC/idela synergy is influenced by genetic background. Conclusions: In pilot studies, idela sensitized HR B-ALL cells to GC chemotherapy and is a promising strategy for further evaluation in a larger cohort of specimens. Our results highlight the potential impact of genetic heterogeneity within childhood B-ALL upon differential therapeutic responses to standard steroid chemotherapy and demonstrate a potential precision medicine approach to augment GC sensitivity via combination with selective PI3Kδ inhibition. Disclosures Tasian: Gilead Sciences: Research Funding; Aleta Biotherapeutics: Membership on an entity's Board of Directors or advisory committees; Incyte Corportation: Research Funding.

Considering Genetic Heterogeneity in the Association Analysis Finds Genes Associated With Nicotine Dependence.

While substantial progress has been made in finding genetic variants associated with nicotine dependence (ND), a large proportion of the genetic variants remain undiscovered. The current research focuses have shifted toward uncovering rare variants, gene-gene/gene-environment interactions, and structural variations predisposing to ND, the impact of genetic heterogeneity in ND has been nevertheless paid less attention. The study of genetic heterogeneity in ND not only could enhance the power of detecting genetic variants with heterogeneous effects in the population but also improve our understanding of genetic etiology of ND. As an initial step to understand genetic heterogeneity in ND, we applied a newly developed heterogeneity weighted U (HWU) method to 26 ND-related genes, investigating heterogeneous effects of these 26 genes in ND. We found no strong evidence of genetic heterogeneity in genes such as CHRNA5. However, results from our analysis suggest heterogeneous effects of CHRNA6 and CHRNB3 on nicotine dependence in males and females. Following the gene-based analysis, we further conduct a joint association analysis of two gene clusters, CHRNA5-CHRNA3-CHRNB4 and CHRNB3-CHRNA6. While both CHRNA5-CHRNA3-CHRNB4 and CHRNB3-CHRNA6 clusters are significantly associated with ND, there is a much stronger association of CHRNB3-CHRNA6 with ND when considering heterogeneous effects in gender (p-value = 2.11E-07).

Genetic Characteristics of Polycythemia Vera and Essential Thrombocythemia in Korean Patients.

Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of genetic heterogeneity on its molecular pathogenesis has not been fully elucidated. Thus, in this study, we aim to characterize the genetic complexity in Korean patients with polycythemia vera (PV) and essential thrombocythemia (ET). We conducted association studies using 84 single-nucleotide polymorphisms (SNPs) in 229 patients (96 with PV and 133 with ET) and 170 controls. Further, whole-genome sequencing was performed in six patients (two with JAK2 V617F and four with wild-type JAK2), and putative somatic mutations were validated in a further 69 ET patients. Clinical and laboratory characteristics were also analyzed. Several germline SNPs and the 46 haplotype were significantly associated with PV and ET. Three somatic mutations in MPDZ, IQCH, and CALR genes were selected and validated. The frequency of the CALR mutation was 58.0% (40/69) in ET patients, who did not carry JAK2/MPL mutations. Moreover, compared with JAK2 V617F-positive patients, those with CALR mutations showed lower hemoglobin and hematocrit levels (P = 0.004 and P = 0.002, respectively), higher platelet counts (P =0.008), and a lower frequency of cytoreductive therapy (P = 0.014). This study was the first comprehensive investigation of the genetic characteristics of Korean patients with PV and ET. We found that somatic mutations and the 46 haplotype contribute to PV and ET pathogenesis in Korean patients.

Pan-proteomics, a concept for unifying quantitative proteome measurements when comparing closely-related bacterial strains

ABSTRACTThe comparison of proteomes between genetically heterogeneous bacterial strains may offer valuable insights into physiological diversity and function, particularly where such variation aids in the survival and virulence of clinically-relevant strains. However, reports of such comparisons frequently fail to account for underlying genetic variance. As a consequence, the current knowledge regarding bacterial physiological diversity at the protein level may be incomplete or inaccurate. To address this, greater consideration must be given to the impact of genetic heterogeneity on proteome comparisons. This may be possible through the use of pan-proteomics, an analytical concept that permits the ability to qualitatively and quantitatively compare the proteomes of genetically heterogeneous organisms. Limited examples of this emerging technology highlight currently unmet analytical challenges. In this article we define pan-proteomics, where its value lies in microbiology, and discuss the technical considerations critical to its successful execution and potential future application.

Updated UK Recommendations for HER2 assessment in breast cancer

Human epidermal growth factor receptor 2 (HER2) overexpression is present in approximately 15% of early invasive breast cancers, and is an important predictive and prognostic marker. The substantial benefits achieved...

Functional and Genetic Heterogeneity of Distinct Leukemic Stem Cell Populations in CD34- Human Acute Myeloid Leukemia

Lack of progress in curing AML is likely, in part, to be due to the genetic and functional heterogeneity of AML. ~13 Tier 1 mutations occur per patient sample arrayed in 2-5 clones (CGARN, N Engl J Med, 2013). Not all AML cell populations may be equally chemosensitive; for example, leukemia-propagating leukemic stem cells (LSC) are more chemoresistant. (Ishikawa et al., Nat Biotechnol, 2007). Additionally, the impact of genetic heterogeneity on LSC function is unclear.In ~ 70% of primary human AML with >2% CD34+ cells, LSCs exist within both CD34+CD38- and CD34+CD38+ compartments (Taussig et al., Blood, 2008), and have progenitor-like transcriptional programmes (Goardon et al., Cancer Cell, 2011). ~30% of AML with <2% CD34+ cells (CD34- AML) are genetically distinct, enriched for mutations in NPM1 and co-associated mutations (FLT3, IDH1/2, TET2, and DNMT3A). Here, LSC activity has been detected in both CD34+ and CD34- compartments (Taussig et al., Blood, 2010, Martelli et al., Blood, 2010, Sarry et al., J Clin Invest, 2011). Questions remain about CD34- AML LSC populations: (i) What is the relationship between CD34- and CD34+ LSCs? (ii) What are the nearest counterpart normal haemopoietic cells to LSCs at a global transcriptional level? (iii) What is the impact of genetic heterogeneity on LSC function? Do all clones have equal LSC potential?Of a sequential cohort of 49 CD34- samples, 55% of 38 samples karyotyped had normal karyotype. 29/49 (59%) had mutated NPM1. Co-occurring mutations were FLT3 (54%), IDH1/2 (54%) and DNMT3A (26%). 11/28 samples with sufficient cells engrafted AML confirmed on mutation analysis. In 8/11 samples (7 were NPM1-mutated) sufficient available cells were available for detailed studies. LSC populations in serial transplant assays were present in both minor CD34+ and CD34-; CD34- populations were CD117+ and CD244+ or CD244-. Limit dilution analysis showed similar LSC frequencies in CD34+ and CD34- fractions from the same patient. Unexpectedly, there was no hierarchy with respect to CD34 expression and CD34 expression did not mark functionally distinct LSC populations. RNA-sequencing of 5 CD34+ and 14 CD34- LSC populations from 8 patient samples showed only 42 differentially protein coding genes out of 15539 expressed genes.We used ANOVA analysis to identify 300 top-ranking differentially expressed genes between normal stem/progenitor and myeloid and erythroid precursor populations. Using this signature, principal component analysis showed CD34- AML LSCs (CD34+ and CD34-) are closest to CD34-CD117+CD244+ populations that are promyelocytes have no D14 progenitor function in CFC assays and express late granulocytic macrophage (GM) genes. CD244 separates normal CD34-CD117+ populations into GM (CD244+) from erythroid (CD244-) precursors so allowing greater precision in mapping CD34-AML LSC to normal GM counterparts. CD34-AML LCS were not only enriched for a GM precursor signature, but also for a transcriptional signature seen in normal HSC. CD34- AML LSC expressed 63/100 transcription factor (TF) genes expressed in HSC including HOX and HOX co-factors. Interestingly, LSCs in CD34- AML had a distinct RNA-Seq profile from CD34+ progenitor-like LSCs populations.To explore genetic and functional heterogeneity of LSC populations, bulk and single cell genotyping of LSC populations revealed: (i) branching subclonal structures; with up to 5 genetically distinct LSC clones/patient; (ii) intermediate genotypes where the order of mutation acquisition was identified; (iii) some but not all patient LSC clones could be propagated in mice suggesting that current immunodeficient murine strains do not accurately model human AML. Thus, studies of LSC function have to combine both studies in mice and of primary human samples.In summary, within CD34- AML there are multiple, non-hierarchically arranged LSC populations with transcriptional programmes most closely related to normal CD34- GM precursors. Unlike these normal mature cells, LSCs also express HSC transcriptional signatures. Functional and genetic analysis of single cells and populations from patient LSC, non-LSC compartments and of xenografts reveals clonal structure, order of acquisition of mutations, how subclones are distributed in different immunophenotypic populations, some with different functional properties and, differences in subclonal representation between patients and xenografts. DisclosuresNo relevant conflicts of interest to declare.

The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling.

Primary clear cell renal cell carcinoma (ccRCC) genetic heterogeneity may lead to an underestimation of the mutational burden detected from a single site evaluation. We sought to characterize the extent of clonal branching involving key tumor suppressor mutations in primary ccRCC and determine if genetic heterogeneity could limit the mutation profiling from a single region assessment. Ex vivo core needle biopsies were obtained from three to five different regions of resected renal tumors at a single institution from 2012 to 2013. DNA was extracted and targeted sequencing was performed on five genes associated with ccRCC (von-Hippel Lindau [VHL], PBRM1, SETD2, BAP1, and KDM5C). We constructed phylogenetic trees by inferring clonal evolution based on the mutations present within each core and estimated the predictive power of detecting a mutation for each successive tumor region sampled. We obtained 47 ex vivo biopsy cores from 14 primary ccRCC's (median tumor size 4.5 cm, IQR 4.0–5.9 cm). Branching patterns of various complexities were observed in tumors with three or more mutations. A VHL mutation was detected in nine tumors (64%), each time being present ubiquitously throughout the tumor. Other genes had various degrees of regional mutational variation. Based on the mutations' prevalence we estimated that three different tumor regions should be sampled to detect mutations in PBRM1, SETD2, BAP1, and/or KDM5C with 90% certainty. The mutational burden of renal tumors varies by region sampled. Single site assessment of key tumor suppressor mutations in primary ccRCC may not adequately capture the genetic predictors of tumor behavior.

Abstract B129: Clinical implications of inter- and intra- prostatic heterogeneity.

Abstract Men with localized prostate cancer vary widely in clinical outcome, with a 30-50% failure rate after primary treatment. There is thus significant interest in developing genomically refined prognostic groups. We sought to evaluate the extent of genetic heterogeneity, both between patients (inter-prostate) and within individual prostate glands (intra-prostate) to assess the impact of genetic heterogeneity on risk stratification within a tight clinical cohort. Copy number aberrations (CNAs) from 75 Gleason 7 patients were determined by OncoScan SNP microarrays. We measure the percentage of genome involved in a CNA, termed percent genome aberration (PGA), a proxy for genomic instability. Additionally, whole genome sequencing was applied to 10 intermediate-risk prostate tumours and matched blood, including multiple manually macro-dissected regions from 5 of the prostates (range 2 to 9). Somatic single nucleotide variants (SNVs) and genomic rearrangements (GR) were extracted from each patient. We find a high degree of inter-prostatic heterogeneity between the 75 Gleason 7 patients, with the number of CNAs per patient ranging from 0 to 929, corresponding to PGA 0 to 16.7%. Known prognostic markers can differentiate between patients at higher risk for biochemical recurrence, but only account for a fraction of the cohort. Notably, when these prognostic genes are examined within multiple regions of five independent tumours, they differ in copy number between cancerous regions of the same prostate. For example, TP53 is deleted in 1/2, 1/3, 4/9, 0/4, and 4/5 prostate regions. Indeed, phylogenetic analysis of geographically distinct regions revealed multi-clonal disease in two of the five patients; separate analyses based on SNVs, CNAs, and GRs all concluded that these patient have two genetically distinct cancers within their prostate. We demonstrate dramatic levels of inter- and intra- prostate genetic heterogeneity within pathologically identical or similar cancers. The observed intra-prostatic genomic heterogeneity, both in terms of multi-focal and multi-clonal disease, has critical implications for clinical management. Prognostic information obtained by biopsy may be inconsistent depending on the site of biopsy, and applying personalized medicine to prostate cancer will be challenging. This study highlights the need for further evaluation of how intra-prostatic heterogeneity is related to patient prognosis. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B129. Citation Format: Emilie Lalonde, Paul C. Boutros, Michael Fraser, Richard de Borja, Nicholas J. Harding, Dominique Trudel, Alice Meng, Pablo H. Hennings-Yeomans, Andrew McPherson, Amin Zia, Jianxin Wang, Timothy Beck, Natalie S. Fox, Taryne Chong, Michelle Sam, Jeremy Johns, Lee Timms, Nicholas Buchner, Sohrab Shah, Cenk Sahinalp, Thomas J. Hudson, John D. McPherson, Theodorus van der Kwast, Robert G. Bristow. Clinical implications of inter- and intra- prostatic heterogeneity. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B129.

Endothelial Nitric Oxide Synthase (NOS3) Polymorphisms in African Americans With Heart Failure: Results From the A-HeFT Trial

Background Genetic heterogeneity at the endothelial nitric oxide synthase (NOS3) locus influences heart failure outcomes. The prevalence of NOS3 variants differs in black and white cohorts, but the impact of these differences is unknown. Methods and Results Subjects (n = 352) in the Genetic Risk Assessment of Heart Failure (GRAHF) substudy of the African-American Heart Failure Trial were genotyped for NOS3 polymorphisms: –786 T/C promoter, intron 4a/4b, and Glu298Asp and allele frequencies and compared with a white heart failure cohort. The effect of treatment with fixed-dose combination of isosorbide dinitrates and hydralazine (FDC I/H) on event-free survival and composite score (CS) of survival, hospitalization, and quality of life (QoL) was analyzed within genotype subsets. In GRAHF, NOS3 genotype frequencies differed from the white cohort ( P < .001). The –786 T allele was associated with lower left ventricular ejection fraction (LVEF) ( P = .01), whereas the intron 4a allele was linked to lower diastolic blood pressure and higher LVEF ( P = .03). Only the Glu298Asp polymorphism influenced treatment outcome; therapy with FDC I/H improved CS ( P = .046) and QoL ( P = .03) in the Glu298Glu subset only. Conclusions In black subjects with heart failure, NOS3 genotype influences blood pressure and left ventricular remodeling. The impact of genetic heterogeneity on treatment with FDC I/H requires further study.

Evaluation of Linkage and Association of HPC2/ELAC2 in Patients with Familial or Sporadic Prostate Cancer

To investigate the relationship between HPC2/ELAC2 and prostate cancer risk, we performed the following analyses: (1) a linkage study of six markers in and around the HPC2/ELAC2 gene at 17p11 in 159 pedigrees with hereditary prostate cancer (HPC); (2) a mutation-screening analysis of all coding exons of the gene in 93 probands with HPC; (3) family-based and population-based association study of common HPC2/ELAC2 missense variants in 159 probands with HPC, 249 patients with sporadic prostate cancer, and 222 unaffected male control subjects. No evidence for linkage was found in the total sample, nor in any subset of pedigrees based on characteristics that included age at onset, number of affected members, male-to-male disease transmission, or race. Furthermore, only the two previously reported missense changes (Ser217Leu and Ala541Thr) were identified by mutational analysis of all HPC2/ELAC exons in 93 probands with HPC. In association analyses, family-based tests did not reveal excess transmission of the Leu217 and/or Thr541 alleles to affected offspring, and population-based tests failed to reveal any statistically significant difference in the allele frequencies of the two polymorphisms between patients with prostate cancer and control subjects. The results of this study lead us to reject the three alternative hypotheses of (1) a highly penetrant, major prostate cancer-susceptibility gene at 17p11, (2) the allelic variants Leu217 or Thr541 of HPC2/ELAC2 as high-penetrance mutations, and (3) the variants Leu217 or Thr541 as low-penetrance, risk-modifying alleles. However, we did observe a trend of higher Leu217 homozygous carrier rates in patients than in control subjects. Considering the impact of genetic heterogeneity, phenocopies, and incomplete penetrance on the linkage and association studies of prostate cancer and on the power to detect linkage and association in our study sample, our results cannot rule out the possibility of a highly penetrant prostate cancer gene at this locus that only segregates in a small number of pedigrees. Nor can we rule out a prostate cancer-modifier gene that confers a lower-than-reported risk. Additional larger studies are needed to more fully evaluate the role of this gene in prostate cancer risk.