mutation profile
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2021 ◽  
Author(s):  
Kathryn A Ryan ◽  
Robert J Watson ◽  
Kevin R Bewley ◽  
Christopher A Burton ◽  
Oliver Carnell ◽  
...  

The mutation profile of the SARS-CoV-2 Omicron variant poses a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2, 99.99% identical to Wuhan-Hu-1, to protect against disease caused by the Omicron variant. We established that infection with Omicron in naive Syrian hamsters resulted in a less severe disease than a comparable dose of prototype SARS-CoV-2 (Australia/VIC01/2020), with fewer clinical signs and less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of Omicron 50 days after an initial infection with Australia/VIC01/2020. The data provide evidence for immunity raised against prototype SARS-CoV-2 being protective against Omicron in the Syrian hamster model. Further investigation is required to conclusively determine whether Omicron is less pathogenic in Syrian hamsters and whether this is predictive of pathogenicity in humans.


2021 ◽  
Vol 102 (12) ◽  
Author(s):  
Ruofan Wang ◽  
Ashton T. Belew ◽  
Vasudevan Achuthan ◽  
Najib El Sayed ◽  
Jeffrey J. DeStefano

Reverse transcriptases (RTs) are typically assayed using optimized Mg2+ concentrations (~5–10 mM) several-fold higher than physiological cellular free Mg2+ (~0.5 mM). Recent analyses demonstrated that HIV-1, but not Moloney murine leukaemia (MuLV) or avain myeloblastosis (AMV) virus RTs has higher fidelity in low Mg2+. In the current report, lacZα-based α-complementation assays were used to measure the fidelity of several RTs including HIV-1 (subtype B and A/E), several drug-resistant HIV-1 derivatives, HIV-2, and prototype foamy virus (PFV), all which showed higher fidelity using physiological Mg2+, while MuLV and AMV RTs demonstrated equivalent fidelity in low and high Mg2+. In 0.5 mM Mg2+, all RTs demonstrated approximately equal fidelity, except for PFV which showed higher fidelity. A Next Generation Sequencing (NGS) approach that used barcoding to determine mutation profiles was used to examine the types of mutations made by HIV-1 RT (type B) in low (0.5 mM) and high (6 mM) Mg2+ on a lacZα template. Unlike α-complementation assays which are dependent on LacZα activity, the NGS assay scores mutations at all positions and of every type. Consistent with α-complementation assays, a ~four-fold increase in mutations was observed in high Mg2+. These findings help explain why HIV-1 RT displays lower fidelity in vitro (with high Mg2+ concentrations) than other RTs (e.g. MuLV and AMV), yet cellular fidelity for these viruses is comparable. Establishing in vitro conditions that accurately represent RT’s activity in cells is pivotal to determining the contribution of RT and other factors to the mutation profile observed with HIV-1.


2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Liang Huang ◽  
Yu Xie ◽  
Shusuan Jiang ◽  
Weiqing Han ◽  
Fanchang Zeng ◽  
...  

Long noncoding RNAs (lncRNAs) exert an increasingly important effect on genome instability and the prognosis of cancer patients. The present research established a computational framework originating from the mutation assumption combining lncRNA expression profile and somatic mutation profile in the genome of renal cancer to assess the effect of lncRNAs on the gene instability of renal cancer. A total of 45 differentially expressed lncRNAs were evaluated to be genome-instability-associated from the high and low cumulative somatic mutations groups. Then we established a prognosis model based on three genome-instability-associated lncRNAs (AC156455.1, AC016405.3, and LINC01234)-GlncScore. The GlncScore was then verified in testing cohort and the total TCGA renal cancer cohort. The GlncScore was evaluated to have an accurate prediction for the survival of patients. Furthermore, GlncScore was associated with somatic mutation patterns, indicating its capacity of reflecting genome instability in renal cancer. In conclusion, this study evaluated the effect of lncRNAs on genome instability of renal cancer and provided new hidden cancer biomarkers related to genome instability in renal cancer.


Author(s):  
Mallika Dhanda ◽  
Amit Agarwal ◽  
Kausik Mandal ◽  
Sushil Gupta ◽  
M. Sabaretnam ◽  
...  

2021 ◽  
pp. 105192
Author(s):  
Jubby Marcela Gálvez Bermúdez ◽  
Henry Mauricio Chaparro-Solano ◽  
Ángela María Pinzón-Rondón ◽  
Ludwig L. Albornoz ◽  
Juan Mauricio Pardo-Oviedo ◽  
...  
Keyword(s):  

Cancers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 5906
Author(s):  
Kristyna Prochazkova ◽  
Nikola Ptakova ◽  
Reza Alaghehbandan ◽  
Sean R. Williamson ◽  
Tomáš Vaněček ◽  
...  

(1) Background: There are limited data concerning inter-tumoral and inter-metastatic heterogeneity in clear cell renal cell carcinoma (CCRCC). The aim of our study was to review published data and to examine mutation profile variability in primary and multiple pulmonary metastases (PMs) in our cohort of four patients with metastatic CCRCC. (2) Methods: Four patients were enrolled in this study. The clinical characteristics, types of surgeries, histopathologic results, immunohistochemical and genetic evaluations of corresponding primary tumor and PMs, and follow-up data were recorded. (3) Results: In our series, the most commonly mutated genes were those in the canonically dysregulated VHL pathway, which were detected in both primary tumors and corresponding metastasis. There were genetic profile differences between primary and metastatic tumors, as well as among particular metastases in one patient. (4) Conclusions: CCRCC shows heterogeneity between the primary tumor and its metastasis. Such mutational changes may be responsible for suboptimal treatment outcomes in targeted therapy settings.


2021 ◽  
pp. 1-6
Author(s):  
Alexander T. Nelson ◽  
Anne Bendel ◽  
Maggie Skrypek ◽  
Sachin Patel ◽  
Uri Tabori ◽  
...  

<b><i>Introduction:</i></b> Low-grade neuroepithelial tumors are a heterogeneous group of central nervous system tumors that are generally indolent in nature but in rare instances can progress to include leptomeningeal dissemination. <b><i>Case Presentation:</i></b> We present a case of a patient with a low-grade neuroepithelial tumor of indeterminate type with symptomatic leptomeningeal dissemination despite 3 chemotherapy regimens and radiotherapy. Somatic targetable mutation testing showed an FGFR1_TACC1 fusion. Therapy with pazopanib/topotecan was initiated, and disease stabilization was achieved. He received pazopanib/topotecan for a total of 2 years and is now &#x3e;2 years from completion of treatment and continues to do well with no evidence of disease. <b><i>Discussion:</i></b> This case highlights the utility of targetable mutation testing in therapeutic decision-making and the novel use of systemic pazopanib/topotecan therapy for refractory low-grade neuroepithelial tumor within the context of this clinical situation and specific mutation profile.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1216-1216
Author(s):  
Irena Tan ◽  
Matthew Schwede ◽  
Paul Phan ◽  
Raymond Yin ◽  
Tian Y Zhang ◽  
...  

Abstract Background: The combination of HMA and venetoclax is now standard of care for patients with AML who are not candidates for intensive chemotherapy. Elderly patients are more likely to have secondary AML (sAML), although the presence of an antecedent hematologic malignancy is often not apparent by history. Lindsley et al (Blood, 2015) showed that a somatic mutation in SRSF2, SF3B1, U2AF1, ZRSR2, ASXL1, EZH2, BCOR, or STAG2 is &gt;95% specific for sAML and associated with worse outcomes. While outcomes with HMA/ven in patients meeting standard criteria for sAML have recently been reported (Pullarkat, ASCO 2021), we set out to conduct a real-world analysis of sAML patients receiving HMA/ven, including those with a secondary mutation profile (SMP) as described by Lindsley et al. We hypothesized that-when treated with HMA/ven-outcomes of patients with SMP may be most similar to those with de novo AML. Methods: Patients diagnosed with AML at Stanford Cancer Institute from 4/2017-3/2021 and treated with front-line HMA/ven were retrospectively reviewed. These included patients previously treated with HMA monotherapy for an antecedent hematologic malignancy and those who had previously received ≤ 3 cycles of HMA monotherapy for AML. Responses were classified per the modified International Working Group response criteria. Overall survival (OS) was assessed for all patients, and for patients who had a complete response (CR) or CR with incomplete hematologic recovery (CRi), duration of response (DoR) was also assessed. Statistical analyses were performed in R using the logrank test, with hazard ratios (HR) computed using the Cox proportional hazards model. For multivariate analyses, p-values for a specific variable were calculated using Cox proportional hazards regression. Results: 82 patients met criteria for inclusion; 78 had valid response assessments and 49 (62.8%) had achieved a CR or CRi at first response assessment. Median age was 72 years, with 3 patients younger than 60. 62 patients were male, median ECOG performance status (PS) was 1, median Charlson Comorbidity Index (CCI) was 6, median time to death or end of follow-up from the start of treatment was 366 days, and 58% of patients had adverse risk AML per ELN guidelines. Fig 1a demonstrates demographics for de novo, sAML (excluding SMP), and patients with SMP AML. 13 patients met criteria for AML-MRC, 23 patients had prior history of antecedent hematologic malignancy (18 with MDS or CMML, 5 with MDS/MPN overlap or MPN), 12 had tAML, and 20 patients possessed a SMP and did not meet criteria for the other three categories of sAML. 14 patients with de novo AML were characterized by the absence of any of the above factors. Patients with de novo AML were less likely to have adverse risk disease (29% vs. 64% in others) and had lower CCI scores (mean 5.1 vs. 6.2) but had no significant differences in age, gender, follow-up time, or PS. There was no statistically significant difference in rates of CR/CRi between the different subgroups or the different types of sAML; 69% of patients with de novo AML, 79% of SMP patients, and 57% of patients with other types of sAML achieved a CR or CRi. However, SMP patients had response durations and OS patterns similar to patients with de novo AML (Fig 1b and 1c), and when grouped with de novo patients, both DoR (HR = 3.5, p = 0.047, Fig 1d) and OS (HR = 2.1, p = 0.042, Fig 1e) were significantly longer than those of the sAML patients. Neither DoR nor OS were significantly longer when the SMP patients were grouped with sAML patients (respectively: HR = 3.3, p = 0.22, Fig 1f; HR = 1.5, p = 0.37, Fig 1g). In multivariate Cox proportional regression adjusting for age, ELN risk category, CCI, and PS, worse OS for sAML patients was maintained relative to the SMP and de novo patients (HR 2.9, p = 0.036), although the difference in DoR was no longer significant (HR 4.4, p= 0.10). Conclusions: Patients meeting standard definitions of sAML had worse outcomes than those with de novo AML when treated with HMA/ven in a retrospective, real-world analysis. Although a secondary mutation profile as described by Lindsley et al may be helpful in identifying patients with sAML, when treated with HMA/ven, patients with this profile have outcomes that align more closely with those of patients with de novo AML. Figure 1 Figure 1. Disclosures Mannis: Astex, Forty Seven Inc/Gilead, Glycomimetics, and Jazz Pharmaceuticals: Research Funding; AbbVie, Agios, Astellas Pharma, Bristol Myers Squibb, Genentech, MacroGenics, Pfizer, and Stemline: Consultancy.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1321-1321
Author(s):  
Preetesh Jain ◽  
Krystle Nomie ◽  
Vitaly Segodin ◽  
Evgeniy Egorov ◽  
Yixin Yao ◽  
...  

Abstract Background - The tumor microenvironment (TME) plays a vital role in the growth and survival of mantle cell lymphoma (MCL) cells. However, characterization of the TME transcriptomic profile in MCL, its prognostic impact and response to Bruton's tyrosine kinase inhibitors (BTKi) is unknown. Unlike other lymphomas, the TME in MCL patients has not been fully characterized at the transcriptomic and genomic levels. To further understand the relevance of tumor-immune landscape in tissue microenvironments in the context of BTKi, we performed multi-omic profiling of the TME in tissues from MCL patients. Methods - Tissue biopsies were collected from MCL patients treated with BTKi. The study was conducted under an Institutional Review Board-approved protocol at The University of Texas MD Anderson Cancer Center. A total of 42 patients treated with BTKi were included. Among evaluable patients, DNA and RNA extraction was performed from fresh biopsies from lymph nodes and non-nodal tissues (including bone marrow). Whole exome (WES) and bulk RNA sequencing (RNA-seq) were performed to assess the somatic mutation profile, copy number abnormalities and gene expression profile to identify TME gene clusters. RNA sequencing data from an independent cohort of MCL patients from Scott et al (n = 122) was analyzed. Joint WES and RNA-seq, mutation calling, expression analysis, and cell type deconvolution from the transcriptome were performed using the BostonGene automated pipeline. Overall survival was calculated after starting BTKi therapy. Results - We obtained 42 MCL tissue samples (28 lymph nodes, 13 various tissues and one bone marrow) from patients treated with BTKi. Samples were obtained at/after starting treatment with BTKi at clinical progression. Unsupervised clustering based on the activities of the proposed transcriptomic signatures identified four distinct MCL subtypes based on tumor-immune cell gene signatures. We identified the four distinct MCL microenvironment signatures - normal lymph node like (N; n = 27), immune cell-enriched or "Hot" (IE; n = 46), mesenchymal (M; n = 44) and immune depleted/deserted or 'cold' (D; n = 51). The tumor proliferation rate signature and PI3K pathways were significantly overexpressed in immune-depleted (D) TME group. Evaluable patients were further classified based on response to BTKi as sensitive (n = 17), primary resistant (n = 11) or acquired resistant (n = 11). The TME was further dichotomized into immune cell rich and immune desert categories based on commonly involved immune cells and pathways. BTKi resistant MCL primarily exhibited immune depleted TME subtype. To explore the somatic mutation profile in relation to TME clusters, we performed a multiomic analysis combining WES data with RNA sequencing data and depicted according to the four TME clusters. Somatic mutations in TP53, NSD2, NOTCH1, KMT2D, SMARCA4, which were previously reported in ibrutinib-resistant MCL and/or in refractory high-risk MCL patients, were predominant in the immune-depleted TME cluster (D). Conclusions - Overall, we defined BTKi sensitivity and resistance by immune-hot and immune-cold TME portraits, respectively. The immune-depleted TME subtype (D) was characterized by dominant proliferation gene signature, overexpressed PI3K pathway, BTKi resistance and poor outcomes in MCL patients. Disclosures Jain: Lilly: Consultancy; kite: Consultancy. Nomie: BostonGene, Corp: Current Employment, Current holder of stock options in a privately-held company. Segodin: boston gene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Egorov: BostonGene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Kotlov: BostonGene Corp: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Vega: CRISPR Therapeutics and Geron: Research Funding; i3Health, Elsevier, America Registry of Pathology, Congressionally Directed Medical Research Program, and the Society of Hematology Oncology: Research Funding. Svekolkin: BostonGene Corp.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Bagaev: BostonGene Corp.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties: BostonGene. Frenkel: boston gene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Attaulakhanov: boston gene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Fowler: BostonGene, Corp: Current Employment, Current holder of stock options in a privately-held company; Bristol Myers Squibb, F. Hoffmann-La Roche Ltd, TG Therapeutics and Novartis: Membership on an entity's Board of Directors or advisory committees, Research Funding. Flowers: Sanofi: Research Funding; Amgen: Research Funding; EMD: Research Funding; Iovance: Research Funding; Janssen: Research Funding; Cancer Prevention and Research Institute of Texas: CPRIT Scholar in Cancer Research: Research Funding; Bayer: Consultancy, Research Funding; BeiGene: Consultancy; Pfizer: Research Funding; Celgene: Consultancy, Research Funding; Denovo: Consultancy; Novartis: Research Funding; Nektar: Research Funding; Epizyme, Inc.: Consultancy; Morphosys: Research Funding; Genmab: Consultancy; AbbVie: Consultancy, Research Funding; Takeda: Research Funding; TG Therapeutics: Research Funding; Xencor: Research Funding; Ziopharm: Research Funding; Burroughs Wellcome Fund: Research Funding; Eastern Cooperative Oncology Group: Research Funding; National Cancer Institute: Research Funding; Biopharma: Consultancy; Pharmacyclics/Janssen: Consultancy; Kite: Research Funding; Guardant: Research Funding; SeaGen: Consultancy; Cellectis: Research Funding; Karyopharm: Consultancy; Gilead: Consultancy, Research Funding; Genentech/Roche: Consultancy, Research Funding; Allogene: Research Funding; Adaptimmune: Research Funding; Spectrum: Consultancy; Acerta: Research Funding; 4D: Research Funding; Pharmacyclics: Research Funding. Wang: BGICS: Honoraria; Newbridge Pharmaceuticals: Honoraria; BioInvent: Research Funding; VelosBio: Consultancy, Research Funding; Juno: Consultancy, Research Funding; InnoCare: Consultancy, Research Funding; Hebei Cancer Prevention Federation: Honoraria; Janssen: Consultancy, Honoraria, Research Funding; Pharmacyclics: Consultancy, Research Funding; Mumbai Hematology Group: Honoraria; Scripps: Honoraria; The First Afflicted Hospital of Zhejiang University: Honoraria; Loxo Oncology: Consultancy, Research Funding; Moffit Cancer Center: Honoraria; Lilly: Research Funding; Bayer Healthcare: Consultancy; OMI: Honoraria; Imedex: Honoraria; Epizyme: Consultancy, Honoraria; Celgene: Research Funding; Physicians Education Resources (PER): Honoraria; Miltenyi Biomedicine GmbH: Consultancy, Honoraria; Kite Pharma: Consultancy, Honoraria, Research Funding; Chinese Medical Association: Honoraria; Clinical Care Options: Honoraria; Dava Oncology: Honoraria; CStone: Consultancy; DTRM Biopharma (Cayman) Limited: Consultancy; Genentech: Consultancy; Oncternal: Consultancy, Research Funding; Molecular Templates: Research Funding; CAHON: Honoraria; BeiGene: Consultancy, Honoraria, Research Funding; AstraZeneca: Consultancy, Honoraria, Research Funding; Anticancer Association: Honoraria; Acerta Pharma: Consultancy, Honoraria, Research Funding.


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