Publications by authors named "Alex Farrell"

Myeloid cell leukemia 1 (MCL-1) is a member of the B-cell lymphoma 2 protein family and has anti-apoptotic functions. Deregulation of MCL-1 has been reported in several cancers, including lung and breast cancer. In the present study, the association of MCL-1 expression with molecular features in colorectal cancer (CRC) has been highlighted.

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Olfactory neuroblastoma (ONB), sinonasal undifferentiated carcinoma (SNUC), and sinonasal neuroendocrine carcinoma (SNEC) are rare malignancies arising from the sinonasal tract with limited therapeutic options. The expression of the somatostatin receptor 2 gene (), which is expressed in other neuroendocrine neoplasms and is therapeutically actionable, has been reported in these tumors. Here, we analyzed gene expression and its associations with genomic features, established biomarkers predicting of immune response, and the tumor immune microenvironment in a cohort of ONB, SNUC, and SNEC tumor samples (26, 13, and 8 samples, respectively) from a real-world database.

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Immunotherapy has changed the treatment paradigm for many types of cancer, but immune checkpoint inhibitors (ICIs) have not shown benefit in prostate cancer (PCa). Chronic inflammation contributes to the immunosuppressive prostate tumor microenvironment (TME) and is associated with poor response to ICIs. The primary source of inflammatory cytokine production is the inflammasome.

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Background: Gene copy number gain (CNG) is a continuous variable. The relevant cutpoint for HER2, KRAS and MET CNG in non-mall cell lung cancer remains uncertain. As de novo driver oncogenes are largely mutually exclusive, oncogene overlap analysis can be used to explore CNG thresholds.

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Purpose: Transcriptional profiling of pancreatic cancers has defined two main transcriptional subtypes: classical and basal. Initial data suggest shorter survival for patients with basal tumors and differing treatment sensitivity to FOLFIRINOX and gemcitabine plus nab-paclitaxel by transcriptional subtype.

Experimental Design: We examined 8,743 patients with RNA sequencing from pancreatic cancers performed at Caris Life Sciences.

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The expression of the protein Mesothelin (MSLN) is highly variable in several malignancies, including colorectal cancer (CRC), and high levels are associated with aggressive clinicopathological features and worse patient survival. Colorectal cancer is both a common and deadly cancer; being the third most common in incidence and second most common cause of cancer-related death. While systemic therapy remains the primary therapeutic option for most patients with stage IV (metastatic; m) CRC, their disease eventually becomes treatment refractory, and 85% succumb within 5 years.

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Background: Non-canonical WNT family (WNT5A pathway) signaling via WNT5A through ROR1 and its partner, ROR2, or Frizzled2 (FZD2) is linked to processes driving tumorigenesis and therapy resistance. We utilized a large dataset of urothelial carcinoma (UC) tumors to characterize non-canonical WNT signaling through WNT5A, ROR1, ROR2, or FZD2 expression.

Methods: NextGen Sequencing of DNA (592 genes or WES)/RNA (WTS) was performed for 4125 UC tumors submitted to Caris Life Sciences.

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Article Synopsis
  • The study investigates the effectiveness of immune checkpoint inhibitors (ICIs) in patients with deficient mismatch repair (dMMR) colorectal and endometrial cancers, focusing on how different types of mismatch repair alterations affect patient responses.
  • Results showed that patients with mutS co-loss (MSH2 and MSH6) had significantly longer median overall survival compared to those with mutL co-loss (MLH1 and PMS2) in both colorectal cancer (54.6 vs. 36 months) and endometrial cancer (81.5 vs. 48.2 months).
  • Additionally, the neoantigen load (NAL) was found to be higher in mutS co-loss cases, suggesting it could be a key factor
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Article Synopsis
  • The expression of a specific protein varies significantly in different malignancies, particularly colorectal cancer (CRC), where high levels are linked to aggressive disease and worse survival rates.
  • Colorectal cancer is a significant health issue, being the third most common cancer and the second leading cause of cancer-related deaths, particularly in patients with stage IV disease whose treatments often fail.
  • Current research focuses on examining the correlation between this protein's levels and clinical outcomes in CRC subtypes, discovering associations with immune response, gene mutation rates, and potential new therapeutic strategies for patients with high protein expression in microsatellite-stable (MSS) CRC.
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TFE3-rearranged renal cell carcinoma (rRCC) is a rare subtype of renal cell carcinomas belonging to the MiT family translocation RCC. To further elucidate the co-alterations that occur along with TFE3 fusions in rRCC, we characterized the genomic, transcriptional, and immune landscapes in comparison to clear cell (ccRCC) and papillary renal cell carcinoma (pRCC). Next-generation sequencing of RNA (whole transcriptome) and DNA (592-gene panel or whole exome) for rRCC (N = 20), pRCC (N = 20), and ccRCC samples (N = 392) was performed.

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Background: Recent studies have correlated surgical skill measured by video-based assessment with improved clinical outcomes. Certain automated measures of operative performance in robotic surgery can be gathered beyond video review called objective performance indicators (OPIs). We explore the relationship between OPIs, surgeon experience, and postoperative recovery, hypothesizing that more efficient dissection will be associated with experience.

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We consider a Darwinian (evolutionary game theoretic) version of a standard susceptible-infectious model in which the resistance of the disease causing pathogen to a treatment that prevents death to infected individuals is subject to evolutionary adaptation. We determine the existence and stability of all equilibria, both disease-free and endemic, and use the results to determine conditions under which the treatment will succeed or fail. Of particular interest are conditions under which a successful treatment in the absence of resistance adaptation (i.

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Objectives: To identify differential survival outcomes and immune checkpoint inhibitor (ICI) response in MLH1 hypermethylated versus MLH1 mutated ("Lynch-like") endometrial tumors and determine whether their molecular profiles can elucidate the differential outcomes.

Methods: 1673 mismatch repair deficient endometrial tumors were analyzed by next-generation sequencing and whole transcriptome sequencing (Caris Life Sciences, Phoenix, AZ). PD-L1, ER, and PR were tested by immunohistochemistry and immune cell infiltrates were calculated using MCP-counter.

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Influenza is an ribonucleic acid virus with a genome that comprises eight segments. Experiments show that the vast majority of virions fail to express one or more gene segments and thus cannot cause a productive infection on their own. These particles, called semi-infectious particles (SIPs), can induce virion production through complementation when multiple SIPs are present in an infected cell.

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Vulvar squamous cell cancer (VSC) accounts for 90% of vulvar cancers. Next-generation sequencing studies of VSC imply human papillomavirus (HPV) and p53 status play separate roles in carcinogenesis and prognosis. We sought to describe the genomic landscape and analyze the immunologic profiles of VSC with respect to HPV and p53 status.

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Objective: HER2 status is not routinely evaluated in endometrioid endometrial cancer (E-EMCA), though it is frequently overexpressed or amplified in high grade E-EMCA and uterine serous carcinoma. Defining characteristics and survival outcomes of HER2+ E-EMCA could reveal subsets of patients who may benefit from targeted therapies.

Methods: 2927 E-EMCA tumors from the Caris Life Sciences database were analyzed by next-generation sequencing and whole exome sequencing, whole transcriptome sequencing, and immunohistochemistry for molecular and genomic features in a CLIA/CAP-certified laboratory (Caris Life Sciences, Phoenix, AZ).

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Background: Genomic signatures contributing to high tumour mutational burden (TMB-H) independent from mismatch-repair deficiency (dMMR) or microsatellite instability-high (MSI-H) status are not well studied. We aimed to characterise molecular features of microsatellite stable (MSS) TMB-H gastrointestinal tumours.

Methods: Molecular alterations of 48 606 gastrointestinal tumours from Caris Life Sciences (CARIS) identified with next-generation sequencing were compared among MSS-TMB-H, dMMR/MSI-H, and MSS-TMB-low (L) tumours, using χ or Fisher's exact tests.

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The stochastic nature of epidemic dynamics on a network makes their direct study very challenging. One avenue to reduce the complexity is a mean-field approximation (or mean-field equation) of the dynamics; however, the classic mean-field equation has been shown to perform sub-optimally in many applications. Here, we adapt a recently developed mean-field equation for SIR epidemics on a network in continuous time to the discrete time case.

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Previous works using different mathematical techniques, however, show that the concavity of the trade-off relationship can alter the expected life history strategies. Thus we developed a model and found that the concavity of the reproduction-survival curve can still have a large impact on life history strategies in an ecological model with Darwinian evolution.

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Within-host models are useful tools for understanding the processes regulating viral load dynamics. While existing models have considered a wide range of within-host processes, at their core these models have shown remarkable structural similarity. Specifically, the structure of these models generally consider target cells to be either uninfected or infected, with the possibility of accommodating further resolution (e.

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Ultra-high vacuum systems must often be constructed of materials with ultra-low outgassing rates to achieve pressure of 10 Pa and below. Any component placed into the ultra-high vacuum system must also be constructed of materials with ultra-low outgassing rates. Baking stainless steel vacuum components to a temperature range of 400 °C to 450 °C while under vacuum is an effective method to reduce the outgassing rate of vacuum components for use in ultra-high vacuum systems.

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In simple SI epidemic and endemic models, three classes of incidence functions are identified for their potential to be associated with host extinction: weakly upper density-dependent incidences are never associated with host extinction. Power incidences that depend on the number of susceptibles and infectives by powers strictly between 0 and 1 are associated with initial-constellation-dependent host extinction for all parameter values. Homogeneous incidences, of which frequency-dependent incidence is a very particular case, and power incidences are associated with global host extinction for certain parameter constellations and with host survival for others.

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For epidemic models, it is shown that fatal infectious diseases cannot drive the host population into extinction if the incidence function is upper density-dependent. This finding holds even if a latency period is included and the time from infection to disease-induced death has an arbitrary length distribution. However, if the incidence function is also lower density-dependent, very infectious diseases can lead to a drastic decline of the host population.

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Few integrated analysis models examine significant U.S. transportation greenhouse gas emission reductions within an integrated energy system.

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