Browse Articles

The impact of genetic analysis on the early detection of colorectal cancer

Agrawal et al. | Aug 24, 2023

The impact of genetic analysis on the early detection of colorectal cancer

Although the 5-year survival rate for colorectal cancer is below 10%, it increases to greater than 90% if it is diagnosed early. We hypothesized from our research that analyzing non-synonymous single nucleotide variants (SNVs) in a patient's exome sequence would be an indicator for high genetic risk of developing colorectal cancer.

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Investigation of unknown causes of uveal melanoma uncovers seven recurrent genetic mutations

Nanda et al. | Aug 25, 2022

Investigation of unknown causes of uveal melanoma uncovers seven recurrent genetic mutations

Uveal melanoma (UM) is a rare subtype of melanoma but the most frequent primary cancer of the eye in adults. The goal of this study was to research the genetic causes of UM through a comprehensive frequency analysis of base-pair mismatches in patient genomes. Results showed a total of 130 genetic mutations, including seven recurrent mutations, with most mutations occurring in chromosomes 3 and X. Recurrent mutations varied from 8.7% to 17.39% occurrence in the UM patient sample, with all mutations identified as missense. These findings suggest that UM is a recessive heterogeneous disease with selective homozygous mutations. Notably, this study has potential wider significance because the seven genes targeted by recurrent mutations are also involved in other cancers.

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Predicting smoking status based on RNA sequencing data

Yang et al. | Aug 30, 2024

Predicting smoking status based on RNA sequencing data
Image credit: Yang and Stanley 2024

Given an association between nicotine addiction and gene expression, we hypothesized that expression of genes commonly associated with smoking status would have variable expression between smokers and non-smokers. To test whether gene expression varies between smokers and non-smokers, we analyzed two publicly-available datasets that profiled RNA gene expression from brain (nucleus accumbens) and lung tissue taken from patients identified as smokers or non-smokers. We discovered statistically significant differences in expression of dozens of genes between smokers and non-smokers. To test whether gene expression can be used to predict whether a patient is a smoker or non-smoker, we used gene expression as the training data for a logistic regression or random forest classification model. The random forest classifier trained on lung tissue data showed the most robust results, with area under curve (AUC) values consistently between 0.82 and 0.93. Both models trained on nucleus accumbens data had poorer performance, with AUC values consistently between 0.65 and 0.7 when using random forest. These results suggest gene expression can be used to predict smoking status using traditional machine learning models. Additionally, based on our random forest model, we proposed KCNJ3 and TXLNGY as two candidate markers of smoking status. These findings, coupled with other genes identified in this study, present promising avenues for advancing applications related to the genetic foundation of smoking-related characteristics.

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Modulation of VEGF and TGF beta in 5-FU induced inflammation in MCF-7 using an herbal formulation

Vinay Nair et al. | Jun 03, 2022

Modulation of VEGF and TGF beta in 5-FU induced inflammation in MCF-7 using an herbal formulation

Acquired drug resistance is an increasing challenge in treating cancer with chemotherapy. One mechanism
behind this resistance is the increased inflammation that supports the progression and development of
cancer that arises because of the drug’s presence. Integrative oncology is the field that focuses on including natural products alongside traditional therapy to create a treatment that focuses on holistic patient well-being.
In this study, the authors demonstrate that the use of an herbal formulation, consisting of turmeric and green tea, alongside a traditional chemotherapeutic drug, 5-fluorouracil (FU) significantly decreases the level of cytokines produced in breast cancer cells when compared to the levels produced when exposed solely to the chemo drug. The authors conclude that this combination of treatment, based on the principle of integrative oncology, shows potential for reducing the resistance against treatment conferred through increased inflammation. Consequently, this suggests a prospective way forward in improving the efficacy of cancer treatment.

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POC-MON: A Novel and Cost-Effective Pocket Lemon Sniff Test (PLST) for Early Detection of Major Depressive Disorder

Cruz et al. | Jul 07, 2020

POC-MON: A Novel and Cost-Effective Pocket Lemon Sniff Test (PLST) for Early Detection of Major Depressive Disorder

Effective treatment of depression requires early detection. Depressive symptoms overlap with olfactory regions, which led to several studies of the correlation between sense of smell and depression. The alarming rise of depression, its related crimes, suicides, and lack of inexpensive, quick tools in detecting early depression — this study aims in demonstrating decreased olfaction and depression correlation. Forty-two subjects (ages 13-83) underwent POC-MON (Pocket Lemon) assessment — an oven-dried lemon peel sniff test, subjected to distance measurement when odor first detected (threshold) and completed Patient Health Questionnaires (PHQ-9). POC-MON and PHQ-9 scores yielded a correlation of 20% and 18% for the right and left nostrils, respectively. Among male (n=17) subjects, the average distance of POC-MON and PHQ-9 scores produced a correlation of 14% and 16% for the right and left nostrils, respectively. Females (n=25) demonstrated a correlation of 28% and 21% for the right and left nostrils, respectively. These results suggest the correlation between olfaction and depression in diagnosing its early-stage, using a quick, inexpensive, and patient-friendly tool — POC-MON.

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Varying Growth Hormone Levels in Chondrocytes Increases Proliferation Rate and Collagen Production by a Direct Pathway

Bennett et al. | Sep 03, 2019

Varying Growth Hormone Levels in Chondrocytes Increases Proliferation Rate and Collagen Production by a Direct Pathway

Bennett and Joykutty test whether growth hormone directly or indirectly affected the rate at which cartilage renewed itself. Growth hormone could exert a direct effect on cartilage or chondrocytes by modifying the expression of different genes, whereas an indirect effect would come from growth hormone stimulating insulin-like growth factor. The results from this research support the hypothesis that growth hormone increases proliferation rate using the direct pathway. This research can be used in the medical sciences for people who suffer from joint damage and other cartilage-related diseases, since the results demonstrated conditions that lead to increased proliferation of chondrocytes. These combined results could be applied in a clinical setting with the goal of allowing patient cartilage to renew itself at a faster pace, therefore keeping those patients out of pain from these chondrocyte-related diseases.

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Who is at Risk for a Spinal Fracture? – A Comparative Study of National Health and Nutrition Examination Survey Data

He et al. | Mar 01, 2018

Who is at Risk for a Spinal Fracture? – A Comparative Study of National Health and Nutrition Examination Survey Data

One common age-related health problem is the loss of bone mineral density (BMD), which can lead to a variety of negative health outcomes, including increased risk of spinal fracture. In this study, the authors investigate risk factors that may be predictive of an individual's risk of spinal fracture. Their findings provide valuable information that clinicians can use in patient evaluations.

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The Effects of Antibiotics on Nutrient Digestion

Murea et al. | Oct 06, 2017

The Effects of Antibiotics on Nutrient Digestion

One disadvantage of antibiotic therapy is the potential for unpleasant gastrointestinal side effects. Here, the authors test whether some common antibiotics directly interfere with the digestion of protein, fat, or sugars. This study provides motivation to more carefully investigate the interactions between antibiotics and gut enzymes in order to inform treatment decisions and improve patient outcomes.

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