Hemant K. Roy’s research while affiliated with Baylor College of Medicine and other places

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Publications (430)


S293 Trends in the Incidence of Early-Onset Colorectal Cancer in Texas from 2000–2019
  • Article

October 2024

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6 Reads

The American Journal of Gastroenterology

Adegboyega Olayode

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Abiodun Oluyomi

O52 Rectal MicroRNA as a screening test for colon Neoplasia: a pilot study

July 2024

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3 Reads

Gut

Introduction Colorectal cancer (CRC) ranks as the second leading cause of cancer deaths in the UK. It is eminently preventable through identification and colonoscopic removal of the precursor lesion, the advanced adenoma (AAs). However, screening is both inefficient and inaccurate. For example, fecal immunohistochemical test (FIT) has a ~25% sensitivity for AAs. On the other hand, colonoscopy has a prevalence of ~6–8% meaning that >90% of screening colonoscopies are squandered with CRC prevention perspective. Finding better risk stratification is critical. Our group has focused on detection of field carcinogenesis, the notion that the genetic/epigenetic milieu that leads to a focal neoplasm can be detected throughout the colon including the readily accessible rectum. This is the clinical rationale for full colonoscopy for polyps on flex sigmoidoscopy or post-polypectomy surveillance (‘condemned mucosa’). MicroRNAs (miRs) are small (18–25 nucleotide) molecules that can impact specific gene expression. There are ~3000 species and miRs are resistant to degradation so ideal for detection in the colon. Methods Human Subjects: After IRB approved informed consent, we recruited patients undergoing colonoscopy and obtained 6 biopsies of the endoscopically normal rectal mucosa. Of the ~150 subjects we identified 9 with advanced adenomas elsewhere in the colon (cases) and selected 15 matched (negative colonoscopies) controls.RNA Seq: RNeasy mini kits (Ambion) for mRNA sequencing. Sequencing was performed using the Illumina® NovaSeqTM platform. Differential miR was analyzed. We assessed performance via the area under the receiver operator characteristic curve (AUROC). Results We identified 2268 miRNA. Of those 165 miRNA values were statistically significant (p<0.05), were >1.2 fold or <0,8 dysregulated. There were 46 microRNAs downregulated and 119 upregulated. The top three miRs were hsa-miR-181b-5p with hsa-let-7d-3p and hsa-miR-4661–5p. The performance is in the table 1 below:View this table: • View inline • View popup Abstract O52 Table 1 We did leave one out validation to determine 95% confidence interval. For the single hsa-miR-181b-5p and with addition of hsa-let-7d-3p it was [0.76, 0.86] and [0.88, 0.95] respectively. Conclusions We show for the first time that a panel of 2 rectal miRs had an excellent performance for diagnosis. It is striking that this simple panel outperformed classic tests such as FIT or Cologuard (~25% and ~45% respectively). This proof of concept study suggests a simple rectal swab may be able to personalize CRC screening.







Linear regression model of chromatin D and age in control and case groups.
Packing scaling D is sensitive to field carcinogenesis. (a) Chromatin packing scaling D in cells brushed from tumor site, healthy-appearing tissue located 4 cm away from tumor and from rectum (n = 10) showed significantly increase (p = 1.5 × 10–6,6.9 × 10–5, 3.6 × 10–7 respectively) compared to control patients (n = 20) but no significant difference among the three locations. (b) Rectal D is increased in patients with dysplasia regardless of anatomic location, right-sided (p = 0.017) and left-sided adenoma (p = 0.002) compared to control.
Rectal chromatin domain changes are sensitive to progression of CRC. Rectal D is increased progressively from control < diminutive adenoma (< 5 mm) < nondiminutive adenoma (5–9 mm) < advanced adenoma (> 10 mm) < Hereditary predisposition to CRC (HNPCC) < Cancer.
(a) Chromatin structural changes estimated by csPWS Rectal D correlated with colonic risk history. (b) 5-year cumulative CRC risk model and packing scaling D regression analysis, r² = 0.94. Hx, History; NDA, non-diminutive adenoma; AA, advanced adenoma.
Normal appearing rectal epithelial cells in control and AA. Red segmentations show chromatin D maps of the nucleus regions.

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Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications
  • Article
  • Full-text available

April 2024

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33 Reads

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9 Citations

Colonoscopy is accurate but inefficient for colorectal cancer (CRC) prevention due to the low (~ 7 to 8%) prevalence of target lesions, advanced adenomas. We leveraged rectal mucosa to identify patients who harbor CRC field carcinogenesis by evaluating chromatin 3D architecture. Supranucleosomal disordered chromatin chains (~ 5 to 20 nm, ~1 kbp) fold into chromatin packing domains (~ 100 to 200 nm, ~ 100 to 1000 kbp). In turn, the fractal-like conformation of DNA within chromatin domains and the folding of the genome into packing domains has been shown to influence multiple facets of gene transcription, including the transcriptional plasticity of cancer cells. We deployed an optical spectroscopic nanosensing technique, chromatin-sensitive partial wave spectroscopic microscopy (csPWS), to evaluate the packing density scaling D of the chromatin chain conformation within packing domains from rectal mucosa in 256 patients with varying degrees of progression to colorectal cancer. We found average packing scaling D of chromatin domains was elevated in tumor cells, histologically normal-appearing cells 4 cm proximal to the tumor, and histologically normal-appearing rectal mucosa compared to cells from control patients (p < 0.001). Nuclear D had a robust correlation with the model of 5-year risk of CRC with r² = 0.94. Furthermore, rectal D was evaluated as a screening biomarker for patients with advanced adenomas presenting an AUC of 0.85 and 85% sensitivity and specificity. artificial intelligence-enhanced csPWS improved diagnostic performance with AUC = 0.90. Considering the low sensitivity of existing CRC tests, including liquid biopsies, to early-stage cancers our work highlights the potential of chromatin biomarkers of field carcinogenesis in detecting early, significant precancerous colon lesions.

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Citations (38)


... The development of Chromatin-sensitive Partial Wave Spectroscopic Microscopy (csPWS) [2,3] marked a significant milestone, enabling the nanosensing of cellular or intracellular structures with unprecedented details. This has opened new avenues for cancer research, allowing the early including lung and colorectal cancer, and has demonstrated high efficacy in detecting Stage-I lung cancer (AUC = 0.92 in Site 1 and 0.81 in Site 2) [3] and advanced adenoma (AUC = 0.90) [10]. Furthermore, cancer heterogeneity poses a significant challenge to cancer research, while automated segmentation facilitates the gathering and evaluation of a large number of nuclear features from extensive cell populations. ...

Reference:

Deep learning-driven automatic nuclei segmentation of live-cell chromatin-sensitive partial wave spectroscopic microscopy imaging
Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications

... In efforts to refine Apc-based mouse models, use of the colon epithelium specific CDX2P regulatory elements with the loxP-CreER T2 system has enabled Apc inactivation in the adult mouse colon epithelium 9,10 . In previous work, we showed that loss of intestinal keratin 8 (K8) makes the colon more susceptible to tumor development upon a second carcinogenic hit with AOM 11 . ...

Colorectal cancer murine models: Initiation to metastasis
  • Citing Article
  • February 2024

Cancer Letters

... This highlights the need for more comprehensive health data collection in low SDI areas, which would help better understand and resolve these health disparities. Although studies of liver cancer in low SDI areas have linked high incidence with hepatitis infection and arsenic-contaminated water sources [35], there is a need to address PC risk factors, especially smoking, obesity, and diabetes, which are common in both high and low SDI regions [36][37][38], to develop strategies to reduce the health disparities in PC burden globally. As discussed earlier, successful interventions in other diseases-such as HPV vaccination for cervical cancer, colorectal cancer screening, and anti-smoking legislation-have demonstrated the value of targeted public health policies. ...

Race/ethnicity and sex differences in the association between area-level arsenic exposure concentration and hepatocellular carcinoma (HCC) incidence rates in Texas. An ecological study
  • Citing Article
  • November 2023

Environmental Research

... Last, to revolutionize oral cancer diagnosis and make the most of the potential of fractal analysis in oral oncology, it could be integrated with machine learning and other artificial intelligence-enhanced tools, as demonstrated in the case of breast and colon cancers [54,55]. ...

Early screening of colorectal cancer using feature engineering with artificial intelligence-enhanced analysis of nanoscale chromatin modifications

... Further, chromatin in the nucleus is known to be organized into several thousand PDs -compact regions that maintain heritability across cell divisions -varying in size (averaging 250 kb). These domains exhibit a chromatin volume concentration (CVC) of approximately 0.35 and demonstrate mass-fractal intradomain chromatin conformation with the genomic length N, scaling with the radius of the occupied physical volume R as N ∝ R D where experimentally measured D values range from 5/3 to 3 across packing domains [3,8]. Thus, packing scaling D provides insight into how nanoscale materials are organized within PDs in a fixed volume. ...

Early detection of lung cancer using artificial intelligence-enhanced optical nanosensing of chromatin alterations in field carcinogenesis

... In recent year, the association between modifiable lifestyle factors, including physical activity, diet patterns, smoking, drinking, obesity, and CRC has attracted increasing attentions [3][4][5][6][7]. Despite significant advances in understanding the risk factors for CRC, including lifestyle behaviors, dietary patterns, and genetic predispositions, recent studies have also highlighted the long-term influence of circadian rhythm on CRC, suggesting that its impact may be as significant as these traditional lifestyle behaviors [8][9][10].Some evidence has demonstrated that sleep problems are prevalent in the general population. A recent meta-analysis involving over 1.1 million individuals from the United States, Netherlands, and United Kingdom indicated that 13.3% of adult participants reported poor sleep quality [11]. ...

Circadian Disruption and Colorectal Cancer Incidence in Black Women
  • Citing Article
  • November 2022

Cancer Epidemiology, Biomarkers & Prevention

... A study that assessed whether exercise-induced myokines would mitigate the COVID-19 infectivity of the bronchial epithelium through angiotensin-converting enzyme 2 -ACE2 intonation demonstrated evidence suggesting exercise has a protective effect against COVID-19 (33). ...

Exercise-induced myokines downregulates the ACE2 level in bronchial epithelial cells: Implications for SARS-CoV-2 prevention

... Similarly, an increase in collagen deposition was also observed in the Picrosirius red (PSR) stained colon (Fig. 6B) (Segnani et al. 2015). Moreover, there was a significant reduction in mucin-producing goblet cells in the AOM/DSS group as compared to the CONTROL group (Fig. 6C) (Pothuraju et al. 2022). While some regions retained a physiological distribution of goblet cells, the tumour tissue demonstrates a marked depletion of these cells, consistent with neoplastic transformation and mucosal barrier disruption ( Fig. 6C and F; Loktionov 2022). ...

Depletion of transmembrane mucin 4 (Muc4) alters intestinal homeostasis in a genetically engineered mouse model of colorectal cancer

Aging

... 48 Participants with a higher quartile of vitamin D scores had a reduced incidence of CRC according to a cohort study of African American women. 49 A meta-analysis linked increased vitamin D consumption to a decreased incidence of CRC. 50 Kwan et al. investigated the impact of vitamin D and calcium on the expression tumor cells in patients with CRC. ...

Predicted Vitamin D Status and Colorectal Cancer Incidence in the Black Women's Health Study
  • Citing Article
  • October 2021

Cancer Epidemiology, Biomarkers & Prevention

... One such mechanism involves enhancing mucus production. The mucus acts as a protective lining in the intestines, thwarting harmful substances and pathogens from breaching the intestinal wall [137]. Postbiotics stimulate mucus production, reinforcing the gut barrier and fortifying its defenses [138]. ...

Mucins, gut microbiota, and postbiotics role in colorectal cancer