Review
Gastroenterology & Hepatology
Riccardo Nevola, Rachele Ruocco, Livio Criscuolo, Angela Villani, Maria Alfano, Domenico Beccia, Simona Imbriani, Ernesto Claar, Domenico Cozzolino, Ferdinando Carlo Sasso, Aldo Marrone, Luigi Elio Adinolfi, Luca Rinaldi
Summary: Hepatocellular carcinoma (HCC) is the most common liver neoplasm with increasing incidence rates. Long-term outcomes of potentially curative treatments are affected by high recurrence rates, with early recurrence being caused by the spread of the primary neoplasm and related to tumor burden, and late recurrence being independent of the primary neoplasm. Early HCC recurrence has a poorer prognosis than late recurrence, and different predictors exist for each type of recurrence. Understanding predictive factors and recurrence risk stratification is important for guiding treatment strategies and post-treatment surveillance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Chemistry, Analytical
Lorico D. S. Lapitan Jr, Mariusz Pietrzak, Marek Krawczyk, Elzbieta Malinowska
Summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death globally in 2020. The complexity of the disease and the low survival rate are due to late-stage diagnosis. Therefore, developing simple, sensitive, and rapid screening methods for early detection is necessary. Recent studies have shown promising HCC biomarkers and ultrasensitive biosensor technologies that could significantly improve diagnosis.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Biotechnology & Applied Microbiology
Maciej Migdal, Eugeniusz Tralle, Karim Abu Nahia, Lukasz Bugajski, Katarzyna Zofia Kedzierska, Filip Garbicz, Katarzyna Piwocka, Cecilia Lanny Winata, Michal Pawlak
Summary: Our study induced hepatic injury in adult zebrafish using thioacetamide (TAA). We isolated three major liver cell types - hepatocytes, endothelial cells, and hepatic stellate cells - and identified cell-type-specific chromatin accessibility and transcriptional changes in the early stage of liver injury. The results showed that TAA induced transcriptional shifts in all three cell types, with liver endothelial cells exhibiting the most pronounced response to liver injury at the transcriptome and chromatin level.
Review
Oncology
Nitin N. Katariya, Blanca C. Lizaola-Mayo, David M. Chascsa, Emmanouil Giorgakis, Bashar A. Aqel, Adyr A. Moss, Pedro Luiz Serrano Uson Junior, Mitesh J. Borad, Amit K. Mathur
Summary: This review examines the use of immune checkpoint inhibitors in advanced hepatocellular carcinoma, particularly in the context of liver transplantation. While many questions remain unanswered, immunotherapy plays an important role in the treatment of hepatocellular carcinoma, and further clinical trials will help refine its indications and parameters.
Article
Radiology, Nuclear Medicine & Medical Imaging
Takeshi Yokoo, Nobuaki Masaki, Neehar D. Parikh, Barton F. Lane, Ziding Feng, Mishal Mendiratta-Lala, Chee Hwee Lee, Gaurav Khatri, Tracey L. Marsh, Kirti Shetty, Colin T. Dunn, Taim Al-Jarrah, Anum Aslam, Matthew S. Davenport, Purva Gopal, Nicole E. Rich, Anna S. Lok, Amit G. Singal
Summary: This study evaluated the sensitivity and specificity of dynamic contrast-enhanced abbreviated MRI for the detection of early-stage hepatocellular carcinoma (HCC). The results showed that dynamic abbreviated MRI had high sensitivity and specificity in detecting early-stage HCC in patients with compensated cirrhosis, but lower sensitivity in those with decompensated cirrhosis.
Review
Oncology
Justin Z. Wang, Farshad Nassiri, Alexander P. Landry, Vikas Patil, Jeff Liu, Kenneth Aldape, Andrew Gao, Gelareh Zadeh
Summary: Meningiomas, the most common primary brain tumors in adults, have been understudied compared to other central nervous system (CNS) tumors, but recent studies have identified key alterations in the molecular landscape of these tumors, leading to the development of a molecular-based classification scheme that surpasses histopathological grading in terms of accuracy and predictive power. This classification scheme divides meningiomas into four consensus molecular groups, based on molecular characteristics and clinical outcomes. Further research is being conducted to validate these groups and establish a standardized nomenclature for routine clinical use.
JOURNAL OF NEURO-ONCOLOGY
(2023)
Article
Surgery
Yutaka Endo, Kazunari Sasaki, Zorays Moazzam, Henrique A. Lima, Laura Alaimo, Muhammad Musaab Munir, Chanza F. Shaikh, Austin Schenk, Minoru Kitago, Timothy M. Pawlik
Summary: This study aimed to identify characteristics of liver transplantation for elderly patients and assess the therapeutic benefit derived from liver transplantation over liver resection. The results showed that elderly patients who underwent liver transplantation had similar 5-year survival rates compared to non-elderly recipients. Liver transplantation was associated with a lower risk of death compared to liver resection.
BRITISH JOURNAL OF SURGERY
(2023)
Article
Surgery
Malay B. Shah, Diego A. Villagomez Rubio, Gabriel Orozco, Siddharth Desai, Alexandre Ancheta, Meera Gupta, Xiaonan Mei, B. Mark Evers, Roberto Gedaly, Robert M. Cannon
Summary: In elderly patients with early-stage hepatocellular carcinoma, orthotopic liver transplantation (OLT) provides a survival advantage compared to liver-directed ablative therapies alone.
JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS
(2022)
Article
Gastroenterology & Hepatology
Ji H. Nahm, Hye S. Lee, Haeryoung Kim, Sun Y. Yim, Ji-hyun Shin, Jeong E. Yoo, Sang H. Ahn, Jin S. Choi, Ju-Seog Lee, Young N. Park
Summary: This study developed a nomogram for predicting late recurrence of hepatocellular carcinoma (HCC) based on clinicopathological and molecular factors. The combination of pSTAT3, pERK1/2 and SYK immunoexpression with high lobular inflammatory activity and cirrhosis was found to predict late HCC recurrence.
LIVER INTERNATIONAL
(2021)
Article
Oncology
Linh M. Duong, Hui Cai, Martha J. Shrubsole, Christina E. Bailey, Kamran Idrees, Xiao-Ou Shu
Summary: Robotic surgery is not inferior to laparoscopic surgery in treating early-stage HCC and may be associated with improved long-term survival.
Article
Medicine, General & Internal
Wenying Jiang, Yunxing Wang, Changtao Yu, Deling Sui, Gang Du, Youchun Li
Summary: This study aimed to establish a new model to predict the prognosis of hepatocellular carcinoma (HCC). Differential expression profiles of mRNA, miRNA, and lncRNA between early and late stage HCC were analyzed, and key molecules associated with prognosis and important immune cell types in HCC were identified. A nomogram incorporating age, gender, stage, and all important factors was constructed to predict the survival of HCC.
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2023)
Article
Oncology
Henrique A. A. Lima, Yutaka Endo, Zorays Moazzam, Laura Alaimo, Mary Dillhoff, Alex Kim, Joal Beane, Aslam Ejaz, Jordan Cloyd, Vivian Resende, Timothy M. M. Pawlik
Summary: This study analyzed data from the National Cancer Database and found heterogenous effects of Medicaid expansion on the treatment of early-stage hepatocellular carcinoma. Specifically, there was an increased utilization of surgical treatment after expansion for patients without insurance or with Medicaid.
ANNALS OF SURGICAL ONCOLOGY
(2023)
Article
Chemistry, Physical
Ningtao Cheng, Bin Lou, Hongyang Wang
Summary: Early detection of hepatocellular carcinoma (HCC) is crucial for improving cure rates. Researchers have developed a novel nanobiosensing technique using surface-enhanced Raman scattering (SERS) to detect disease-relevant biomolecules in human serum. With the help of a deep learning algorithm, this technique can accurately capture key biomolecular phenotypes of early-stage HCC, showing high predictive accuracy, sensitivity, and specificity.
Article
Oncology
Van-Chu Nguyen, Trong Hieu Nguyen, Thanh Hai Phan, Thanh-Huong Thi Tran, Thu Thuy Thi Pham, Tan Dat Ho, Hue Hanh Thi Nguyen, Minh-Long Duong, Cao Minh Nguyen, Que-Tran Bui Nguyen, Hoai-Phuong Thi Bach, Van-Vu Kim, The-Anh Pham, Bao Toan Nguyen, Thanh Nhan Vo Nguyen, Le Anh Khoa Huynh, Vu Uyen Tran, Thuy Thi Thu Tran, Thanh Dang Nguyen, Dung Thai Bieu Phu, Boi Hoan Huu Phan, Quynh-Tho Thi Nguyen, Dinh-Kiet Truong, Thanh-Thuy Thi Do, Hoai-Nghia Nguyen, Minh-Duy Phan, Hoa Giang, Le Son Tran
Summary: This study demonstrates the potential of liquid biopsy assays based on ctDNA detection for early noninvasive detection of hepatocellular carcinoma (HCC). By analyzing cancer-related mutations and fragment length profiles, a classification model was built to differentiate HCC patients from healthy individuals, achieving high accuracy and sensitivity.
Review
Genetics & Heredity
An Tong, Xiangjie Di, Xia Zhao, Xiao Liang
Summary: In this article, we reviewed studies on the genomics and epigenetics of Ovarian clear cell carcinoma (OCCC), including gene mutation, copy number variations, DNA methylation, and histone modifications. OCCC is a rare subtype of epithelial ovarian cancer with unique molecular characteristics, specific biological and clinical behavior, poor prognosis, and high resistance to chemotherapy.
FRONTIERS IN GENETICS
(2023)
Article
Biochemical Research Methods
Nishant Kumar, Sumeet Patiyal, Shubham Choudhury, Ritu Tomer, Anjali Dhall, Gajendra P. S. Raghava
Summary: In this study, a high-precision method for predicting, designing, and scanning T1DM associated peptides was developed. By using alignment and machine learning techniques, this method provides accurate results. A web server and standalone server were also developed for practical use.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Sumeet Patiyal, Anjali Dhall, Khushboo Bajaj, Harshita Sahu, Gajendra P. S. Raghava
Summary: This paper describes a method called Pprint2 for predicting RNA-interacting residues in proteins. The study found that positively charged amino acids are more prominent in these residues. By using evolutionary profiles and convolutional neural network, the researchers developed a final model that performed well on the validation dataset.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Immunology
Ritu Tomer, Sumeet Patiyal, Anjali Dhall, Gajendra P. S. Raghava
Summary: In this study, computational tools were used to predict CD associated epitopes and motifs in protein-based foods and therapeutics. The analysis revealed that proline (P) and glutamine (Q) are highly abundant in CD associated peptides. Machine learning based models and motif-based approach were developed, and the best models and motifs were integrated into a web server and standalone software package CDpred.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Anjali Dhall, Sumeet Patiyal, Shubham Choudhury, Shipra Jain, Kashish Narang, Gajendra P. S. Raghava
Summary: Tumor Necrosis Factor alpha (TNF-a) is a pleiotropic pro-inflammatory cytokine that plays a crucial role in immune cell signaling pathways. This study aimed to predict and design TNF-a inducing epitopes using an in silico tool. The proposed models achieved high predictive performance in identifying TNF-a inducing peptides in both human and mouse hosts. Additionally, potential TNF-a inducing peptides were identified in proteins of HIV-1, HIV-2, SARS-CoV-2, and human insulin.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Leimarembi Devi Naorem, Neelam Sharma, Gajendra P. S. Raghava
Summary: This study aims to develop a model for accurately predicting IL-5 inducing antigenic regions in proteins. The study identified certain residues, such as Ile, Asn, and Tyr, that dominate IL-5 inducing peptides. Alignment-based methods provided high precision but limited coverage, while alignment-free methods, including machine learning models, improved performance. The hybrid model combining alignment-based and alignment-free methods achieved excellent results on the validation dataset.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Sadhana Tripathi, Neelam Sharma, Leimarembi Devi Naorem, Gajendra P. S. Raghava
Summary: Over the years, numerous vaccines have been developed against viral infections, but a comprehensive database providing detailed information on viral vaccines has been lacking. In this review, we introduce our freely accessible database ViralVacDB, which includes details of viral vaccines, their types, routes of administration, and approving agencies. This repository systematically covers additional information on 422 viral vaccines, including 145 approved vaccines and 277 in clinical trials. We believe that this database will greatly benefit researchers and professionals in pharmaceuticals and immuno-informatics.
DRUG DISCOVERY TODAY
(2023)
Article
Endocrinology & Metabolism
Dashleen Kaur, Akanksha Arora, Sumeet Patiyal, Gajendra Pal Singh Raghava
Summary: Hmrbase2 is a comprehensive platform that provides extensive information on hormones, which is essential for the therapeutics and diagnostics of hormonal diseases.
HORMONES-INTERNATIONAL JOURNAL OF ENDOCRINOLOGY AND METABOLISM
(2023)
Article
Biochemical Research Methods
Deriesha Gaines, Elia Brodsky, Harpreet Kaur, Gergana G. Nestorova
Summary: Advancing biomedical studies requires the development of advanced technologies for the rapid extraction of nucleic acid. We characterized an RNA capture pin (RCP) tool that enables non-destructive, rapid purification and enrichment of mRNA for genetic analysis. The RCP, functionalized with dT15 capture sequences, demonstrated high RNA capture efficiency and selectivity, with 70% messenger RNA, 10% ribosomal RNA, and 20% non-coding RNA. Evaluation of long-term stability showed that gold-thiol RNA capture pins retained 40% of the oligos after 4 months of storage, while streptavidin-coated pins showed a significant decrease in dT15 surface coverage after 2 weeks of storage at 4°C.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Xiang Deng, Shaoli Das, Harpreet Kaur, Evan Wilson, Kevin Camphausen, Uma Shankavaram
Summary: To assist cancer researchers in validation, exploration, analysis, and visualization of molecular profiles in cancer patient samples, we developed Glioma-BioDP, a user-friendly web tool for exploring and visualizing RNA and protein expression profiles in low- and high-grade gliomas. Glioma-BioDP includes expression data from The Cancer Genome Atlas and allows querying by mRNA, microRNA, and protein levels. Advanced query interface enables exploring the association of expression profiles with molecular and histological subtypes, surgical resection status, and survival. The tool facilitates the validation and generation of hypotheses for novel therapies and personalized treatment for gliomas.
BMC MEDICAL GENOMICS
(2023)
Review
Biochemistry & Molecular Biology
Nishant Kumar, Nisha Bajiya, Sumeet Patiyal, Gajendra P. S. Raghava
Summary: This paper provides a comprehensive review of the identification of B-cell epitopes (BCEs), covering experimental techniques, historical perspectives, and computational methods. The overall challenge of identifying BCEs is also discussed.
Article
Biochemical Research Methods
Akanksha Arora, Sumeet Patiyal, Neelam Sharma, Naorem Leimarembi Devi, Dashleen Kaur, Gajendra P. S. Raghava
Summary: Non-invasive diagnostics and therapies are important for minimizing patient discomfort. Exosomal proteins are identified as potential biomarkers. This study presents a model for predicting exosomal proteins based on machine learning and sequence motifs. The hybrid model outperforms existing methods and a web server and standalone software have been developed for researchers to predict and discover exosomal proteins.
Article
Genetics & Heredity
Poonam Sen, Harpreet Kaur
Summary: This study conducted a comparative transcriptomics analysis on seven asymptomatic and eight severe COVID-19 patients. The results showed differential gene expression between severe and asymptomatic patients, with the upregulation of biological processes and pathways related to viral infection and inflammation in severe patients. These findings can aid researchers in finding effective therapeutic targets and assist clinicians in managing COVID-19 patients and their post-COVID-19 effects.
Article
Biochemical Research Methods
Akshara Pande, Sumeet Patiyal, Anjali Lathwal, Chakit Arora, Dilraj Kaur, Anjali Dhall, Gaurav Mishra, Harpreet Kaur, Neelam Sharma, Shipra Jain, Salman Sadullah Usmani, Piyush Agrawal, Rajesh Kumar, Vinod Kumar, Gajendra P. S. Raghava
Summary: In the past 30 years, numerous protein features have been discovered for protein annotation. To integrate these features, we developed a method called Pfeature, which can compute over 200,000 features for predicting protein function, residue-level annotation, and chemically modified peptides. Pfeature includes six major modules: composition, binary profiles, evolutionary information, structural features, patterns, and model building.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biology
Anjali Dhall, Sumeet Patiyal, Harpreet Kaur, Gajendra P. S. Raghava
Summary: Advancements in cancer immunotherapy have shown significant outcomes in treating cancers. To design effective immunotherapy, it's important to understand immune response of a patient based on its genomic profile. However, analyses to do that requires proficiency in the bioinformatic methods. Here, we are providing a web-based resource that gives scientists with no bioinformatics expertise, the ability to obtain the prognostic biomarkers for different cancer types at different levels.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)