Exploring transcription modalities from bimodal, single-cell RNA sequencing data DOI Creative Commons
Enikő Regényi, Mir‐Farzin Mashreghi,

Christof Schütte

et al.

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(4)

Published: Sept. 28, 2024

Abstract There is a growing interest in generating bimodal, single-cell RNA sequencing (RNA-seq) data for studying biological pathways. These are predominantly utilized understanding phenotypic trajectories using velocities; however, the shape information encoded two-dimensional resolution of such not yet exploited. In this paper, we present an elliptical parametrization RNA-seq data, from which derived statistics that reveal four different modalities. modalities can be interpreted as manifestations changes rates splicing, transcription or degradation. We performed our analysis on cell cycle and colorectal cancer dataset. both datasets, found genes picked up by differential gene expression (DGEA), consequently unnoticed, visibly delineate phenotypes. This indicates that, addition to DGEA, searching exhibit discovered could aid recovering set phenotypes apart. For communities biomarkers cellular phenotyping, bimodal broaden search space genes, furthermore, allow incorporating processing into regulatory analyses.

Language: Английский

Mitochondrial Dynamics Regulators in Cancer Metabolism and Progression DOI Creative Commons
Ahmed Shaaban,

Al-Hassan Soliman Wadan,

Mohamed El‐Sadek

et al.

Mitochondrial Communications, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Mitochondrial metabolism in laryngeal cancer: Therapeutic mechanisms and prospects DOI

Yunjing Hou,

Xin Yang, Hongxue Meng

et al.

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, Journal Year: 2025, Volume and Issue: unknown, P. 189335 - 189335

Published: April 1, 2025

Language: Английский

Citations

0
Unraveling Crucial Mitochondria-Related Genes in the Transition from Ulcerative Colitis to Colorectal Cancer DOI Creative Commons

Fanqi Wang,

Limin Xie,

Yuan Tang

et al.

Drug Design Development and Therapy, Journal Year: 2024, Volume and Issue: Volume 18, P. 3175 - 3189

Published: July 1, 2024

Purpose: To clarify the significance of mitochondria-related differentially expressed genes (MTDEGs) in UC carcinogenesis through a bioinformatics analysis and provide potential therapeutic targets for patients with associated colorectal cancer. Methods: Microarray GSE37283 was utilized to investigate (DEGs) neoplasia (UCN). MTDEGs were identified by intersecting DEGs human mitochondrial genes. Utilizing LASSO random forest analyses, we three crucial Subsequently, using ROC curve predictive ability key Following, confirmed AOM/DSS mice model Real-time PCR. Finally, single-sample gene set enrichment (ssGSEA) employed explore correlation between hub immune cells infiltration carcinogenesis. Results: The (HMGCS2, MAVS, RDH13) may exhibit significant diagnostic specificity transition from UCN. PCR assay further that expressions HMGCS2 RDH13 significantly downregulated UCN than mice. ssGSEA revealed highly CD56dim natural killer cells. Conclusion: RDH13, HMGCS2, MAVS become indicators biomarkers Our research has enhance our understanding mechanisms underlying UC. Keywords: ulcerative colitis, cancer, autoimmunity diseases, mitochondria, NKT

Language: Английский

Citations

1
Prognostic Prediction and Immune Microenvironment Characterization in Uveal Melanoma: A Novel Mitochondrial Metabolism-Related Gene Signature DOI Creative Commons

W.-J. Cai,

Ru-Ru Chen,

Zi-Bin Liu

et al.

ACS Omega, Journal Year: 2024, Volume and Issue: 9(42), P. 43034 - 43045

Published: Oct. 10, 2024

Uveal Melanoma (UM), a highly aggressive and metastatic intraocular cancer with strong propensity for liver metastasis, presents limited therapeutic alternatives unfavorable survival outcomes. Despite its low incidence, the underlying mechanisms of UM pathogenesis precise role mitochondrial metabolism in remain inadequately understood. Utilizing Cox proportional hazards regression analysis was used to assess prognostic relevance, consensus clustering employed molecular subtyping. A risk signature constructed using Least Absolute Shrinkage Selection Operator (LASSO) regression. We further conducted comparative analyses on clinicopathological characteristics, somatic mutation profiles, drug sensitivity, gene expression patterns, tumor microenvironment features across different subtypes. Moreover, nomogram developed evaluated. Among 1234 mitochondria metabolism-related genes (MMRGs), 343 were identified as significantly associated prognosis UM. These prognosis-associated MMRGs facilitated classification into two distinct subtypes, which displayed notable differences pathological staging. Furthermore, an index termed MMRGs-derived (MMI) derived from eight MMRGs, serving quantitative measure poor MMI demonstrated significant associations mutations, responsiveness, microenvironment, where higher levels corresponded worse prognosis, advanced stages, increased immune cell infiltration. The built upon provided potential tool clinical assessment patients. This study value predicting stratification within UM; however, additional basic research is warranted validate their applicability elucidate related mechanisms.

Language: Английский

Citations

1
Mitochondria: a crucial factor in the progression and drug resistance of colorectal cancer DOI Creative Commons
Ying Zhao,

Xiaomin Guo,

Li Zhang

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 23, 2024

Colorectal cancer (CRC), as one of the malignant tumors with highest incidence and mortality rates worldwide in recent years, originating primarily from mucosal tissues colon or rectum, has potential to rapidly develop into invasive cancer. Its pathogenesis is complex, involving a multitude factors including genetic background, lifestyle, dietary habits. Early detection treatment are key improving survival for patients CRC. However, pervasive problem that can become severely resistant treatment, which greatly increases complexity challenge treatment. Therefore, unraveling overcoming resistance CRC focus research. Mitochondria, energy centers cell, play crucial role cellular metabolism, supply, apoptosis process. In CRC, Mitochondrial dysfunction not only impairs normal cell function but also promotes tumor resistance. deep understanding relationship between mitochondrial mechanisms development, well by it chemotherapy drugs, development targeted therapies, enhancing drug efficacy, outcomes quality life patients.

Language: Английский

Citations

1
Targeting mitochondrial damage: shining a new light on immunotherapy DOI Creative Commons
Wenjuan Zeng, Menghui Wang, Yuxin Zhang

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 15

Published: July 22, 2024

Mitochondrial damage has a particular impact on the immune system and tumor microenvironment, which can trigger cell stress, an inflammatory response, disrupt function, thus all of accelerate progression tumor. Therefore, it is essence to comprehend how function microenvironment interact with mitochondrial dysfunction for cancer treatment. Preserving integrity mitochondria or regulating cells, such as macrophages, may enhance efficacy therapy. Future research should concentrate interactions among mitochondria, system, identify new therapeutic strategies.

Language: Английский

Citations

0
HOXC11-mediated regulation of mitochondrial function modulates chemoresistance in colorectal cancer DOI Creative Commons

Shicheng Chu,

Xiang Ren,

Lianmeng Cao

et al.

BMC Cancer, Journal Year: 2024, Volume and Issue: 24(1)

Published: July 30, 2024

Chemoresistance remains a significant challenge in colorectal cancer (CRC) treatment, necessitating deeper understanding of its underlying mechanisms. HOXC11 has emerged as potential regulator various cancers, but role CRC chemoresistance unclear.

Language: Английский

Citations

0
The role of soluble epoxide hydrolase in the intestine DOI

Yanbei Ren,

Ting Wang, Jiuheng Yin

et al.

Cell Biology International, Journal Year: 2024, Volume and Issue: 48(11), P. 1612 - 1620

Published: Aug. 20, 2024

The soluble epoxide hydrolase (sEH; encoded by the EPHX2 gene) is an α/β fold protein that is, widely distributed throughout body. Recent studies have highlighted sEH, in metabolism of polyunsaturated fatty acids, plays a part pathogenesis various diseases, including cardiovascular disease, Alzheimer's disease and intestine-associated disease. This review discusses current findings on role sEH development intestine- colitis, colorectal cancer, other intestinal as well potential underlying mechanisms involved.

Language: Английский

Citations

0
Laherradurin Inhibits Colorectal Cancer Cell Growth by Induction of Mitochondrial Dysfunction and Autophagy Induction DOI Creative Commons
Izamary Delgado-Waldo, Svetlana Dokudovskaya,

Yahir A. Loissell-Baltazar

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(19), P. 1649 - 1649

Published: Oct. 3, 2024

LAH, an acetogenin from the Annonaceae family, has demonstrated antitumor activity in several cancer cell lines and vivo models, where it reduced tumor size induced programmed death. We focused on effects of LAH mitochondrial dynamics, mTOR signaling, autophagy, apoptosis colorectal (CRC) cells to explore its anticancer potential. Methods: CRC were treated with respiration glycolysis measured using Seahorse XF technology. The changes dynamics observed through fluorescent imaging, while Western blot analysis was used examine key autophagy markers. Results: significantly inhibited complex I activity, inducing ATP depletion a compensatory increase glycolysis. This disruption caused fragmentation, trigger for as shown by increased LC3-II expression suppression. Apoptosis also confirmed cleavage caspase-3, contributing viability. Conclusions: LAH’s are driven function, triggering both apoptosis. These findings highlight potential therapeutic compound further exploration treatment.

Language: Английский

Citations

0
CYP19A1 regulates chemoresistance in colorectal cancer through modulation of estrogen biosynthesis and mitochondrial function DOI Creative Commons
Yang Wang, Qiang Ji, N. Cao

et al.

Cancer & Metabolism, Journal Year: 2024, Volume and Issue: 12(1)

Published: Oct. 28, 2024

Abstract Chemoresistance remains a major challenge in the effective treatment of colorectal cancer (CRC), contributing to poor patient outcomes. While molecular mechanisms underlying chemoresistance are complex and multifaceted, emerging evidence suggests that altered mitochondrial function hormone signaling play crucial roles. In this study, we investigated role CYP19A1, key enzyme estrogen biosynthesis, regulating CRC. Using combination vitro functional assays, transcriptomic analysis, clinical data mining, demonstrate CYP19A1 expression is significantly upregulated CRC cells patient-derived samples compared normal controls. Mechanistically, found regulates through modulation I activity, which mediated by CYP19A1-dependent biosynthesis. Notably, targeted inhibition using specific inhibitors effectively reversed chemotherapeutic drugs. Moreover, analysis TCGA dataset revealed high correlates with overall survival chemotherapy-treated patients. Taken together, our findings uncover novel for signaling, highlight potential targeting CYP19A1/estrogen/complex axis as therapeutic strategy overcome improve

Language: Английский

Citations

0