The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens

D Oreper, S Klaeger, S Jhunjhunwala… - Seminars in …, 2023 - Elsevier
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer
therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of …

Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ

Y Long, B Zhang, S Tian, JJ Chan, J Zhou, Z Li… - Genome …, 2023 - genome.cshlp.org
Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with
different 3′ ends, which is dynamic across different cell types or conditions. Many …

Therapeutic targeting of CPSF3-dependent transcriptional termination in ovarian cancer

P Shen, K Ye, H Xiang, Z Zhang, Q He, X Zhang… - Science …, 2023 - science.org
Transcriptional dysregulation is a recurring pathogenic hallmark and an emerging
therapeutic vulnerability in ovarian cancer. Here, we demonstrated that ovarian cancer …

RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in …

M Okubo, S Noguchi, T Awaya, M Hosokawa, N Tsukui… - Human genetics, 2023 - Springer
Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain
genetically undiagnosed, because intronic variations are not detected by standard methods …

ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues

X Ma, S Cheng, R Ding, Z Zhao, XD Zou… - Nucleic Acids …, 2023 - academic.oup.com
Functional interpretation of disease-associated non-coding variants remains a significant
challenge in the post-GWAS era. Our recent study has identified 3′ UTR alternative …

Crosstalk between metabolic and epigenetic modifications during cell carcinogenesis

Y Gao, X Zhang, Y Du, T Ni, S Hao - iScience, 2024 - cell.com
Genetic mutations arising from various internal and external factors drive cells to become
cancerous. Cancerous cells undergo numerous changes, including metabolic …

Intergenic splicing-stimulated transcriptional readthrough is suppressed by nonsense-mediated mRNA decay in Arabidopsis

Y Kurihara, Y Makita, M Kawauchi… - Communications …, 2022 - nature.com
Recent emerging evidence has shown that readthrough transcripts (RTs), including
polycistronic mRNAs, are also transcribed in eukaryotes. However, the post-transcriptional …

Cooperative strand displacement circuit with dual-toehold and bulge-loop structure for single-nucleotide variations discrimination

D Bai, X Zhou, W Luo, H Yu, S Bai, Y Wu, L Song… - Biosensors and …, 2022 - Elsevier
Nucleic acid nanotechnologies based on toehold-mediated strand displacement are ideally
suited for single-nucleotide variations (SNVs) detection. But only a limited number of means …

The landscape of cryptic antisense transcription in human cancers reveals an oncogenic noncoding RNA in lung cancer

Z Zhao, Y Chen, X Cheng, L Huang, H Wen, Q Xu… - Science …, 2023 - science.org
Cryptic transcription initiation has been previously linked to activation of oncogenic
transcripts. However, the prevalence and impact of cryptic antisense transcription from the …

Recurrent disruption of tumour suppressor genes in cancer by somatic mutations in cleavage and polyadenylation signals

Y Kainov, F Hamid, EV Makeyev - eLife, 2024 - elifesciences.org
The expression of eukaryotic genes relies on the precise 3'-terminal cleavage and
polyadenylation of newly synthesized pre-mRNA transcripts. Defects in these processes …