Biology subjects

Montanes, J. C.

Publications and source records attributed to Montanes, J. C..

4 recordsLinked to original sources

bioRxiv2026

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

Classical cancer germline-antigens (CGAs) are proteins that are expressed in the male germinal line but not in somatic tissues, and that can also become expressed in tumors. However, the vast majority of testis-specific transcripts are long non-coding RNAs (lncRNAs) rather than protein-coding genes. Since recent studies have shown that many lncRNAs contain non-canonical open reading frames (ncORFs) that are translated into small proteins, or microproteins, there could be a large class of non-canonical cancer-germline antigens (ncCGAs) that remains to be discovered. Here, we integrate ribosome profiling from human testis and cancer cell lines with paired tumor/normal transcriptomes from 917 patients across eight common cancer types to define a comprehensive catalog of ncCGAs. This set comprises 235 ncCGAs encoded by lncRNAs or mRNA untranslated regions (5UTRs and 3UTRs), compared to 192 canonical CGAs (cCGAs) with similar expression patterns. We show that ncCGAs are evolutionary young, consistent with recent de novo emergence in the rapidly evolving male germline. Moreover, a large fraction is expressed across multiple patients and cancer types, indicating recurrent reactivation mechanisms in tumors. We further find that ncCGAs are frequently located in cancer-amplified regions or associated with MYC or E2F-regulated pathways, which may explain their expression in cancer. Finally, we provide strong evidence that a subset of ncCGAs give rise to potentially immunogenic HLA class I bound peptides. Together, our results describe a previously unexplored class of tumor-restricted antigens with potential applications in cancer immunotherapy.

cancer biology↗

bioRxiv2026

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The analysis of ribosome profiling (Ribo-Seq) data has provided evidence that many eukaryotic mRNAs contain translated upstream or downstream ORFs (uORFs/dORFs), but the biological significance of this translation activity remains, for the most part, unknown. One of the principal limitations has been the lack of Ribo-Seq data from several closely related species, precluding the identification of cases in which translation is phylogenetically conserved. Here, by combining Ribo-Seq data from 100 different experiments, we identify 2,332 translated uORFs and 1,008 translated dORFs in S. cerevisiae, which result in microproteins that tend to be highly hydrophobic or positively charged. To study their phylogenetic conservation, we have generated Nanopore direct RNA sequencing data, together with Ribo-Seq data, from six additional Saccharomyces species, spanning an evolutionary period of around 16 million years. We have identified 195 translated S. cerevisiae uORFs that are also translated in other Saccharomyces species; these uORFs are translated at levels comparable to the main coding sequence and display signatures of purifying selection at the level of the encoded microproteins. In contrast, dORFs are translated at very low levels and they are rarely conserved, suggesting much more limited microprotein functionalization. We have also discovered that uORF translation is associated with the formation of alternative transcript isoforms encompassing the region containing the uORFs but not the main protein coding sequence, implying that some microproteins can be produced independently of the main protein product. This work significantly advances our understanding of how initially pervasive uORF translation can result in new microproteins, providing many new candidates for further functional studies.

genomics↗

bioRxiv2024

GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing

Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For more than twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, becoming a foundation for biomedical and genomics communities worldwide. Nevertheless, collections of important yet poorly-understood gene classes like long non-coding RNAs (lncRNAs) remain incomplete and scattered across multiple, uncoordinated catalogs. To address this, GENCODE has undertaken the most comprehensive lncRNA annotation effort to date. This is founded on the manually supervised computational annotation of full-length targeted long-read sequencing, on matched embryonic and adult tissues, of orthologous regions in human and mouse. Altogether 17,931 human genes (140,268 transcripts) and 22,784 mouse genes (136,169 transcripts) have been added to the GENCODE catalog representing a 2-fold and 6-fold growth in transcripts, respectively - the greatest increase in the number of annotated human genes since the sequencing of the human genome. Our targeted design assigned human-mouse orthologs at a rate beyond previous studies, tripling the number of human disease-associated lncRNAs that have mouse orthologs. Novel lncRNA genes consistently exhibit biological signals of functionality, and they greatly enhance the functional interpretability of the human genome. While poorly expressed in bulk RNA-Seq samples, many of them are highly expressed in specific cell populations, maybe even contributing to cell-type determination. The expanded GENCODE lncRNA annotations mark a critical step toward deciphering the human and mouse genomes.

genomics↗

bioRxiv2021

siRNA enrichment in Argonaute 2-depleted Blattella germanica

BackgroundRNA interference (RNAi) is a cellular mechanism used to fight various threats, including transposons, aberrant RNA, and some types of viruses. It relies on dsRNA detection and, through a mechanism involving Dicer-2 (Dcr-2) and Argonaute 2 (AGO2), together with a small RNA fragment (siRNA) as a complementary guide, binds to an RNA and cleaves it. MethodsUsing the cockroach Blattella germanica as a model, we examined AGO2 activity by depleting its mRNA levels using RNAi and analyzing the phenotypes produced. ResultsSilencing AGO2 expression had no remarkable effect on nymphal development or reproduction. dsRNA treatment triggered an immediate and transitory increase in AGO2 expression, independently of Dcr-2 action. In addition, we analyzed the siRNAs generated after injecting a heterologous dsRNA in control and AGO2-depleted animals. The results revealed that siRNAs were distributed non-uniformly along the dsRNA sequence. In AGO2-depleted animals, the proportion of 22 nucleotide reads was higher and accumulations of reads appeared in areas less well-represented in the controls. We also detected a slight preference for cytosine as the first nucleotide in controls to be lost in AGO2-depleted individuals. Conclusions/General significanceThe siRNAs produced from a dsRNA are heterogeneously distributed along the length of the dsRNA and this arrangement depends on the sequence. AGO2 exerts its role as nuclease on the siRNA duplexes independently of its action on the homologous mRNA. This study sheds light on an extremely useful process for reverse genetics in laboratories, in addition to the design of more effective, specific, and eco-friendly pest-control strategies. Highlights- RNA interference is used to fight cellular threats including transposons and viruses - Silencing AGO2 in Blattella germanica does not affect development or reproduction - siRNA distribution along the dsRNA sequence is non-uniform and sequence dependent - AGO2 depletion increased the proportion of 22 nt reads in certain areas

physiology↗