Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies

Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

Under normal conditions, cells of almost all tissue types express the same predominant canonical transcript isoform at each gene locus. In cancer, however, splicing regulation is often disturbed, leading to cancer-specific switches in the most dominant transcripts (MDT). To address the pathogenic impact of these switches, we have analyzed isoform-specific protein-protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the International Cancer Genomics Consortium (ICGC). Our study revealed large variations in the number of cancer-specific MDT (cMDT) with the highest frequency in cancers of female reproductive organs. Interestingly, in contrast to the mutational load, cancers arising from the same primary tissue had a similar number of cMDT. Some cMDT were found in 100% of all samples in a cancer type, making them candidates for diagnostic biomarkers. cMDT tend to be located at densely populated network regions where they disrupted protein interactions in the proximity of pathogenic cancer genes. A gene ontology enrichment analysis showed that these disruptions occurred mostly in protein translation and RNA splicing pathways. Interestingly, samples with mutations in the spliceosomal complex tend to have higher number of cMDT, while other transcript expressions correlated with mutations in non-coding splice-site and promoter regions of their genes. This work demonstrates for the first time the large extent of cancer-specific alterations in alternative splicing for 27 different cancer types. It highlights distinct and common patterns of cMDT and suggests novel pathogenic transcripts and markers that induce large network disruptions in cancers

CanIsoNet: a database to study the functional impact of isoform switching events in diseases

MOTIVATION: Alternative splicing, as an essential regulatory mechanism in normal mammalian cells, is frequently disturbed in cancer and other diseases. Switches in the expression of most dominant alternative isoforms can alter protein interaction networks of associated genes giving rise to disease and disease progression. Here, we present CanIsoNet, a database to view, browse and search isoform switching events in diseases. CanIsoNet is the first webserver that incorporates isoform expression data with STRING interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in various diseases. RESULTS: Data in CanIsoNet can be browsed by disease or searched by genes or isoforms in annotation-rich data tables. Various annotations for 11 811 isoforms and 14 357 unique isoform switching events across 31 different disease types are available. The network density score for each disease-specific isoform, PFAM domain IDs of disrupted interactions, domain structure visualization of transcripts and expression data of switched isoforms for each sample is given. Additionally, the genes annotated in ClinVar are highlighted in interactive interaction networks. AVAILABILITY AND IMPLEMENTATION: CanIsoNet is freely available at https://www.caniso.net. The source codes can be found under a Creative Common License at https://github.com/kahramanlab/CanIsoNet_Web. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online

Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets

BACKGROUND Immune checkpoint inhibitors and antiangiogenic agents are used for first-line treatment of advanced papillary renal cell carcinoma (pRCC) but pRCC response rates to these therapies are low. OBJECTIVE To generate and characterise a functional ex vivo model to identify novel treatment options in advanced pRCC. DESIGN, SETTING, AND PARTICIPANTS We established patient-derived cell cultures (PDCs) from seven pRCC samples from patients and characterised them via genomic analysis and drug profiling. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Comprehensive molecular characterisation in terms of copy number analysis and whole-exome sequencing confirmed the concordance of pRCC PDCs with the original tumours. We evaluated their sensitivity to novel drugs by generating drug scores for each PDC. RESULTS AND LIMITATIONS PDCs confirmed pRCC-specific copy number variations such as gains in chromosomes 7, 16, and 17. Whole-exome sequencing revealed that PDCs retained mutations in pRCC-specific driver genes. We performed drug screening with 526 novel and oncological compounds. Whereas exposure to conventional drugs showed low efficacy, the results highlighted EGFR and BCL2 family inhibition as the most effective targets in our pRCC PDCs. CONCLUSIONS High-throughput drug testing on newly established pRCC PDCs revealed that inhibition of EGFR and BCL2 family members could be a therapeutic strategy in pRCC. PATIENT SUMMARY We used a new approach to generate patient-derived cells from a specific type of kidney cancer. We showed that these cells have the same genetic background as the original tumour and can be used as models to study novel treatment options for this type of kidney cancer

Testes development and maturity classification of albacore (Thunnus alalunga (Bonaterre, 1788)) from the Eastern Mediterranean Sea

The criteria of testicular maturity during the spawning season and for maturity rates are described according to age for 140 male albacore (Thunnus alalunga, Bonnaterre, 1788) sampled between April and August, 2002-2008 in the Eastern Mediterranean Sea. Histology of gonad samples was used to determine maturity status. Spermatogenesis and its relation to reproductive biology are reported. Fish ranged in fork length (FL) from 63 to 90 cm. The reproductive classes were based upon changes in the testicular morphology and stages of the germinative cells, i.e. immature, developing, maturing, spawning, and spent. Mature stages of testes including the smallest sample of a 63 cm male were observed from May to August of each year during the study. The reported evidence indicates that the size and age of first sexual maturity values of males of the Eastern Mediterranean population are nearly the same as in the Western Mediterranean population, but lower than in the Atlantic stock. The results of this histological investigation, conducted for the first time on this species in the Mediterranean Sea, will enable more precise future estimations for sustainability of the male albacore stock in the Eastern Mediterranean

Doğu Akdeniz’de Uzun Kanat Orkinos Balığının Bazı Populasyon Parametreleri

Bu çalışmada, ekonomik yönden yüksek değere sahip olan uzun kanat orkinos balığının büyüme, üreme ve beslenme özelliklerinin belirlenmesi amaçlanmıştır. Antalya Körfezi’nde, Mayıs 2006 ve Temmuz 2008 tarihleri arasındaki balıkçılık sezonunda toplam 819 adet uzun kanat orkinos bireyi toplanılmıştır. İncelenen balık boyları 55.5-101 cm ve ağırlıkları ise 3.93-12.75 kg arasında değişmektedir. Çatal boy - total ağırlık ilişkisi dişi bireyler için W= 0.00042L2.246, erkek bireyler için W= 0.00022L2.396 ve tüm örnekler için W= 0.00016L2.467 bulunmuştur. Dişi ve erkeklerde negatif allometrik büyüme gözlenmiştir. Yaş ve büyüme analizi için dorsal yüzgecin ilk diken ışını alınmıştır. Avlanan bireylerin yaşları 1+ ile 9+ yaşlar arasında değişmektedir. En baskın yaş grupları, 4+ (29.43%), 5+ (27.79%) ve 3+ (23.43%) yaş gruplarıdır. Von Bertalanffy’nin boyca ve ağırlıkça büyüme sabitlerinden L∞ = 93.198 cm, W∞ = 11.552, k = 0.295 yıl-1 ve to = -1.213 yıl olarak tespit edilmiştir. Erkek bireylerin büyümesi dişilere göre daha fazladır. Gonad histolojik analizinden, ortalama gonadosomatik indeks (GSI) ve kondisyon faktörü (K) değerlerinin aylık değişiminden, bu balıkların Haziran-Temmuz döneminde yumurtladıkları saptanmıştır. Balıkların midelerinde bulunan en büyük av grupları %95.1 cephalopodlar, %47.5 teleost ve %39.3 crustaceans oluşturmaktadır. Toplam 14 türe ait 633 birey tespit edilmiştir. Cephalopodlardan başlıca besin grupları içerisinde sepiolida ordosundan %56.40 Heteroteuthis dispar ilk sırada olup, teuthida ordosundan Onychoteuthis banksii %12.32 ile takip etmektedir. Tespit edilen türler genellikle yavaş hareket eden küçük boylu bireylerdir. Ayrıca incelenen midelerde ~%10 oranında beyaz plastik parçalarına rastlanmış olması açık denizlerde bile olsa kirliliğin denizlerdeki en üst predadatörlere kadar uzanabiliyor olduğunu göstermektedir