Merja Perälä

Oxidative stress response (OSR) is suggested as a therapeutic target in triple negative breast cancer (TNBC). However, the cell type specificity and spatial distribution of OSR genes and proteins remain poorly defined. We re-analyzed public datasets, demostrating high OSR gene expression in TNBC tumor cells. We generated a multiplex immunofluorescence dataset of 345 TNBC samples that showed OSR proteins GCLC and NQO1 are differentially expressed across tumor, immune, and stromal cells, and elevated in inflamed regions. We identified a mesenchymal-like tumor cell state characterized by co-expression of GCLC and vimentin (GCLC⁺VIM⁺), with increased proliferation and reduced anastasis-associated signatures, suggesting a vulnerability to chemotherapy. Consistently, TNBC cell lines with higher GCLC expression showed increased sensitivity to cisplatin. Moreover, patients with higher proportions of GCLC⁺VIM⁺ tumor cells had longer overall survival. Our findings indicate that OSR proteins are expressed in spatially and phenotypically distinct tumor microenvironments, and that the GCLC⁺VIM⁺ tumor cell state is associated with favorable outcomes in TNBC.

Inhibiting oxidative stress response (OSR) proteins has been suggested as a therapeutic strategy in triple negative breast cancer (TNBC). However, the cell type specificity and spatial distribution of OSR genes and proteins, such as GCLC and NQO1, is unknown. Using single cell and spatial transcriptomics datasets we found that OSR genes were highly expressed in TNBC tumor cells, which localized in spatial clusters. Multiplex immunofluorescence imaging of 345 TNBC samples from 186 patients demonstrated that OSR proteins GCLC and NQO1 exhibit distinct expression profiles across tumor, immune, and stromal cell populations and are elevated in inflamed histological regions. Tumor cell OSR protein expression was associated with the composition of the adjacent cellular neighborhood. Furthermore, we identified GCLC and vimentin positive (GCLC+VIM+) mesenchymal-like tumor cells, residing near immune cells and exhibiting increased proliferation and decreased anastasis signatures, suggesting sensitivity to chemotherapy. Across a panel of thirteen TNBC cell lines, GCLC expression was positively correlated with sensitivity to cisplatin. Cox regression analysis revealed that patients with higher proportions of GCLC+VIM+ tumor cells had a longer overall survival. Collectively, our results demonstrate that individual OSR proteins are expressed in distinct microenvironments and tumor cell states, potentially contributing to patient outcomes.

Finland has steadily developed its biobanking infrastructures since the early 2010s. This article presents a systematic overview of the number of biological samples that have been provided for research since 2013 when the Finnish Biobank Act came into force. Using data from individual biobanks and from permits issued by Fimea (formerly Valvira), we present the most up-to-date and complete account of sample use at a national level. Between 2014 and 2023 a total of 1,474,881 samples were provided through 998 sample requests. A better understanding of the use of biological samples at the national level can help highlight the important impact biobanking has as an infrastructure for supporting research. We argue that developing standards can help in developing national biobanking strategies and identify areas where biobanking can be further developed. We also conclude that the ability to combine tissue samples and health data flexibly and efficiently is essential and needs to be secured also within the context of the European Health Data Space (EHDS).

Cartilage collagens type II and type IX exist in two alternative forms which arise from alternative splicing and alternative use of promoters, respectively. In the present study we analyzed temporal and spatial expression patterns of the two isoforms of type II and type IX collagen transcripts as well as those of α2(IX) and α3(IX) collagen mRNAs in limb cartilages and eyes during mouse embryonic development. Northern and RNase protection assays revealed temporal coregulation of the two alternative isoforms in limbs, but not in the eye where no long form of α1(IX) collagen mRNA was detected. Although in situ hybridization of limbs revealed identical expression patterns of the long form of type II collagen and the short form of α1(IX) collagen mRNA in the perichondrium and periosteum of 14.5–18.5-day embryos, the patterns were distinctly different at day 12.5 of development: the long form of type II collagen mRNA was expressed throughout the developing cartilaginous anlage whereas the short form of α1(IX) collagen mRNA was expressed in the surrounding mesenchyme. Some differences were also detected in the temporal and spatial expression patterns between the α1(IX), α2(IX), and α3(IX) collagen mRNAs. In the eyes, α2(IX) collagen mRNA had highest expression levels at day 12.5, whereas α1(IX) and α3(IX) collagen mRNAs peaked later, at day 16.5. In the limbs, α1(IX) and α3(IX), but not α2(IX), collagen mRNAs were detected in periosteal cells after 16.5 days of development. In transgenic Del1 mice, harboring type II collagen transgenes with a small deletion mutation, expression of mutant mRNA affected neither the alternative splicing of wild-type or mutant transcripts nor the ratio of the two alternative forms of the α1(IX) collagen mRNA. Despite some distinct similarities, the two alternative forms of type II and type IX collagen must, therefore, be under differential control during mouse development.

Several techniques were used to study the co-ordination of mRNA levels for five constituent chains of cartilage collagen fibrils during mouse development. Short cDNA clones were first constructed for mouse and human α3(IX) and for mouse proα1(XI) collagen mRNA species. Northern analysis of developing mouse embryos revealed that the mRNA species for α1, α2 and α3 chains of type IX collagen peaked earlier than those for proα1(II) and proα1(XI) collagen chains. Quantification of these mRNA species by slot-blot hybridization confirmed this developmental regulation: the mRNA ratios for type II/type IX/type XI collagens changed from 5.7:1:0.6 (at embryonic day 12.5) to 10.6:1:0.9 (in newborn mice). However, the genes coding for the three chains of type IX collagen seemed to be under more co-ordinated regulation during mouse development. In addition to high mRNA levels in cartilages and the eye, low levels of type IX collagen transcripts were identified in brain and skin of newborn mouse using RNase protection and reverse transcriptase–PCR assays. Finally, hybridization in situ revealed identical tissue distributions of the three type IX collagen mRNA species during early chondrogenesis but somewhat more widespread expression of the α1(IX) and α3(IX) mRNA species during endochondral ossification at day 16.5 of embryonic development. These results suggest a relatively tight co-ordination of the α1(IX), α2(IX), and α3(IX) collagen mRNA species in chondrocytes, but a lack of co-ordination in several non-cartilaginous tissues.