Selective breeding is a cornerstone of genetic improvement in aquaculture, yet long term documentation of realized genetic progress in marine fish remains limited. This study quantifies two decades of genetic improvement for growth in gilthead sea bream (Sparus aurata), drawing on more than twenty years of data (2002 to 2023) from an ongoing large scale commercial breeding program in Greece. A total of 123,992 fish from 1843 full sib families, spanning approximately five to six overlapping generations, were recorded for harvest body weight. Genetic parameters and trends were estimated using a linear mixed animal model that included genetic group effects and relevant environmental terms. A moderate heritability of 0.35 +/- 0.02 was estimated for harvest weight, supporting effective response to selection. Predicted breeding values increased steadily over time, corresponding to a cumulative gain of 248 g (76.1%) in harvest weight across the assessed period, equivalent to an average annual improvement of 3.6% or about 15% per generation. Accumulated inbreeding remained low (1.3% in 2023), with a mean increase of 0.39% per generation, demonstrating sustainable management of genetic diversity. These results provide the first long term evidence of sustained genetic progress for growth in gilthead sea bream, highlighting the capacity of structured and well managed selective breeding programs to deliver continuous and economically relevant improvement while maintaining population integrity, supporting more efficient and sustainable aquaculture production systems.

Multiple myeloma (MM) is a hematological malignancy originating from plasma cells. Genetically, MM is categorized into two subtypes: hyperdiploid and non-hyperdiploid tumors, with distinct chromosomal characteristics. Human myeloma cell lines (HMCLs) are instrumental in understanding MM and identifying therapeutic targets. However, their utility depends on their resemblance to patient-derived cells. We analyzed protein expression of cell surface markers, including myeloma drug targets and immunotherapy-relevant markers, in nine HMCLs using flow cytometry. RNAseq analysis was performed to correlate protein expression with transcriptomic data. While five cell surface markers (CD47, CD49d, CD138, CD269 (BCMA), and GPRC5D) were highly expressed and three (CD19, CD20, and CD117) were low or negative across cell lines, heterogenous expression was observed for the 16 remaining markers. A comparative study with patient-derived transcriptomic data indicated that four of our six in-house HMCLs closely resembled patient disease. Furthermore, our hyperdiploid HMCLs correlated better with hyperdiploid than non-hyperdiploid patient samples. Here, we also describe three previously uncharacterized HMCLs; IH-1, URVIN and FOLE. Our findings underscore the importance of evaluating surface protein expression in HMCLs when modeling MM. The observed variations in expression levels emphasize the need for a strategic selection of cell lines based on the study’s objectives.

Penaeid shrimp farming plays a pivotal role in ensuring future food security and promoting economic sustainability. Compared to the extensive long history of domestication observed in terrestrial agriculture species, the domestication and selective breeding of penaeids are relatively recent endeavors. Selective breeding aimed at improving production traits holds significant promise for enhancing efficiency and reducing the environmental impact of shrimp farming, thereby contributing to its long-term sustainability. Assessing genotype-by-environment (G-by-E) interactions is essential in breeding programs to ensure that improved penaeid shrimp strains perform consistently across different production environments, with genomic selection proving more effective than sib-testing alone in mitigating environmental sensitivity. Genome editing tools like CRISPR/Cas9 offer significant potential to accelerate genetic gains in penaeid shrimp by enabling rapid introduction of desired genetic changes, with recent advancements showing promising results in achieving high transfection efficiency in shrimp embryos. Additionally, artificial intelligence and machine learning are being leveraged to streamline phenotyping and enhance decision-making in shrimp breeding and farming, improving efficiency and accuracy in managing traits and predicting disease outbreaks. Herein, we provide an overview and update on the domestication of penaeid shrimp, including the current status of domestication for principal farmed species, key milestones in domestication history, targeted breeding traits in selective breeding programs, the advantages of integrating genomeic selection for enhancing production traits, and future directions for selective breeding of penaeid shrimp. ### Competing Interest Statement The authors have declared no competing interest.

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 110 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells partake in inducing myeloid inflammation previously associated with androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting.### Competing Interest StatementThe authors have declared no competing interest.

Streptococcus iniae is a causative agent of streptococcal disease that negatively impacts tilapia ( Oreochromis spp.) production worldwide. Previously, our collaborative research team demonstrated substantial genetic variation for resistance to S. iniae and confirmed the ability to improve resistance through selective breeding. Although positive gains in resistance have been achieved, the underlying mechanism(s) involved in the observed resistance are unknown. To address this knowledge gap, the objective of this work was to describe differences in mortality and pathology between S. iniae resistant and susceptible Nile tilapia. Marker assisted selection was used to produce tilapia from resistant and susceptible parents. The tilapia were challenged with S. iniae and organ samples were collected from challenged individuals for histology prior to and 24 h post-challenge. The resistance phenotype was confirmed as demonstrated by 100% survival in the resistant tilapia and only 10% survival in the susceptible tilapia following S. iniae challenge. Lesions observed in the anterior kidney, spleen, and brain of susceptible tilapia were consistent with classic S. iniae infection including histiocytic meningitis, splenitis, nephritis, and the presence of gram-positive cocci. The severity of these lesions was greatly reduced in the resistant tilapia and no S. iniae were observed in the tissues. Changes described through histological assessment of S. iniae challenged tilapia provide a foundation for subsequent research to elucidate the mechanisms governing the improved survival and reduced lesion formation in the resistant tilapia.

Prostate tumor heterogeneity is a major obstacle when studying the biological mechanisms of molecular markers. Increased gene expression levels of secreted frizzled-related protein 4 (SFRP4) is a biomarker in aggressive prostate cancer. To understand how SFRP4 relates to prostate cancer we performed comprehensive spatial and multiomics analysis of the same prostate cancer tissue samples. The experimental workflow included spatial transcriptomics, bulk transcriptomics, proteomics, DNA methylomics and tissue staining. SFRP4 mRNA was predominantly located in cancer stroma, produced by fibroblasts and smooth muscle cells, and co-expressed with extracellular matrix components. We also confirmed that higher SFRP4 gene expression is associated with cancer aggressiveness. Gene expression of SFRP4 was affected by gene promotor methylation. Surprisingly, the high mRNA levels did not reflect SFRP4 protein levels, which was much lower. This study contributes previously unknown insights of SFRP4 mRNA in the prostate tumor environment that potentially can improve diagnosis and treatment. Leveraging spatial and bulk transcriptomics, DNA methylomics and proteomics on the same prostate cancer tissue samples, this study provides insights on the tissue origin and role of SFRP4 gene expression in aggressive prostate cancer.

Understanding the molecular characteristics and changes of the tumor microenvironment (TME) associated with aggressive prostate cancer (PCa) is essential for precise diagnosis and treatment. We interrogated spatially resolved integrated transcriptomics and metabolomics data to build molecular strafiers discriminating patients with aggressive, potentially relapsing, and metastasizing PCa. We report a relapse associated (RA) gene expression signature characterized by upregulated immune response related gene expression scoring high in cancer, stroma, and glandular tissue of relapsing patients. Further, we identified a signature specific to a distinct sub-group of morphologically non-cancerous glands in prostate tissue from patients with relapsing cancer. This signature, named chemokine-enriched-gland (CEG) signature, was characterized by upregulated gene expression of pro-inflammatory chemokines. Glands with a high CEG score were enriched for club-like cells and surrounding stroma was infiltrated by immune cells. Tissue regions scoring high for both CEG and RA signatures were associated with reduced levels of citrate and zinc and loss of normal prostate secretory gland functions via reduced expression of genes necessary for citrate secretion. In summary we report that aggressive PCa is associated with an increased inflammatory status linked to chemokine production and club-like cell enrichment in potentially pre-cancerous prostate glands displaying an aberrant metabolism. ### Competing Interest Statement The authors have declared no competing interest.

Prostate cancer treatment resistance is a significant challenge facing the field. Genomic and transcriptomic profiling have partially elucidated the mechanisms through which cancer cells escape treatment, but their relation toward the tumor microenvironment (TME) remains elusive. Here we present a comprehensive transcriptomic landscape of the prostate TME at multiple points in the standard treatment timeline employing single-cell RNA-sequencing and spatial transcriptomics data from 120 patients. We identify club-like cells as a key epithelial cell subtype that acts as an interface between the prostate and the immune system. Tissue areas enriched with club-like cells have depleted androgen signaling and upregulated expression of luminal progenitor cell markers. Club-like cells display a senescence-associated secretory phenotype and their presence is linked to increased polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) activity. Our results indicate that club-like cells are associated with myeloid inflammation previously linked to androgen deprivation therapy resistance, providing a rationale for their therapeutic targeting. The prostate cancer tumour microenvironment in the context of treatment remains to be explored. Here, single-cell RNA-sequencing and spatial transcriptomics analysis of samples at multiple treatment points from 120 patients suggests that club-like cells may contribute to treatment resistance.

Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polymorphism (SNPs) linked to quantitative trait loci (QTL) related to survival to S. iniae challenge. With this purpose, Nile tilapia from the Spring Genetics breeding program were sent to a controlled S. iniae challenge test where phenotypes were scored as dead for fish that died during challenge test and survivors for the fish alive at the termination of the test. Additionally, fin-clip samples from all fish in the test were collected for DNA extraction. Out of 1904 fish in the challenge test, tissue samples of 321 fish were sent for genotyping using double digest restriction site associated DNA sequencing (ddRADseq). After quality control and filtering, 9,085 SNPs were used to perform a genome-wide association study (GWAS). A significant signal in LG8 was observed indicating association with survival to S. iniae challenge, with SNPs explaining from 12% to 26% of the genetic variance. To demonstrate the usefulness of marker assisted selection (MAS) to selectively breed fish for survival to S. iniae, offspring of breeding candidates classified as "resistant" and "susceptible" based on haplotypes of the four most significant markers were sent to a controlled S. iniae challenge test. At the end of the test, the differences in mortality between the two groups were strikingly different with a final cumulative percent mortality of less than 1% and 73% for offspring from "resistant" and "susceptible" parents, respectively. These results demonstrate that MAS for improved resistance to S. iniae is feasible.

Background Locally advanced breast cancer is a heterogeneous disease with respect to response to neoadjuvant chemotherapy (NACT) and survival. It is currently not possible to accurately predict who will benefit from the specific types of NACT. DNA methylation is an epigenetic mechanism known to play an important role in regulating gene expression and may serve as a biomarker for treatment response and survival. We investigated the potential role of DNA methylation as a prognostic marker for long-term survival (> 5 years) after NACT in breast cancer. Methods DNA methylation profiles of pre-treatment ( n = 55) and post-treatment ( n = 75) biopsies from 83 women with locally advanced breast cancer were investigated using the Illumina HumanMethylation450 BeadChip. The patients received neoadjuvant treatment with epirubicin and/or paclitaxel. Linear mixed models were used to associate DNA methylation to treatment response and survival based on clinical response to NACT (partial response or stable disease) and 5-year survival, respectively. LASSO regression was performed to identify a risk score based on the statistically significant methylation sites and Kaplan–Meier curve analysis was used to estimate survival probabilities using ten years of survival follow-up data. The risk score developed in our discovery cohort was validated in an independent validation cohort consisting of paired pre-treatment and post-treatment biopsies from 85 women with locally advanced breast cancer. Patients included in the validation cohort were treated with either doxorubicin or 5-FU and mitomycin NACT. Results DNA methylation patterns changed from before to after NACT in 5-year survivors, while no significant changes were observed in non-survivors or related to treatment response. DNA methylation changes included an overall loss of methylation at CpG islands and gain of methylation in non-CpG islands, and these changes affected genes linked to transcription factor activity, cell adhesion and immune functions. A risk score was developed based on four methylation sites which successfully predicted long-term survival in our cohort ( p = 0.0034) and in an independent validation cohort ( p = 0.049). Conclusion Our results demonstrate that DNA methylation patterns in breast tumors change in response to NACT. These changes in DNA methylation show potential as prognostic biomarkers for breast cancer survival.

An understanding of the genetic relationship between traits of economic importance for a widely cultured species such as Nile tilapia (Oreochromis niloticus) is important, in particular the relationship between disease resistance and growth. Francisellosis results in economic losses for the industry, and we confirmed that Francisellosis resistance is under additive genetic control in our population. Analysing four generations, significant additive genetic variation was found for survival to F. orientalis challenge (P < 0.001; Log-likelihood-ratio test) with an estimated heritability of h2 = 0.31 ± 0.05 across all generations. The random effect common to full-sibs was also significant, but of lower magnitude (c2 = 0.075 ± 0.02) (P < 0.001; Log-likelihood-ratio test). Results of assortative mating groups confirmed that genetic gain could be obtained for survival to F. orientalis challenge since offspring of fish selected with high estimated breeding values exhibited higher survival to F. orientalis challenge. The genetic correlation between harvest weight and survival to F. orientalis challenge was very low (rg = −0.02 ± 0.13) and not significantly different from zero (Log-likelihood-ratio test p > 0.05). The genetic correlation between survival to F. orientalis challenge and survival to S. agalactiae Ib challenge was positive but not significantly different from zero (rg = 0.14 ± 0.11; Log-likelihood-ratio test p > 0.05). The genetic correlation between harvest weight and survival to S. agalactiae challenge was negative but also not significantly different (rg = − 0.19 ± 0.10; Log-likelihood-ratio test p > 0.05). Lack of significant favourable genetic relationships between economically important traits favours multi-trait selection since selection for growth alone does not improve survival to F. orientalis challenge or survival to S. agalactiae challenge.

We investigated genomic and transcriptomic changes in paired tumor samples of 29 in-house multiple myeloma (MM) patients and 28 patients from the MMRF CoMMpass study before and after treatment. A change in clonal composition was found in 46/57 (82%) of patients, and single-nucleotide variants (SNVs) increased from median 67 to 86. The highest increase in prevalence of genetic aberrations was found in RAS genes (60% to 72%), amp1q21 (18% to 35%), and TP53 (9% to 18%). The SBS-MM1 mutation signature was detected both in patients receiving high and low dose melphalan. A total of 2589 genes were differentially expressed between early and late samples (FDR < 0.05). Gene set enrichment analysis (GSEA) showed increased expression of E2F, MYC, and glycolysis pathways and a decreased expression in TNF-NFkB and TGFbeta pathways in late compared to early stage. Single sample GSEA (ssGSEA) scores of differentially expressed pathways revealed that these changes were most evident in end-stage disease. Increased expression of several potentially targetable genes was found at late disease stages, including cancer-testis antigens, XPO1 and ABC transporters. Our study demonstrates a transcriptomic convergence of pathways supporting increased proliferation and metabolism during disease progression in MM.

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Cytoscape is often used for visualization and analysis of metabolic pathways. For example, based on KEGG data, a reader for KEGG Markup Language (KGML) is used to load files into Cytoscape. However, although multiple genes can be responsible for the same reaction, the KGML-reader KEGGScape only presents the first listed gene in a network node for a given reaction. This can lead to incorrect interpretations of the pathways. Our new method, FunHoP, shows all possible genes in each node, making the pathways more complete. FunHoP collapses all genes in a node into one measurement using read counts from RNA-seq. Assuming that activity for an enzymatic reaction mainly depends upon the gene with the highest number of reads, and weighting the reads on gene length and ratio, a new expression value is calculated for the node as a whole. Differential expression at node level is then applied to the networks. Using prostate cancer as model, we integrate RNA-seq data from two patient cohorts with metabolism data from literature. Here we show that FunHoP gives more consistent pathways that are easier to interpret biologically. Code and documentation for running FunHoP can be found at https://github.com/kjerstirise/FunHoP.

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that lysine-specific demethylase 1A (Kdm1a/Lsd1) is absolutely required for Paneth cell differentiation. Lsd1-deficient crypts, devoid of Paneth cells, are still able to form organoids without a requirement of exogenous or endogenous Wnt. Mechanistically, we find that LSD1 enzymatically represses genes that are normally expressed only in fetal and neonatal epithelium. This gene profile is similar to what is seen in repairing epithelium, and we find that Lsd1-deficient epithelium has superior regenerative capacities after irradiation injury. In summary, we found an important regulator of neonatal intestinal development and identified a druggable target to reprogram intestinal epithelium toward a reparative state.

Two bacterial pathogens that impact worldwide tilapia production through direct mortalities and treatment costs are Streptococcus iniae and S. agalactiae. An economically important trait is rapid growth; however, it is not known if this trait is correlated to Streptococcus disease resistance. The objectives of this study were to: 1) determine the relationship between growth of Nile tilapia (Oreochromis niloticus) and survival to both S. iniae and S. agalactiae capsular type Ib; 2) verify previous results demonstrating heritability of resistance to S. agalactiae Ib and S. iniae through positive assortative mating; and 3) determine the response to selection obtained from genetic trend analysis and estimates of heritability. Data from eight generations of tilapia were used in this study including growth data for all generations, S. iniae mortality data from three generations, and S. agalactiae Ib mortality data from five generations. Additive genetic variation was found for all three traits: harvest weight heritability was 0.23, S. iniae heritability was 0.43 and S. agalactiae heritability was 0.21. Significant effects common to full-sibs were found for all traits and were of higher magnitude for harvest weight (c(2) = 0.11) than for both S. iniae (c(2) = 0.04) and S. agalactiae (c(2) = 0.05). The genetic correlation between harvest weight and S. iniae survival was low (r(g) = 0.15 +/- 0.12) and not significantly different from zero. The genetic correlation between harvest weight and S. agalactiae Ib survival was intermediate and negative, but not significantly different from zero (r(g) = -0.21 +/- 0.11), suggesting there is no relationship between growth and resistance to Streptococcus sp. These results demonstrate that multi-trait selection is needed to balance growth and resistance to both Streptococcus sp. to provide commercial tilapia farmers with a fast-growing fish with reduced susceptibilities to these two important pathogens.

We present Model-based Analysis for ChIA-PET (MACPET) which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared to MACS in terms of motif occurrence, spatial resolution and false discovery rate. Significant binding sites discovered by MACPET are involved in a higher number of significant 3D interactions than those discovered by MACS. MACPET is freely available on Bioconductor.

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G(0)) were ranked on genomic breeding values for WSSV resistance. Two G(1) populations were produced, one from G(0) breeders with high and the other with low estimated breeding values. A third population was produced from "random" mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G(1)) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

The head kidney is a key organ that plays a fundamental role in the regulation of the fish immune response and in the maintenance of endocrine homeostasis. Previous studies indicate that the supplementation of exogenous dietary components, such as krill meal (KM), soybean meal (SM), Bactocell® (BA), and butyrate (BU), can have a significant effect on the immune function of the head kidney. The aim of this study was to investigate the differential effect of these four dietary ingredients on the transcriptional profiles of the head kidney of the Atlantic salmon. This study revealed that just a small number of genes were responsive to the feeding regime after a long-term (12 weeks) treatment, and evidenced that the most significant alterations, both in terms of the number of affected genes and magnitude of changes in gene expression, were detectable in the BU- and KM-fed groups compared with controls, while the SM diet had a nearly negligible effect, and BA had no significant effects at all. Most of the differentially expressed genes were involved in the immune response and, in line with data previously obtained from pyloric caeca, major components of the complement system were significantly affected. These alterations were accompanied by an increase in the density of melanomacrophage centers in the KM- and SM-fed group and their reduction in the BU-fed group. While three types of dietary supplements (BU, KM, and SM) were able to produce a significant modulation of some molecular players of the immune system, the butyrate-rich diet was revealed as the one with the most relevant immune-stimulating properties in the head kidney. These preliminary results suggest that further investigations should be aimed towards the elucidation of the potential beneficial effects of butyrate and krill meal supplementation on farmed salmon health and growth performance.