Samaneh Eickelschulte

Accurate risk stratification is essential to prevent over- and undertreatment in newly diagnosed prostate cancer (PCa). In a pilot study with 49 men (36 PCa patients, 13 controls), we integrated non-invasive data modalities collected in a real-world clinical setting: radiomics from multiparametric magnetic resonance imaging (T2/ADC index-lesion features), routine and extended serological parameters, multimodal liquid biopsy features (copy number variations, chromosomal instability, methylation, fragmentation in plasma/urinary cfDNA), plus clinical and lifestyle factors. Pairwise Spearman analyses revealed significant inter-modality correlations. Our holistic PCa characterization showed that imaging phenotypes reflect tumor stage and molecular aggressiveness: lower ADC metrics correlated inversely with genomic cfDNA features, while ADC/T2 lesion volumes correlated positively with molecular signals. These results indicate that routine imaging and serological data may capture systemic tumor biology. Our proof-of-concept demonstrates feasibility of combining multiple data modalities in real-world clinical workflows and supports developing integrative models for non-invasive PCa risk stratification.

Background and Objective: Prostate cancer (PCa) is a heterogeneous disease, impeding early detection and risk stratification. Liquid biopsies (LBx) enable minimally invasive tumor profiling, but circulating tumor-derived DNA (ctDNA) detection remains difficult, especially in early-stage PCa. This study aimed at developing a multimodal LBx approach, analyzing genomic and epigenomic cell-free DNA (cfDNA) features in plasma and urine from newly diagnosed PCa patients for early detection, tumor characterization, and risk stratification of aggressive PCa. Methods: Plasma and urine samples were included from 55 localized PCa (lPCa) patients, 18 advanced PCa (aPCa) patients, and 36 cancer-free controls. Low-coverage whole-genome sequencing and methylated DNA immunoprecipitation sequencing were performed to assess fragmentation, chromosomal instability, and methylation in cfDNA. Key findings and Limitations: The complementary (epi)genomic analysis of plasma and urinary cfDNA achieved a 45% ctDNA detection rate in newly diagnosed PCa. Major differences were observed between aPCa and controls, reflecting increasing signals with tumor progression. Epigenomic cfDNA features differentiated lPCa from aPCa, and ctDNA was detected in 46% of PCa patients with prostate-specific antigen <10 ng/ml, suggesting potential for risk stratification. However, sensitivity in early PCa remains a major limitation. Conclusions and Clinical Implications: This study highlights the potential of multimodal LBx approaches, integrating genomic and epigenomic cfDNA features, for minimally invasive characterization of primary PCa and potential metastasis at initial diagnosis. While promising for risk stratification, sensitivity requires optimization for early detection. Incorporating LBx into clinical workflows could complement diagnostics and support clinical decision-making for personalized treatments tailored to patients’ PCa risk profiles.

Background: Prostate cancer (PCa) is a highly heterogeneous disease, with cases ranging from indolent to highly aggressive forms. Ongoing research focuses on identifying new biomarkers to improve early risk stratification in PCa, addressing current limitations to accurately evaluate disease progression. A promising new approach to aid PCa risk stratification is digital spatial profiling (DSP) of PCa tissue. Methods: A total of 94 regions of interest from 38 PCa patients at first diagnosis were analyzed for the expression of 44 proteins, including components of the PI3K-AKT, MAPK, and cell death signaling pathways as well as immune cell markers. An additional validation cohort consisting of 154 PCa patients with long-term follow-up data was analyzed using immunohistochemistry (IHC) to assess the consistency of the identified biomarkers across a larger sample set. Results: DSP identified proliferation marker Ki-67 and phospho-c-Jun N-terminal protein kinase (p-JNK), a member of the MAPK signaling pathway, as significantly upregulated proteins in aggressive PCa (Gleason scores 4 and 5) compared to indolent disease (Gleason score 3). The upregulation of p-JNK was confirmed through IHC. High p-JNK expression was associated with a shorter time to biochemical recurrence (log-rank, p=0.1). Conclusion: Our results indicate that p-JNK may contribute to PCa progression and serve as an early biomarker for aggressive PCa stratification. Identifying this biomarker through DSP could be crucial in advancing disease management and addressing the critical unmet need for more targeted therapies in the treatment of aggressive PCa. Further studies are recommended to evaluate the role of p-JNK in PCa progression.

Type 2 diabetes (T2D) represents a multifactorial metabolic disease with a strong genetic predisposition. Despite elaborate efforts in identifying the genetic variants determining individual susceptibility towards T2D, the majority of genetic factors driving disease development remain poorly understood. With the aim to identify novel T2D risk genes we previously generated an N2 outcross population using the two inbred mouse strains New Zealand obese (NZO) and C3HeB/FeJ (C3H). A linkage study performed in this population led to the identification of the novel T2D-associated quantitative trait locus (QTL) Nbg15 (NZO blood glucose on chromosome 15, Logarithm of odds (LOD) 6.6). In this study we used a combined approach of positional cloning, gene expression analyses and in silico predictions of DNA polymorphism on gene/protein function to dissect the genetic variants linking Nbg15 to the development of T2D. Moreover, we have generated congenic strains that associated the distal sublocus of Nbg15 to mechanisms altering pancreatic beta cell function. In this sublocus, Cbx6, Fam135b and Kdelr3 were nominated as potential causative genes associated with the Nbg15 driven effects. Moreover, a putative mutation in the Kdelr3 gene from NZO was identified, negatively influencing adaptive responses associated with pancreatic beta cell death and induction of endoplasmic reticulum stress. Importantly, knockdown of Kdelr3 in cultured Min6 beta cells altered insulin granules maturation and pro-insulin levels, pointing towards a crucial role of this gene in islets function and T2D susceptibility.

Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.

The two closely related RabGTPase-activating proteins (RabGAPs) TBC1D1 and TBC1D4, both substrates for the AMP-activated protein kinase AMPK, play important roles in exercise metabolism and contraction-dependent translocation of the glucose transporter GLUT4 in skeletal muscle. However, the specific contribution of each RabGAP in contraction signaling is mostly unknown. In this study, we investigated the cooperative AMPK/RabGAP signaling axis in the metabolic response to exercise/contraction using a novel mouse model deficient in active skeletal muscle AMPK, combined with knockout of either Tbc1d1, Tbc1d4 or both RabGAPs. AMPK-deficiency in muscle reduced treadmill exercise performance. Additional deletion of Tbc1d1 but not Tbc1d4 resulted in further decrease in exercise capacity. In oxidative Soleus muscle, AMPK deficiency reduced contraction-mediated glucose uptake and deletion of each or both RabGAPs had no further effect. In contrast, in glycolytic EDL muscle, AMPK deficiency reduced contraction-stimulated glucose uptake and deletion of Tbc1d1 but not Tbc1d4 led to a further decrease. Importantly, skeletal muscle deficient in AMPK and both RabGAPs still exhibited residual contraction-mediated glucose uptake, which was completely abolished by inhibition of the GTPase Rac1. Our results demonstrate a novel mechanistic link between glucose transport and the GTPase signaling framework in skeletal muscle in response to contraction.

The two closely related RabGTPase-activating proteins (RabGAPs) TBC1D1 and TBC1D4 play a crucial role in the regulation of GLUT4 translocation in response to insulin and contraction in skeletal muscle. In mice, deficiency in one or both RabGAPs leads to reduced insulin- and contraction-stimulated glucose uptake and to elevated fatty acid (FA) uptake and oxidation in both glycolytic and oxidative muscle fibers without altering mitochondrial copy number and the abundance of proteins for oxidative phosphorylation. Here we present evidence for a novel mechanism of skeletal muscle lipid utilization involving the two RabGAPs and the FA transporter SLC27A4/FATP4. Both RabGAPs control the uptake of saturated and unsaturated long-chain FAs (LCFAs) into skeletal muscle and knockdown (Kd) of a subset of RabGAP substrates, Rab8, Rab10, or Rab14, decreased LCFA uptake into these cells. In skeletal muscle from Tbc1d1 and Tbc1d4 knockout animals, SLC27A4/FATP4 abundance was increased and depletion of SLC27A4/FATP4 but not FAT/CD36 completely abrogated the enhanced FA oxidation in RabGAP-deficient skeletal muscle and cultivated C2C12 myotubes. Collectively, our data demonstrate that RabGAP-mediated control of skeletal muscle lipid metabolism converges with glucose metabolism at the level of downstream RabGTPases and involves regulated transport of LCFAs via SLC27A4/FATP4.