Pawel Herzyk

Purpose: Data on the evolution of molecular alterations during first-line systemic anticancer treatment (SACT) are lacking for biliary tract cancers. Liquid biopsy and radiomics are noninvasive tools that could provide insights into this. Experimental Design: Plasma samples collected at baseline (N = 39) and progressive disease (PD; N = 30) were subjected to a next-generation sequencing (NGS) panel assay covering single-nucleotide variants (SNV) and copy-number variants [CNV; AVENIO ctDNA Expanded Kit (Roche)]. CT scans were reviewed for total tumor burden (TTB) analysis and for an exploratory radiomic analysis. Results: Circulating free DNA (cfDNA) concentration correlated with TTB (P = 0.0003). Intrahepatic cholangiocarcinomas (iCCA) had larger TTB (P = 0.034) and higher number of alterations (P = 0.02). cfDNA concentration or median dominant variant allele frequency (dVAF) did not correlate with outcomes. Baseline MET SNVs (P = 0.07) and ERBB2 CNVs (P = 0.03) were associated with shorter time to progression (TTP). iCCA frequently displayed a heterogeneous molecular response to SACT. Patients with increasing CNV score for EGFR [TTP: 4.1 vs. 9.5 months; P = 0.003 and overall survival (OS): 10.1 vs. 21.6 months; P = 0.02] and MET [TTP: 4.2 vs 10.1 months; P = 0.01 and OS: 9.5 vs. 20.2 months; P = 0.06] had worse outcomes than those with decreasing score during SACT. Cases with PD driven by EGFR and MET were associated with selected baseline radiomic features: neighboring gray-tone difference matrix (NGTDM) coarseness (P = 0.041) and gray-level size zone matrix (GLSZM) zone size entropy (P = 0.028) for EGFR; gray-level run length matrix (GLRLM) short run emphasis (P = 0.034), GLRLM run length variance (P = 0.017), GLRLM run entropy (P = 0.028), and GLSZM large zone emphasis (P = 0.019) for MET. Conclusions: Liquid biopsy identified potential primary (MET SNVs/ERBB2 CNVs) and secondary (EGFR/MET CNVs) resistance mechanisms to platinum-based SACT. Radiomics provided an early correlation with molecular evolution.

Summary: Environmental and endogenous stimuli determine plant developmental transitions including flowering through multiple signaling cascades. Although the key activators and repressors of flowering initiation are defined, the components and mechanisms integrating light signaling and flowering pathways are not fully established. This study investigates the role of TANDEM ZINC‐FINGER/PLUS3 (TZP), a light‐integrating transcriptional regulator, to elucidate how light cues influence the epigenetic regulation of flowering in Arabidopsis thaliana . To dissect the molecular function of TZP, this study employed a combination of genetics, RNA sequencing, chromatin immunoprecipitation sequencing and phenotypic assays. These approaches were used to determine TZP's genomic binding sites, its downstream gene targets and its influence on flowering time and chromatin modifications. TANDEM ZINC‐FINGER/PLUS3 was found to directly associate with the promoter regions of chromatin‐modifying genes, including FLOWERING LOCUS D (a histone H3K4 demethylase) and histone deacetylase 6 (a histone deacetylase). This regulation promotes a chromatin environment that represses FLOWERING LOCUS C ( FLC ) transcription, thereby accelerating flowering. TANDEM ZINC‐FINGER/PLUS3 thus functions upstream of multiple pathways integrating photoperiodic and autonomous floral cues. TANDEM ZINC‐FINGER/PLUS3 mediates crosstalk between light signaling and flowering pathways by modulating chromatin structure at the FLC locus. This provides a mechanistic framework for understanding how environmental signals dynamically influence epigenetic regulation of developmental transitions.

Heart failure with preserved ejection fraction (HFpEF) is a public health problem and an elusive illness for which there are few treatment options. HFpEF is a systemic condition with a broad phenotype including diastolic dysfunction, pulmonary oedema, exercise intolerance, and left ventricular (LV) hypertrophy, collectively resulting in enhanced morbidity and mortality. Master-regulator transcription factor RUNX1 has recently been identified as a mediator of pathological changes in many cardiac diseases, however its role in HFpEF was unknown. Here we show that inhibition of Runx 1 limits adverse cardiac remodelling in a clinically relevant mouse model of HFpEF. Cardiomyocyte-specific tamoxifen-inducible Runx 1-deficient mice with HFpEF are protected, with preservation of diastolic function, and attenuation of pulmonary oedema, exercise intolerance, and hypertrophy. Furthermore, targeting Runx 1 in HFpEF by using gene transfer or small molecule inhibitors improves diastolic function, both in female and male mice. Overall, our research enhances our understanding of RUNX1 in cardiac disease and demonstrates a novel translational target for the treatment of HFpEF. Keywords: Heart failure with preserved ejection fraction, metabolic heart failure, diastolic dysfunction, hypertrophy, pulmonary oedema, exercise intolerance CLINICAL PERSPECTIVE: Heart failure (HF) is a leading cause of death world-wide and traditionally divided into different subtypes according to cardiac ejection fraction (EF). In contrast to HF with reduced EF (HFrEF), there are limited treatment options for HF with preserved EF which is of considerable concern given that HFpEF is projected to become the dominant HF subtype in the future ¹ . RUNX1 has been demonstrated to play an important role in the development of many cardiac and non-cardiac diseases. As a result, the potential for RUNX1 inhibitors as therapeutic agents across various conditions has become increasingly evident. In this study we established the therapeutic potential of targeting RUNX1 in the context of HFpEF. Targeting RUNX1 in cardiomyocytes markedly attenuates the development of the HFpEF phenotype and therefore this novel translational therapeutic target has great potential to address one of the biggest challenges in cardiac research.

BACKGROUND: Renal denervation lowers blood pressure (BP) in patients with uncontrolled hypertension. We conducted an unbiased genomic screen to identify genetic variants that may associate with BP response to renal denervation (RDN). METHODS: Patients (n=268) with uncontrolled resistant hypertension (baseline BP, 166±21/90±15 mm Hg) who underwent endovascular RDN using the Symplicity catheter (Medtronic, Inc, Santa Rosa, CA) were included. Reduction in 24-hour ambulatory systolic BP was assessed at 6 months and divided into 2 groups: above and below the median response of 6.0 mm Hg, taking preintervention 24-hour ambulatory BP and regression to the mean into account. Whole exome sequencing assessing 249 669 variants, was conducted using Illumina NovaSeq technology read on a NovaSeq S4 Flow Cell device. RESULTS: We did not identify individual gene variants associated with BP response following RDN. These findings were confirmed after adjustment for sex and in a sensitivity analysis looking at tertiles of BP response. We also explored specific variants in AGT , ADD1 , ADRB1, ADRB2 , and SCNN1A that have been proposed as potential candidate genes for response and found no association (all P >0.13). Gene ontology analysis of variants across the 2 responder groups highlighted differences in biologic processes such as cell adhesion and molecular function such as protein tyrosine kinase activity. CONCLUSIONS: The response to RDN, in terms of 24-hour BP reduction, was not associated with the genetic profile of patients with resistant hypertension. These data do not support the use of a genetic score to identify potential responders to RDN.

Summary: Early responses of plants to environmental stress factors prevent damage but can delay growth and development in fluctuating conditions. Optimising these trade‐offs requires tunability of plant responsiveness to environmental signals. We have previously reported that Histone Deacetylase Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the stress responsiveness of Arabidopsis seedlings, but the underlying mechanism remained elusive. Here, we show that HDC1 attenuates transcriptome re‐programming in salt‐treated seedlings, and we identify two genes ( LEA and MAF5 ) that inhibit seedling establishment under salt stress downstream of HDC1. HDC1 attenuates their transcriptional induction by salt via a dual mechanism involving H3K9/14 deacetylation and H3K27 trimethylation. The latter, but not the former, was also abolished in a triple knockout mutant of the linker histone H1, which partially mimics the hypersensitivity of the hdc1‐1 mutant to salt stress. Although stress‐induced H3K27me3 accumulation required both H1 and HDC1, it was not fully recovered by complementing hdc1‐1 with a truncated, H1‐binding competent HDC1 suggesting other players or independent inputs. The combined findings reveal a dual brake function of HDC1 via regulating both active and repressive epigenetic marks on stress‐inducible genes. This natural ‘anti‐panic’ device offers a molecular leaver to tune stress responsiveness in plants.

Summary: Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat‐tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat ‘stress‐ready’ state. Furthermore, the A. hierochuntica global transcriptome as well as heat‐responsive orthologs, display a lower basal and higher heat‐induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV‐B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod‐insensitive, early‐flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

Transport of water, ions and signals from roots to leaves via the xylem vessels is essential for plant life and needs to be tightly regulated. The final composition of the transpiration stream before passage into the shoots is controlled by the xylem-adjacent cell layers, namely xylem parenchyma and pericycle, in the upper part of the root. To unravel regulatory networks in this strategically important location, we generated Arabidopsis lines expressing a nuclear tag under the control of the HKT1 promoter. HKT1 retrieves sodium from the xylem to prevent toxic levels in the shoot, and this function depends on its specific expression in upper root xylem-adjacent tissues. Based on FACS RNA-sequencing and INTACT ChIP-sequencing, we identified the gene repertoire that is preferentially expressed in the tagged cell types and discovered transcription factors experiencing cell-type specific loss of H3K27me3 demethylation. For one of these, ZAT6, we show that H3K27me3-demethylase REF6 is required for de-repression. Analysis of zat6 mutants revealed that ZAT6 activates a suite of cell-type specific downstream genes and restricts Na ⁺ accumulation in the shoots. The combined Files open novel opportunities for ‘bottom-up’ causal dissection of cell-type specific regulatory networks that control root-to-shoot communication under environmental challenge.

Summary: Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and pinpointed extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat and identifying positively selected genes in A. hierochuntica . The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat “stress-ready” state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana . Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

Metabolic reprogramming is a key hallmark of cancer, but less is known about metabolic plasticity of the same tumor at different sites. Here, we investigated the metabolic adaptation of leukemia in two different microenvironments, the bone marrow and the central nervous system (CNS). We identified a metabolic signature of fatty acid synthesis in CNS leukemia, highlighting stearoyl-CoA desaturase (SCD) as a key player. In vivo SCD overexpression increases CNS disease, whereas genetic or pharmacological inhibition of SCD decreases CNS load. Overall, we demonstrated that leukemic cells dynamically rewire metabolic pathways to suit local conditions and that targeting these adaptations can be exploited therapeutically.