Spatial Effects of Infiltrating T cells on Neighbouring Cancer Cells and Prognosis in Stage III CRC patients

Colorectal cancer (CRC) is one of the most frequently occurring cancers, but prognostic biomarkers identifying patients at risk of recurrence are still lacking. In this study, we aimed to investigate in more detail the spatial relationship between intratumoural T cells, cancer cells, and cancer cell hallmarks, as prognostic biomarkers in stage III colorectal cancer patients. We conducted multiplexed imaging of 56 protein markers at single cell resolution on resected fixed tissue from stage III CRC patients who received adjuvant 5-fluorouracil-based chemotherapy. Images underwent segmentation for tumour, stroma and immune cells, and cancer cell 'state' protein marker expression was quantified at a cellular level. We developed a Python package for estimation of spatial proximity, nearest neighbour analysis focusing on cancer cell - T cell interactions at single-cell level. In our discovery cohort (MSK), we processed 462 core samples (total number of cells: 1,669,228) from 221 adjuvant 5FU-treated stage III patients. The validation cohort (HV) consisted of 272 samples (total number of cells: 853,398) from 98 stage III CRC patients. While there were trends for an association between percentage of cytotoxic T cells (across the whole cancer core), it did not reach significance (Discovery cohort: p = 0.07, Validation cohort: p = 0.19). We next utilized our region-based nearest neighbourhood approach to determine the spatial relationships between cytotoxic T cells, helper T cells and cancer cell clusters. In the both cohorts, we found that lower distance between cytotoxic T cells, T helper cells and cancer cells was significantly associated with increased disease-free survival. An unsupervised trained model that clustered patients based on the median distance between immune cells and cancer cells, as well as protein expression profiles, successfully classified patients into low-risk and high-risk groups (Discovery cohort: p = 0.01, Validation cohort: p = 0.003).

Identification of unique rectal cancer-specific subtypes

BACKGROUND

Existing colorectal cancer subtyping methods were generated without much consideration of potential differences in expression profiles between colon and rectal tissues. Moreover, locally advanced rectal cancers at resection often have received neoadjuvant chemoradiotherapy which likely has a significant impact on gene expression.

METHODS

We collected mRNA expression profiles for rectal and colon cancer samples (n = 2121). We observed that (i) Consensus Molecular Subtyping (CMS) had a different prognosis in treatment-naïve rectal vs. colon cancers, and (ii) that neoadjuvant chemoradiotherapy exposure produced a strong shift in CMS subtypes in rectal cancers. We therefore clustered 182 untreated rectal cancers to find rectal cancer-specific subtypes (RSSs).

RESULTS

We identified three robust subtypes. We observed that RSS1 had better, and RSS2 had worse disease-free survival. RSS1 showed high expression of MYC target genes and low activity of angiogenesis genes. RSS2 exhibited low regulatory T cell abundance, strong EMT and angiogenesis signalling, and high activation of TGF-β, NF-κB, and TNF-α signalling. RSS3 was characterised by the deactivation of EGFR, MAPK and WNT pathways.

CONCLUSIONS

We conclude that RSS subtyping allows for more accurate prognosis predictions in rectal cancers than CMS subtyping and provides new insight into targetable disease pathways within these subtypes.

Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders

OBJECTIVE

Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD.

METHODS

By means of label-free mass spectrometry (MS) and mRNA sequencing (mRNA-seq), we report pre-symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extracted unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage.

RESULTS

In this regard, upregulation of both Acyl-CoA Synthetase Long-Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS/FTD tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS/FTD pathology.

CONCLUSIONS

Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.

CT-derived coronary artery calcium density is affected by regional lesion distribution and image reconstruction parameters

PURPOSE

The prognostic relevance of coronary artery calcium (CAC) density, assessed from cardiac CT scans, is established. However, the influence of CAC distribution, volume, image reconstruction, and clinical factors on CAC density warrants further examination.

METHODS

In this study, 120 patients underwent non-contrast ECG-gated cardiac CT scans using a prospectively defined CAC scoring protocol with 1-, 3-, and 5-mm thick image reconstructions, both with and without a 20% image overlap. We segmented CAC in all reconstructions and assessed the relationship between CAC density, volume, and number of detected calcifications/patient.

RESULTS

Overall, 75/120 (63%) patients (66% men, mean age 63 ± 11 years) presented CAC across 342 segments. CAC density, CAC volume, and the number of detected calcifications decreased with increasing slice thickness (p < 0.001 for all); these effects were slightly reduced by image overlap (p < 0.001 for all). Higher CAC density correlated with greater CAC volume (ρ = 0.62; p < 0.001) and more calcified segments per person (ρ = 0.32; p = 0.006). Higher CAC density was also associated with lower patient weight (beta: -0.6, 95%CI: -1.1--0.1, p = 0.022) and increased high-density lipoprotein (HDL) levels (beta: 0.7, 95%CI: 0.0-1.4, p = 0.046). In a multivariable analysis adjusted for clinical covariates, lower CAC density was associated with broader CAC distribution (i.e., a higher number of calcified segments at a given CAC volume; beta-coefficient: -58.9; 95%CI: -84.7 to -33.1; p < 0.001).

CONCLUSION

CAC density is significantly impacted by regional CAC distribution and image reconstruction, potentially confounding its prognostic value. Accounting for these factors may improve patient risk assessment, management, and cardiovascular health outcomes.

Exploring the Potential of Sulfur Moieties in Compounds Inhibiting Steroidogenesis

This study reports on the synthesis and evaluation of novel compounds replacing the nitrogen-containing heterocyclic ring on the chemical backbone structure of cytochrome P450 17α-hydroxylase/12,20-lyase (CYP17A1) inhibitors with a phenyl bearing a sulfur-based substituent. Initial screening revealed compounds with marked inhibition of CYP17A1 activity. The selectivity of compounds was thereafter determined against cytochrome P450 21-hydroxylase, cytochrome P450 3A4, and cytochrome P450 oxidoreductase. Additionally, the compounds showed weak inhibitory activity against aldo-keto reductase 1C3 (AKR1C3). The compounds' impact on steroid hormone levels was also assessed, with some notable modulatory effects observed. This work paves the way for developing more potent dual inhibitors specifically targeting CYP17A1 and AKR1C3.

Multiplexed Immunofluorescence Imaging Reveals an Immune-Rich Tumor Microenvironment in Mucinous Rectal Cancer Characterized by Increased Lymphocyte Infiltration and Enhanced Programmed Cell Death Protein 1 Expression

BACKGROUND

Mucinous rectal cancer is associated with a higher incidence of microsatellite instability and a poorer response to neoadjuvant chemoradiotherapy compared to other subtypes of rectal adenocarcinoma. Immune checkpoint inhibitors are an emerging family of anticancer therapeutics associated with highly variable outcomes in colorectal cancer. Although the immune landscape of mucinous rectal cancer has not been fully explored, the presence of mucin is thought to act as a barrier preventing immune-cell infiltration.

OBJECTIVE

The aim of this study was to determine the immune properties of mucinous rectal cancer and investigate the degree of lymphocyte infiltration in this cohort.

DESIGN

This is a retrospective cohort study that involved multiplexed immunofluorescence staining of tumor microarrays.

SETTINGS

Samples originated from a single university teaching hospital.

PATIENTS

Our cohort included 15 cases of mucinous and 43 cases of nonmucinous rectal cancer.

MAIN OUTCOME MEASURES

Immune cells were classified and quantified. Immune-cell counts were compared between mucinous and nonmucinous cohorts. Immune marker expression within tumor epithelial tissue was evaluated to determine the degree of lymphocyte infiltration.

RESULTS

Cytotoxic ( p = 0.022) and regulatory T cells ( p = 0.010) were found to be overrepresented in the mucinous cohort compared to the nonmucinous group. Programmed cell death protein 1 expression was also found to be significantly greater in the mucinous group ( p = 0.001). CD3 ( p = 0.001) and CD8 ( p = 0.054) expressions within the tumor epithelium were also higher in the mucinous group, suggesting adequate immune infiltration despite the presence of mucin. In our analysis, microsatellite instability status was not a predictor of immune marker expression.

LIMITATIONS

The relatively small size of the cohort.

CONCLUSIONS

Mucinous rectal cancer is associated with an immune-rich tumor microenvironment, which was not associated with microsatellite instability status. See Video Abstract at http://links.lww.com/DCR/C65 .

IMGENES DE INMUNOFLUORESCENCIA MULTIPLEXADAS REVELAN UN MICROAMBIENTE TUMORAL RICO EN INMUNIDAD EN EL CNCER RECTAL MUCINOSO CARACTERIZADO POR UNA MAYOR INFILTRACIN DE LINFOCITOS Y UNA EXPRESIN MEJORADA DE PD

ANTECEDENTES:El cáncer rectal mucinoso se asocia con una mayor incidencia de inestabilidad de microsatélites y una peor respuesta a la quimiorradioterapia neoadyuvante en comparación con otros subtipos de adenocarcinoma rectal. Los inhibidores de puntos de control inmunitarios son una familia emergente de tratamientos contra el cáncer asociados con resultados muy variables en el cáncer colorrectal. Aunque el panorama inmunitario del cáncer rectal mucinoso no se ha explorado completamente, se cree que la presencia de mucina actúa como una barrera que previene la infiltración de células inmunitarias.OBJETIVO:El objetivo de este estudio fue determinar las propiedades inmunes del cáncer de recto mucinoso e investigar el grado de infiltración de linfocitos en esta cohorte.DISEÑO:Este es un estudio de cohorte retrospectivo que involucró la tinción de inmunofluorescencia multiplexada de micromatrices tumorales.AJUSTES:Las muestras se originaron en un solo hospital docente universitario.PACIENTES:Nuestra cohorte incluyó 15 casos de cáncer de recto mucinoso y 43 casos de cáncer de recto no mucinosoPRINCIPALES MEDIDAS DE RESULTADO:Las células inmunitarias se clasificaron y cuantificaron. Se compararon los recuentos de células inmunitarias entre cohortes mucinosas y no mucinosas. Se evaluó la expresión del marcador inmunitario dentro del tejido epitelial tumoral para determinar el grado de infiltración de linfocitos.RESULTADOS:Se encontró que las células T citotóxicas ( p = 0,022) y reguladoras ( p = 0,010) estaban sobrerrepresentadas en la cohorte mucinosa en comparación con el grupo no mucinoso. También se encontró que la expresión de PD-1 era significativamente mayor en el grupo mucinoso ( p = 0,001). La expresión de CD3 ( p = 0,001) y CD8 ( p = 0,054) dentro del epitelio tumoral también fue mayor en el grupo mucinoso, lo que sugiere una infiltración inmunitaria adecuada a pesar de la presencia de mucina. En nuestro análisis, no se encontró que el estado de inestabilidad de los microsatélites sea un predictor de la expresión del marcador inmunitario.LIMITACIONES:El tamaño relativamente pequeño de la cohorte.CONCLUSIONES:El cáncer rectal mucinoso se asocia con un microambiente tumoral rico en inmunidad, que no se asoció con el estado de inestabilidad de microsatélites. Consulte el Video del Resumen en http://links.lww.com/DCR/C65 . (Traducción- Dr. Yesenia Rojas-Khalil ).

Disordering of Starch Films as a Factor Influencing the Release Rate of Biologically Active Substances

The release of a spin probe (nitroxide radical) from polymer films was studied by electron paramagnetic resonance (EPR). The films were fabricated from starch having different crystal structures (A-, B-, and C-types) and disordering degrees. Film morphology (analysis of the scanning electron microscopy (SEM)) depended on the presence of dopant (nitroxide radical) to a larger extent rather than on crystal structure ordering or polymorphic modification. The presence of nitroxide radical led to additional crystal structure disordering and reduced the crystallinity index from the X-ray diffraction (XRD) data. Polymeric films made of amorphized starch powder were able to undergo recrystallization (crystal structure rearrangement), which manifested itself as an increase in crystallinity index and phase transition of the A- and C-type crystal structures to the B-type one. It was demonstrated that nitroxide radical does not form an individual phase during film preparation. According to the EPR data, local permittivity of starch-based films varied from 52.5 to 60.1 F/m, while bulk permittivity did not exceed 17 F/m, which demonstrates that local concentration of water is increased in the regions near the nitroxide radical. The mobility of the spin probe corresponds to small stochastic librations and is indicative of the strongly a mobilized state. The application of kinetic models made it possible to find out that substance release from biodegradable films consists of two stages: matrix swelling and spin probe diffusion through the matrix. Investigation of the release kinetics for nitroxide radical demonstrated that the course of this process depends on the type of crystal structure of native starch.

Rectal cancer–specific subtyping using transcriptomics datasets derived from treatment-naive patients to assess novel prognostic signatures and key differences to CMS-based subtyping

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Background: Molecular subtyping in colorectal cancer provided novel insights into tumour heterogeneity and delivered new prognostic signatures. Existing methods (such as CMS-based subtyping) were generated without much consideration of differences in expression profiles between colon and rectal cancer tissues. Moreover, stage 2 and 3 rectal cancer patients often receive neo-adjuvant radio-chemotherapy which may impact on gene expression when determined from resection samples. Methods: We investigated possible differences between treatment-naive colon and rectal cancers at the molecular level. We collected mRNA expression profiles for rectal and colon cancer samples available from Gene Expression Omnibus (GEO) database (n=2139) and applied batch-effect correction using ComBat. Results: To explore whether CMS subtypes changed after neoadjuvant chemoradiation in rectal cancers, we analysed rectal tumour samples from 40 patients where both pre-operative biopsies and resections after chemoradiotherapy were available. More than half of samples shifted from CMS1-3 to CMS4 after patients received chemoradiotherapy. We therefore focused our further analysis on treatment-naive rectal cancers. We observed that CMS-based subtyping showed different prognostic potential in treatment-naïve colon vs. rectal cancers. Rectal cancers had significantly better disease-free survival (DFS) when assigned to CMS 2 or 4 compared to colon cancers. This suggested differences in disease biology that were not captured by CMS subtyping. We next aimed to identify molecular subtypes in rectal cancers, and identified three prevalent rectal-specific subtypes (RSS) by applying hierarchical clustering in 182 untreated rectal cancer samples. We used gene co-expression network analysis to define functional gene modules to identify these subtypes. Based on the gene modules’ signatures, we built a classifier to predict our new subtypes in different transcriptomics datasets (n=692). We observed that RSS1 had better disease-free survival (DFS), whereas RSS2 exhibited worse short-term DFS (less than 3 years) and RSS3 showed worse long-term DFS (3+ years). We discovered the deactivation of EGFR, MAPK and WNT pathways on RSS3 as well as high CD8+ infiltration and low CD4+ counts in these tumours. RSS2 exhibits low plasma cell and regulatory T-cell abundance and high activations of TGF-β, NF-κB, and TNF-α. We also observed high EMT, angiogenesis and inflammatory response in this subtype. Lastly, RSS1 showed high expression on MYC target and low activity on angiogenesis genes. Moreover, the immune and inflammatory responses were also lower than in the other subtypes. Conclusions: Rectal-specific subtypes are of prognostic importance and provide new insight into molecular disease pathways and potential targets.

Development of a protein signature to enable clinical positioning of IAP inhibitors in colorectal cancer

Resistance to chemotherapy-induced cell death is a major barrier to effective treatment of solid tumours such as colorectal cancer, CRC. Herein, we present a study aimed at developing a proteomics-based predictor of response to standard-of-care (SoC) chemotherapy in combination with antagonists of IAPs (inhibitors of apoptosis proteins), which have been implicated as mediators of drug resistance in CRC. We quantified the absolute expression of 19 key apoptotic proteins at baseline in a panel of 12 CRC cell lines representative of the genetic diversity seen in this disease to identify which proteins promote resistance or sensitivity to a model IAP antagonist [birinapant (Bir)] alone and in combination with SoC chemotherapy (5FU plus oxaliplatin). Quantitative western blotting demonstrated heterogeneous expression of IAP interactome proteins across the CRC cell line panel, and cell death analyses revealed a widely varied response to Bir/chemotherapy combinations. Baseline protein expression of cIAP1, caspase-8 and RIPK1 expression robustly correlated with response to Bir/chemotherapy combinations. Classifying cell lines into 'responsive', 'intermediate' and 'resistant' groups and using linear discriminant analysis (LDA) enabled the identification of a 12-protein signature that separated responders to Bir/chemotherapy combinations in the CRC cell line panel with 100% accuracy. Moreover, the LDA model was able to predict response accurately when cells were cocultured with Tumour necrosis factor-alpha to mimic a pro-inflammatory tumour microenvironment. Thus, our study provides the starting point for a proteomics-based companion diagnostic that predicts response to IAP antagonist/SoC chemotherapy combinations in CRC.

Correlation of magnetic resonance imaging and post-ablation endoscopy to detect oesophageal thermal injury in patients after atrial fibrillation ablation: MRI-EDEL-study

Aims 

To correlate oesophageal magnetic resonance imaging (MRI) abnormalities with ablation-induced oesophageal injury detected in endoscopy.

Methods and results 

Ablation-naïve patients with atrial fibrillation (AF), who underwent ablation using a contact force sensing irrigated radiofrequency ablation catheter, received a cardiac MRI on the day of ablation, and post-ablation oesophageal endoscopy (OE) 1 day after ablation. Two MRI expert readers recorded presence of abnormal oesophageal tissue signal intensities, defined as increased oesophageal signal in T2-fat-saturated (T2fs), short-tau inversion-recovery (STIR), or late gadolinium enhancement (LGE) sequences. Oesophageal endoscopy was performed by experienced operators. Finally, we correlated the presence of any affection with endoscopically detected oesophageal thermal lesions (EDEL). Among 50 consecutive patients (age 67 ± 7 years, 60% male), who received post-ablation MRI and OE, complete MRI data were available in 44 of 50 (88%) patients. In OE, 7 of 50 (14%) presented with EDEL (Category 1 lesion: erosion n = 3, Category 2 lesion: ulcer n = 4). Among those with EDEL, 6 of 7 (86%) patients presented with increased signal intensities in all three MRI sequences, while only 2 of 37 (5%) showed hyperintensities in all three MRI sequences and negative endoscopy. Correspondingly, sensitivity, specificity, positive predictive value, and negative predictive value (NPV) for MRI (increased signal in T2fs, STIR, and LGE) were 86%, 95%, 75%, and 97%, respectively.

Conclusion 

Increased signal intensity in T2fs, STIR, and LGE represents independent markers of EDEL. In particular, the combination of all three has the highest diagnostic value. Hence, MRI may represent an accurate, non-invasive method to exclude acute oesophageal injury after AF ablation (NPV: 97%).

Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform

Ligand binding to death receptors activates apoptosis in cancer cells. Stimulation of death receptors results in the formation of intracellular multiprotein platforms that either activate the apoptotic initiator Caspase-8 to trigger cell death, or signal through kinases to initiate inflammatory and cell survival signalling. Two of these platforms, the Death-Inducing Signalling Complex (DISC) and the RIPoptosome, also initiate necroptosis by building filamentous scaffolds that lead to the activation of mixed lineage kinase domain-like pseudokinase. To explain cell decision making downstream of death receptor activation, we developed a semi-stochastic model of DISC/RIPoptosome formation. The model is a hybrid of a direct Gillespie stochastic simulation algorithm for slow assembly of the RIPoptosome and a deterministic model of downstream caspase activation. The model explains how alterations in the level of death receptor-ligand complexes, their clustering properties and intrinsic molecular fluctuations in RIPoptosome assembly drive heterogeneous dynamics of Caspase-8 activation. The model highlights how kinetic proofreading leads to heterogeneous cell responses and results in fractional cell killing at low levels of receptor stimulation. It reveals that the noise in Caspase-8 activation-exclusively caused by the stochastic molecular assembly of the DISC/RIPoptosome platform-has a key function in extrinsic apoptotic stimuli recognition.

USE OF CIRCULATING TUMOR DNA FOR DETECTION OF BRAF V600E MUTATION AND TREATMENT MONITORING IN MELANOMA PATIENTS

Detection of BRAF V600E mutation in circulating tumor DNA may be important tool for primary diagnostic and therapeutic monitoring in patients with melanoma. For the first time in Ukraine, the sensitivity of BRAF V600E testing on circulating tumor DNA was analyzed, as well as the possibility of its application for monitoring the course of the disease. Allele-specific semi-quantitative Real-time PCR for BRAF V600E mutation was performed on DNA extracted from 28 plasma samples of 18 patients with known BRAF V600E melanoma. At baseline, BRAF V600E ctDNA was detected in 67% of all patients (n=11/17) and in 75% (n=11/15) of patients with IV stage. In 7 cases we have more than one blood sample from patient. In 2 of 3 patients with positive BRAF V600E ctDNA at the baseline, mutation became undetectable during therapy that was associated with stable disease and partial response. In 2 cases patients had stage II and after surgery BRAF V600E ctDNA was undetectable, but then mutation was detected prior to clinical disease progression (PD) in one case and simultaneously with PD in another. One patient with resected brain metastasis of melanoma with unknown primary also had negative baseline and second sample (after 5 months) but BRAF V600E was detected in third sample (after 11 months) without radiological evidence of progression. ctDNA in plasma is a good source for BRAF V600E primary testing in case of absence or low quality of FFPE tissue and potential instrument for monitoring of disease flowing. Its potential role in management of patients with malignant melanoma requires further evaluation.

Coronary CT angiography in patients with atrial fibrillation: Standard-dose and low-dose imaging with a high-resolution whole-heart CT scanner

OBJECTIVE

To compare image quality, observer confidence, radiation exposure in the standard-dose (SD-CCTA) and low-dose (LD-CCTA) protocols of coronary CT angiography (CCTA) in patients with atrial fibrillation (AF).

MATERIAL AND METHODS

CCTA was performed in 303 patients using a CT scanner with 16-cm coverage (111 scans during sinus rhythm (SR); 192 during AF). LD-CCTA was used in 218 patients; SD-CCTA in 85 patients suspected of having coronary artery disease (CAD). Image quality and observer confidence were evaluated on 5-point scales. Radiation doses were recorded.

RESULTS

Image quality was superior in the SD-CCTA compared to the LD-CCTA (SR 1.45±0.40; AF 1.72±0.46; vs. SR 1.83±0.48; AF 1.92±0.50; p < 0.001). Observers were more confident with SD-CCTA than with LD-CCTA (SR 1.38±0.33; AF 1.61±0.43; vs. SR 1.70±0.45; AF 1.82±0.50; p < 0.001). Radiation doses in AF were significantly higher than in the SR (LD-CCTA, 1.68±0.71 mSv; SD-CCTA, 3.72±1.95 mSv; vs. LD-CCTA, 1.3 ±0.52 mSv; SD-CCTA, 2.67±1.47 mSv; p < 0.001).

CONCLUSION

Using a low-dose protocol in AF, radiation exposure can be decreased by 50 % at the expense of 20 % impaired image quality. A low-dose CCTA protocol can be considered in young patients, whereas the standard-dose protocol is recommended for older patients and those suspected of having CAD.

KEY POINTS

• Whole-heart CT allows visualization of the coronary arteries in atrial fibrillation. • Low-dose CT decreases radiation exposure by 50%, image quality by 20%. • Standard-dose CT seems advantageous when concomitant coronary artery disease is suspected.

The TGF-beta - SMAD pathway is inactivated in cronic lymphocytic leukemia cells

AIM

To study the status of the tumor growth factor beta (TGFB) pathway in chronic lymphocytic leukemia (CLL) cells and to uncover molecular details underlying CLL cell genesis.

OBJECTS AND METHODS

The study was conducted on peripheral blood samples of patients with CLL using the following methods: RNA isolation, analysis of expression of transcription factors using RT2 profiler assay, bioinformatics analysis of publicly available data bases on expression.

RESULTS

We have shown that the TGFB - SMAD canonical pathway is not active in CLL cells. SMAD-responsive genes, such as BCL2L1 (BCL-XL), CCND2 (Cyclin D2), and MYC, are down-regulated in CLL cells compared with peripheral blood B cells of healthy donors.

CONCLUSIONS

The TGFB-mediated signaling is not active in CLL cells due to low (or absent) expression of SMAD1, -4, -5, -9, and ATF-3. Expression and phosphorylation status of SMAD2 and -3 should be further elucidated in the future studies.

Specificity, propagation, and memory of pericentric heterochromatin

The cell establishes heritable patterns of active and silenced chromatin via interacting factors that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts. We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2 demarcate the PCH state. From the experimental data, we developed a predictive mathematical model that explains how chromatin-bound SUV39H1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin dynamics. This “nucleation and looping” mechanism is particularly robust toward transient perturbations and stably maintains the PCH state. These features make it an attractive model for establishing functional epigenetic domains throughout the genome based on the localized immobilization of chromatin-modifying enzymes.