Expanding the phenotype of Harel-Yoon syndrome: A case report suggesting a genotype/phenotype correlation.

Harel-Yoon syndrome (HAYOS) is a unique neurodevelopmental genetic disorder characterized by hypotonia, spasticity, intellectual disability, hypertrophic cardiomyopathy, and global developmental delay. It primarily results from mutations in the ATAD3A gene, pivotal for mitochondrial function. This report presents a 5-year-old girl with HAYOS harboring a de novo heterozygous variant c.1064G>A; (p.G355D) in ATAD3A. Her clinical profile includes delayed milestones, hypotonia, spastic quadriplegia, and ptosis. Notably, dermatologic anomalies such as hypopigmentation, café au lait macules, and freckling are observed, expanding the known phenotype of HAYOS. The inclusion of dermatologic features challenges our understanding of the syndrome and emphasizes the importance of further research to elucidate the molecular connections between ATAD3A mutations and dermatologic manifestations.

Non-Radical Activation of Peracetic Acid by Powdered Activated Carbon for the Degradation of Sulfamethoxazole.

Environmental-friendly and low-cost catalysts for peracetic acid (PAA) activation are vital to promote their application for micropollutant degradation in water. In this study, powdered activated carbon (PAC) was reported to improve the degradation of sulfamethoxazole (SMX). The improvement of SMX degradation in the PAC/PAA system was expected to be because of the PAA activation rather than the co-existing H2O2 activation. Non-radical oxidation pathways, including the mediated electron-transfer process and singlet oxygen (1O2), were evidenced to play the dominant roles in the degradation of micro-organic pollutants. The graphitization of PAC, persistent free radicals, and electron-donating groups like C-OH were proposed to contribute to the activation of PAA. High SMX degradation could be achieved in the acidic and neutral conditions in the PAC/PAA system. Overall, higher dosages of PAC (0-0.02 g/L) and PAA (0-100 µM) benefited the degradation of SMX. The presence of HCO3- could lower the SMX degradation significantly, while Cl-, PO43-, and humic acid (HA) only reduced the SMX degradation efficiency a little. Overall, this study offered an efficient non-radical PAA activation method using PAC, which can be effectively used to degrade micro-organic pollutants.

Immobilized penicillin G acylase with enhanced activity and stability using glutaraldehyde-modified polydopamine-coated Fe3 O4 nanoparticles.

In this work, Fe3 O4 nanoparticles (NPs) were coated with polydopamine (PDA) to structure Fe3 O4 @PDA NPs by the spontaneous oxygen-mediated self-polymerization of dopamine (DA) in an aqueous solution of pH = 8.5. The fabricated Fe3 O4 @PDA NPs were grafted by glutaraldehyde to realize the immobilization of penicillin G acylase (PGA) under mild conditions. The carriers of each stage were characterized and investigated by transmission electron microscopy, X-ray diffraction, Fourier transform infrared, and vibrating sample magnetometry. To improve the catalytic activity and stability of immobilized PGA, the immobilization conditions were investigated and optimized. Under the optimal immobilization conditions, the enzyme loading capacity, enzyme activity, and enzyme activity recovery of immobilized PGA were 114 mg/g, 26,308 U/g, and 78.5%, respectively. In addition, the immobilized PGA presented better temperature and pH stability compared with free PGA. The reusability study ensured that the immobilized PGA showed an excellent repeating application performance. In particular, the recovery rate of immobilized PGA could reach 94.8% and immobilized PGA could retain 73.0% of its original activity after 12 cycles, indicating that the immobilized PGA exhibited a high operation stability and broad application potential in the biocatalysis field.

Genotype-Phenotype Correlation in NF1: Evidence for a More Severe Phenotype Associated with Missense Mutations Affecting NF1 Codons 844-848.

Neurofibromatosis type 1 (NF1), a common genetic disorder with a birth incidence of 1:2,000-3,000, is characterized by a highly variable clinical presentation. To date, only two clinically relevant intragenic genotype-phenotype correlations have been reported for NF1 missense mutations affecting p.Arg1809 and a single amino acid deletion p.Met922del. Both variants predispose to a distinct mild NF1 phenotype with neither externally visible cutaneous/plexiform neurofibromas nor other tumors. Here, we report 162 individuals (129 unrelated probands and 33 affected relatives) heterozygous for a constitutional missense mutation affecting one of five neighboring NF1 codons-Leu844, Cys845, Ala846, Leu847, and Gly848-located in the cysteine-serine-rich domain (CSRD). Collectively, these recurrent missense mutations affect ∼0.8% of unrelated NF1 mutation-positive probands in the University of Alabama at Birmingham (UAB) cohort. Major superficial plexiform neurofibromas and symptomatic spinal neurofibromas were more prevalent in these individuals compared with classic NF1-affected cohorts (both p < 0.0001). Nearly half of the individuals had symptomatic or asymptomatic optic pathway gliomas and/or skeletal abnormalities. Additionally, variants in this region seem to confer a high predisposition to develop malignancies compared with the general NF1-affected population (p = 0.0061). Our results demonstrate that these NF1 missense mutations, although located outside the GAP-related domain, may be an important risk factor for a severe presentation. A genotype-phenotype correlation at the NF1 region 844-848 exists and will be valuable in the management and genetic counseling of a significant number of individuals.

Optimization of penicillin G acylase immobilized on glutaraldehyde-modified titanium dioxide.

In this work, TiO2 , which was modified by glutaraldehyde, was adopted as the carrier; the penicillin G acylase (PGA) was immobilized and the influence of immobilized conditions, such as pH of solution, the concentration of PGA, the immobilization temperature, and the reaction time, on the catalytic performance of the immobilized PGA was investigated and optimized. During this process, potassium penicillin G (PG) was chosen as substrate, and the quantity of 6-aminopenicillanic acid (6-APA) produced by PG at the temperature of 25 °C for 3 Min in neutral solution was conscripted as the evaluation foundation, indexes, containing the loading capacity (ELC), the activity (EA), and activity retention rate (EAR), were calculated based on quantities of produced 6-APA and compared with finding out the suitable conditions. Results showed that when the solution pH, PGA concentration, immobilization temperature, and reaction time were 8.0, 2.5% (v/v), 35 °C, and 24 H, respectively, ELC, EA, and EAR presented optimal values of 9,190 U, 14,969 U/g, and 88.5% relatedly. After that, the stability and reusability of immobilized PGA were studied, and the results documented that the pH resistance, thermal stability, and storage stability of immobilized PGA were significantly improved. This work provided technique support for the practical application of immobilized PGA carrier.

Preparation and characterization of a novel molecularly imprinted polymer for the separation of glycyrrhizic acid.

Molecularly imprinted polymers of glycyrrhizic acid were prepared by solution polymerization using glycyrrhizic acid as the template molecule, N-vinypyrrolidone as functional monomer, N,N-methylene bisacrylamide as cross-linker and ascorbic acid and hydrogen peroxide as initiators. Focused on the adsorption capacity and separation degree of the polymer to glycyrrhizic acid, the effects of the monomers, crosslinker and initiators were investigated and optimized. Finally, the structure of the polymer was characterized by using Fourier transform infrared spectroscopy and scanning electron microscopy. To obtain objective results, non-imprinted molecular polymers prepared under the same conditions were also characterized. The adsorption quantity of the polymer was measured by high-performance liquid chromatography. Under the optimum conditions, the maximum adsorption capacity of glycyrrhizic acid approached 15 mg/g, and the separation degree was as high as 2.5. The adsorption kinetics could be well described by a pseudo-first-order model, while the thermodynamics of the adsorption process could be described by the Langmuir model.

Integrated genomic profiling identifies microRNA-92a regulation of IQGAP2 in locally advanced rectal cancer.

Locally advanced rectal cancer (LARC) is treated with chemoradiation prior to surgical excision, leaving residual tumors altered or completely absent. Integrating layers of genomic profiling might identify regulatory pathways relevant to rectal tumorigenesis and inform therapeutic decisions and further research. We utilized formalin-fixed, paraffin-embedded pre-treatment LARC biopsies (n=138) and compared copy number, mRNA, and miRNA expression with matched normal rectal mucosa. An integrative model was used to predict regulatory interactions to explain gene expression changes. These predictions were evaluated in vitro using multiple colorectal cancer cell lines. The Cancer Genome Atlas (TCGA) was also used as an external cohort to validate our genomic profiling and predictions. We found differentially expressed mRNAs and miRNAs that characterize LARC. Our integrative model predicted the upregulation of miR-92a, miR-182, and miR-221 expression to be associated with downregulation of their target genes after adjusting for the effect of copy number alterations. Cell line studies using miR-92a mimics and inhibitors demonstrate that miR-92a expression regulates IQGAP2 expression. We show that endogenous miR-92a expression is inversely associated with endogenous KLF4 expression in multiple cell lines, and that this relationship is also present in rectal cancers of TCGA. Our integrative model predicted regulators of gene expression change in LARC using pre-treatment FFPE tissues. Our methodology implicated multiple regulatory interactions, some of which are corroborated by independent lines of study, while others indicate new opportunities for investigation.

KRAS and Combined KRAS/TP53 Mutations in Locally Advanced Rectal Cancer are Independently Associated with Decreased Response to Neoadjuvant Therapy.

BACKGROUND: The response of rectal cancers to neoadjuvant chemoradiation (CRT) is variable, but tools to predict response remain lacking. We evaluated whether KRAS and TP53 mutations are associated with pathologic complete response (pCR) and lymph node metastasis after adjusting for neoadjuvant regimen. METHODS: Retrospective analysis of 229 pretreatment biopsies from patients with stage II/III rectal cancer was performed. All patients received CRT. Patients received 0-8 cycles of FOLFOX either before or after CRT, but prior to surgical excision. A subset was analyzed to assess concordance between mutation calls by Sanger Sequencing and a next-generation assay. RESULTS: A total of 96 tumors (42 %) had KRAS mutation, 150 had TP53 mutation (66 %), and 59 (26 %) had both. Following neoadjuvant therapy, 59 patients (26 %) achieved pCR. Of 133 KRAS wild-type tumors, 45 (34 %) had pCR, compared with 14 of 96 (15 %) KRAS mutant tumors (p = .001). KRAS mutation remained independently associated with a lower pCR rate on multivariable analysis after adjusting for clinical stage, CRT-to-surgery interval and cycles of FOLFOX (OR 0.34; 95 % CI 0.17-0.66, p < .01). Of 29 patients with KRAS G12V or G13D, only 2 (7 %) achieved pCR. Tumors with both KRAS and TP53 mutation were associated with lymph node metastasis. The concordance between platforms was high for KRAS (40 of 43, 93 %). CONCLUSIONS: KRAS mutation is independently associated with a lower pCR rate in locally advanced rectal cancer after adjusting for variations in neoadjuvant regimen. Genomic data can potentially be used to select patients for "watch and wait" strategies.

Acute toxicity formation potential of benzophenone-type UV filters in chlorination disinfection process.

Benzophenones (BPs) are a class of widely used UV filters, which have been frequently detected within multiple environmental matrices. Disinfection is a necessary process in water treatment processes. The transformation behaviors and toxicity changes of 14 BP-type UV filters during chlorination disinfection treatment were investigated in this study. A new index, the acute toxicity formation potential, was proposed to evaluate the toxicity changes and potential risks of BP-type UV filters during chlorination treatment. It was found that 13 of 14 BP-type UV filters exhibited toxicity decreases in the chlorination disinfection process, more or less, while one showed a toxicity increase. The toxicity changes were dependent on substitution effects, such that 2,4-di-hydroxylated or 3-hydroxylated BPs exhibited significant toxicity decreases after chlorination treatment due to the ready cleavage of the aromatic ring. Importantly, the acute toxicity changes could be duplicated in an ambient water matrix.

Efficient disinfection of combined sewer overflows by ultraviolet/peracetic acid through intracellular oxidation with preserving cell integrity.

Combined sewer overflows (CSOs) introduce microbial contaminants into the receiving water bodies, thereby posing risks to public health. This study systematically investigated the disinfection performance and mechanisms of the combined process of ultraviolet and peracetic acid (UV/PAA) in CSOs with selecting Escherichia coli (E. coli) as a target microbial contaminant. The UV/PAA process exhibited superior performance in inactivating E. coli in simulated CSOs compared with UV, PAA, and UV/H2O2 processes. Increasing the PAA dosage greatly enhanced the disinfection efficiency, while turbidity and organic matter hindered the inactivation performance. Singlet oxygen (1O2), hydroxyl (•OH) and organic radicals (RO•) contributed to the inactivation of E. coli, with •OH and RO• playing the prominent role. Variations of intracellular reactive oxygen species, malondialdehyde, enzymes activities, DNA contents and biochemical compositions of E. coli cells suggested that UV/PAA primarily caused oxidative damage to intracellular molecules rather than the damage to the lipids of the cell membrane, therefore effectively limited the regrowth of E. coli. Additionally, the UV/PAA process displayed an outstanding performance in disinfecting actual raw CSOs, achieving a 2.90-log inactivation of total bacteria after reaction for 4 min. These results highlighted the practical applicability and effectiveness of the UV/PAA process in the disinfection of CSOs.

Gene polymorphisms predict toxicity to neoadjuvant therapy in patients with rectal cancer.

BACKGROUND: Toxicity from neoadjuvant chemoradiation therapy (NT) increases morbidity and limits therapeutic efficacy in patients with rectal cancer. The objective of this study was to determine whether specific polymorphisms in genes associated with rectal cancer response to NT were correlated with NT-related toxicity. METHODS: One hundred thirty-two patients with locally advanced rectal cancer received NT followed by surgery. All patients received 5-fluorouracil (5-FU) and radiation (RT), and 80 patients also received modified infusional 5-FU, folinic acid, and oxaliplatin chemotherapy (mFOLFOX-6). Grade ≥3 adverse events (AEs) that occurred during 5-FU/RT and during combined 5-FU/RT + mFOLFOX-6 were recorded. Pretreatment biopsy specimens and normal rectal tissues were collected from all patients. DNA was extracted and screened for 22 polymorphisms in 17 genes that have been associated with response to NT. Polymorphisms were correlated with treatment-related grade ≥3 AEs. RESULTS: Overall, 27 of 132 patients (20%) had grade ≥3 AEs; 18 patients had a complication associated only with 5-FU/RT, 3 patients experienced toxicity only during mFOLFOX-6, and 6 patients had grade ≥3 AEs associated with both treatments before surgery. Polymorphisms in the genes x-ray repair complementing defective repair in Chinese hamster cells 1 (XRCC1), xeroderma pigmentosum group D (XPD), and tumor protein 53 (TP53) were associated with grade ≥3 AEs during NT (P < .05). Specifically, 2 polymorphisms-an arginine-to-glutamine substitution at codon 399 (Q399R) in XRCC1 and a lysine-to-glutamine substitution at codon 751 (K751Q) in XPD-were associated with increased toxicity to 5-FU/RT (P < .05), and an arginine-to-proline substitution at codon 72 (R72P) in TP53 was associated with increased toxicity to mFOLFOX-6 (P = .008). CONCLUSIONS: Specific polymorphisms in XRCC1, XPD, and TP53 were associated with increased toxicity to NT in patients with rectal cancer. The current results indicated that polymorphism screening may help tailor treatment for patients by selecting therapies with the lowest risk of toxicity, thus increasing patient compliance.

Mutations in specific codons of the KRAS oncogene are associated with variable resistance to neoadjuvant chemoradiation therapy in patients with rectal adenocarcinoma.

BACKGROUND: Mutations in KRAS and TP53 are common in colorectal carcinogenesis and are associated with resistance to therapy. Rectal cancers carrying both mutations are less likely to respond to neoadjuvant chemoradiation therapy (CRT) compared with wild-type tumors. Codon-specific KRAS mutations are associated with variable resistance to targeted therapies, but their association with rectal cancer response to CRT remains unclear. Our objective was to establish a correlation between specific KRAS mutations and rectal cancer response to CRT and to investigate if the correlation was related to a different association between KRAS and TP53 mutations. METHODS: A total of 148 stage II-III rectal cancer patients underwent preoperative CRT followed by surgery. DNA was extracted from pretreatment tumor biopsies and paired normal surgical tissues and KRAS and TP53 genotyping was performed. Specific KRAS mutations were then correlated with tumor response and with concurrent TP53 mutation. RESULTS: A total of 60 patients had KRAS mutation, 12 in codon 13 and 48 in other locations. Also, 80 patients had TP53 mutation; 27 had concurrent KRAS/TP53 mutations. Tumors with any KRAS mutation were less likely to have a pCR compared with wild-type KRAS (p = 0.006). Specifically, no tumors with KRAS codon 13 mutations had a pCR (p = 0.03). Tumors with KRAS codon 13 mutations also had a higher incidence of concurrent TP53 mutation compared with tumors with other KRAS mutations (p = 0.02). CONCLUSIONS: Mutations in different KRAS codons may have different effects on rectal cancer resistance to CRT. This variable resistance may be related to a different frequency of TP53 mutations in KRAS mutant tumors.

Distribution of residual cancer cells in the bowel wall after neoadjuvant chemoradiation in patients with rectal cancer.

BACKGROUND: The standard treatment for locally advanced rectal cancer is preoperative chemoradiation and total mesorectal excision. After surgery, tumors are classified according to the depth of tumor invasion, nodal involvement, and tumor regression grade. However, these staging systems do not provide information about the distribution of residual cancer cells within the bowel wall. OBJECTIVE: This study aimed to determine the distribution of residual cancer cells in each layer of the bowel wall in rectal cancer specimens. DESIGN: This was a secondary analysis of data from a prospective phase II study. SETTING: This study was performed in a multi-institutional setting. PATIENTS: Included were 153 patients with stage II or stage III rectal cancer. INTERVENTIONS: Patients were treated with chemoradiation and surgery. The surgical specimen tumor tissue was analyzed, and the distribution of residual cancer cells in each layer of the bowel wall was determined. MAIN OUTCOME MEASURES: Statistical analysis was used to examine the correlation of residual cancer cells in each layer of the bowel wall with the clinical/pathologic stage and tumor regression grade. RESULTS: Forty-two of 153 (27%) patients had complete response in the bowel wall (ypT0). Of the remaining 111 patients who had residual cancer cells, 5 (3%) were ypTis, 12 (8%) were ypT1, 41 (27%) were ypT2, 50 (33%) were ypT3, and 3 (2%) were ypT4. Of the 94 patients with ypT2-4 tumors, 12 (13%) had cancer cells in the mucosa, and 53 (56%) had cancer cells in the submucosa; 92 (98%) had cancer cells in the muscularis propria. Pretreatment cT correlated with the distribution of residual cancer cells. Tumor regression grade was not associated with the distribution of residual cancer cells after chemoradiation. LIMITATIONS: : Patients received different chemotherapy regimens. CONCLUSIONS: Residual cancer cells in rectal cancer specimens after chemoradiation are preferentially located close to the invasive front. This should be considered when designing strategies to diagnose complete pathologic response and when investigating the mechanisms of tumor resistance to chemoradiation.

Effect of Multifactor on the Stability of Glucose Solution Emulsified Heavy Fuel Oil.

Water emulsified heavy fuel oil (HFO) has been a promising alternative fuel for reducing oil consumption and preventing environmental pollution. However, the intrinsic challenges such as fuel formula, emulsion stability, and preparation process normally limit its further applications in energy-saving and emission reduction applications. In this study, the glucose obtained from biomass was added to a dispersed-phase aqueous solution of water emulsified HFO to prepare a novel alternative emulsified fuel. First, based on the preliminary experimental design, the effects of glucose and surfactant on the stability of the HFO emulsion were systematically evaluated through the appearance of emulsion separation, droplet size distribution, and rheological characteristics. It indicated that the surfactant ratio, hydrophilic-lipophilic balance value, solution ratio, and glucose/water ratio had significant impacts on emulsion stability. Subsequently, the optimum range of influencing factors of emulsion stability was determined by a single factor experiment and determined by the response surface methodology based on the Box-Behnken design; the optimal values of the above factors were 2.439 v/v%, 5.807, 26.462 v/v%, and 35.729%, respectively. Under these conditions, an optimal glucose solution emulsified HFO with a uniform brown color and long-term stability was obtained, making the unseparated emulsion ratio reach 98% (lasting for 7 days at 85 °C). Meanwhile, it emerged that the influence of multifactor on emulsion stability was not a simple linear correlation, and there were significant interactions between the solution ratio and the surfactant ratio, as well as between the glucose/water ratio and the surfactant ratio.

Influence of PODE1 additive into ethanol-gasoline blends (E10) on fuel properties and phase stability.

Polyoxymethylene dimethyl ethers (PODEn, n = 1-8) as an oxygenated fuel are a promising alternative fuel with a high oxygen concentration, a low C:H ratio, and no C-C bonds in their chemical structure. This could lead to smoke-free combustion. In this study, we chose to focus on PODE1 because of its lower cetane number, which makes it more suitable for use in spark ignition (SI) engines. However, its lower boiling point and octane number remain challenges. A low boiling point may lead to high vapour pressure and require storage and handling comparable to gaseous fuels. We investigated the effect of adding PODE1 to gasoline-ethanol blends (E10) on fuel properties, including distillation curve, octane number, phase stability, C/O/H ratio, heat of combustion, kinematic viscosity, and density. Our results showed that the blended fuels of E10 and PODE1 are stable up to 10 % PODE1, and there was no phase separation. Additionally, up to 10 % PODE1 additive had no significant side effect on the fuel properties of E10, particularly boiling point and octane number. Thus, work offers creative points by proposing a new candidate for additive fuel to gasoline-ethanol blends, which contributes to reducing the soot emission of GDI engines.

New insights into the degradation of micro-pollutants in the hydroxylamine enhanced Fe(II)/peracetic acid process: Contribution of reactive species and effects of pH.

The hydroxylamine-enhanced Fe(II)/peracetic acid (PAA) process is a promising advanced oxidation process (AOP) with the generation of reactive species (RS) including RO•, •OH and Fe(IV). Nevertheless, it is still challenging to identify which RS is the major intermediate oxidant, and the reasons why the optimal condition is pH 4.5 rather than 3.0 are also unclear. Herein, the generation of RS and their contribution to the degradation of three micro-pollutants were explored. The quenching experiments and pseudo first-order kinetic model demonstrated that RO• rather than the other two RS were predominant. Then the overall generation and evolution pathways of RS were depicted. The elevation of pH (3.0-4.5) would accelerate the Fe(II)/Fe(III) redox cycle through the enhanced reduction of Fe(III) by hydroxylamine and induce the conversion of Fe(IV) to RO•, which benefited naproxen degradation. While the adverse Fe(III) precipitation would dominate the reduced degradation performance with the solution pH higher than 4.5. The elevation of PAA and Fe(II) dosages sped up the PAA activation, while excess hydroxylamine could consume the formed RS and exhibited an inhibitory effect. This study helps further understand the role of HA and differentiate the contribution of RS in the emerging PAA-based AOPs.

Magnetic chitosan/TiO2 composite for vanadium(v) adsorption simultaneously being transformed to an enhanced natural photocatalyst for the degradation of rhodamine B.

A magnetic chitosan/TiO2 composite material (MCT) was developed. MCT was successfully synthesized by a one-pot method using chitosan, TiO2, and Fe3O4. The absorption equilibrium time of MCT was 40 min in absorbing vanadium(v), the optimal adsorption pH was 4, and the maximum adsorption capacity of vanadium(v) was 117.1 mg g-1. The spent MCT was applied to photocatalytic reactions for reutilization. The decolorization rates for the degradation of rhodamine B (RhB) by new and spent MCT were 86.4% and 94.3%, respectively. The new and spent MCT exhibited absorption bands at 397 and 455 nm, respectively, which showed that the spent MCT was red-shifted to the cyan light region. These results indicated that the forbidden band widths of the new and spent MCT were about 3.12 and 2.72 eV, respectively. The mechanism of the degradation reaction showed that the hydroxyl radicals as oxidants in the spent MCT mediated the photocatalytic degradation of RhB. In addition, the superoxide anion radical formation of hydroxyl radicals was the main reaction, and the hole generation of hydroxyl radicals was the subordinate reaction. The N-de-ethylated intermediates and organic acids were monitored by MS and HPLC.

Chromosomal copy number alterations are associated with persistent lymph node metastasis after chemoradiation in locally advanced rectal cancer.

BACKGROUND: Lymph node metastasis is an important indicator of oncologic outcome for patients with rectal cancer. Identifying predictive biomarkers of lymph node metastasis could therefore be clinically useful. OBJECTIVE: The aim of this study was to assess whether chromosomal copy number alterations can assist in predicting persistent lymph node metastasis in patients with locally advanced rectal cancer treated with preoperative chemoradiation therapy. DESIGN: This is a nonrandomized, prospective phase II study. SETTING: This study took place in a multi-institutional setting. PATIENTS: Ninety-five patients with stage II (cT3-4, cN0) or stage III (any cT, cN1-2) rectal cancer were included. INTERVENTION: Patients were treated with preoperative chemoradiation therapy followed by total mesorectal excision. Pretreatment biopsy tumor DNA and surgical margin control DNA were extracted and analyzed by oligonucleotide array-based comparative genomic hybridization. Chromosomal copy number alterations were correlated with persistent lymph node metastasis. Finally, a model for predicting persistent lymph node metastasis was built. MAIN OUTCOME MEASURES: The primary outcomes assessed were whether chromosomal copy number alterations are associated with persistent lymph node metastasis in patients with rectal cancer and the accuracy of oligonucleotide array-based comparative genomic hybridization for predicting lymph node metastasis. RESULTS: Twenty-five of 95 (26%) patients had lymph node metastasis after chemoradiation. Losses of 28 chromosomal regions, most notably in chromosome 4, were significantly associated with lymph node metastasis. Our predictive model contained 65 probes and predicted persistent lymph node metastasis with 68% sensitivity, 93% specificity, and positive and negative predictive values of 77% and 89%. The use of this model accurately predicted lymph node status (positive or negative) after chemoradiation therapy in 82 of 95 patients (86%). LIMITATIONS: The patient cohort was not completely homogeneous, which may have influenced their clinical outcome. In addition, although we performed rigorous, statistically sound internal validation, external validation will be important to further corroborate our findings. CONCLUSIONS: Copy number alterations can help identify patients with rectal cancer who are at risk of lymph node metastasis after chemoradiation.

Gene expression variations in microsatellite stable and unstable colon cancer cells.

BACKGROUND: Microsatellite instability (MSI) is a marker of chemoresistance, but it is associated with improved survival compared with microsatellite-stable (MSS) colon cancers. We hypothesized that MSI tumors overexpress chemoresistance-associated genes and underexpress DNA damage/repair genes. We used ultra high-throughput sequencing (UHTS) to assess the expression of representative genes in MSI and MSS colon cancer cell lines. METHODS: Solexa UHTS was used to examine gene expression in HCT116 (MSI) and HT29 (MSS) cells, and normal colonic mucosa (NCM). We compared expression of 40 genes involved in chemoresistance, DNA repair, DNA damage, and drug metabolism pathways. RESULTS: We observed gene expression differences between MSI and MSS cell lines in 8 out of 40 genes involved in mismatch repair (MMR), DNA repair, drug metabolism, and chemoresistance. MMR gene expression was lower in MSI cells, which is consistent with the MSI phenotype, whereas DNA repair genes were highly expressed in these cells. Genes associated with chemoresistance and drug metabolism also had increased expression in MSI cells. No difference in expression of DNA damage genes was observed between MSI and MSS cell lines. CONCLUSION: Using UHTS gene expression analysis, we identified differential expression of genes between MSI and MSS cell lines which may account for resistance to chemotherapy in MSI tumors. UHTS expression analysis has the potential to identify genome-wide predictors of response or resistance to chemotherapy.

Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer.

Rectal cancer response to chemoradiation (CRT) varies from no response to a pathologic complete response (pCR). Identifying predictive biomarkers of response would therefore be useful. We assessed whether chromosomal copy number alterations (CNAs) can assist in predicting pCR. Pretreatment tumor biopsies and paired normal surgical tissues from the proximal resection margin were collected from 95 rectal cancer patients treated with preoperative CRT and total mesorectal excision in a prospective Phase II study. Tumor and control DNA were extracted, and oligonucleotide array-based comparative genomic hybridization (aCGH) was used to identify CNAs, which were correlated with pCR. Ingenuity pathway analysis (IPA) was then used to identify functionally relevant genes in aberrant regions. Finally, a predictive model for pCR was built using support vector machine (SVM), and leave-one-out cross validation assessed the accuracy of aCGH. Chromosomal regions most commonly affected by gains were 20q11.21-q13.33, 13q11.32-23, 7p22.3-p22.2, and 8q23.3-q24.3, and losses were present at 18q11.32-q23, 17p13.3-q11.1, 10q23.1, and 4q32.1-q32.3. The 25 (26%) patients who achieved a pCR had significantly fewer high copy gains overall than non-pCR patients (P = 0.01). Loss of chromosomal region 15q11.1-q26.3 was significantly associated with non-pCR (P < 0.00002; Q-bound < 0.0391), while loss of 12p13.31 was significantly associated with pCR (P < 0.0003; Q-bound < 0.097). IPA identified eight genes in the imbalanced chromosomal regions that associated with tumor response. SVM identified 58 probes that predict pCR with 76% sensitivity, 97% specificity, and positive and negative predictive values of 91% and 92%. Our data indicate that chromosomal CNAs can help identify rectal cancer patients more likely to develop a pCR to CRT.