RNA-seq analysis identifies transcriptomic profiles associated with anal cancer recurrence among people living with HIV

BACKGROUND

Chemoradiation therapy (CRT) is the standard of care for squamous cell carcinoma of the anus (SCCA), the most common type of anal cancer. However, approximately one fourth of patients still relapse after CRT.

METHODS

We used RNA-sequencing technology to characterize coding and non-coding transcripts in tumor tissues from CRT-treated SCCA patients and compare them between 9 non-recurrent and 3 recurrent cases. RNA was extracted from FFPE tissues. Library preparations for RNA-sequencing were created using SMARTer Stranded Total RNA-Seq Kit. All libraries were pooled and sequenced on a NovaSeq 6000. Function and pathway enrichment analysis was performed with Metascape and enrichment of gene ontology (GO) was performed with Gene Set Enrichment Analysis (GSEA).

RESULTS

There were 449 differentially expressed genes (DEGs) observed (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between the two groups. We identified a core of upregulated genes (IL4, CD40LG, ICAM2, HLA-I (HLA-A, HLA-C) and HLA-II (HLA-DQA1, HLA-DRB5) in the non-recurrent SCCA tissue enriching to the gene ontology term 'allograft rejection', which suggests a CD4+ T cell driven immune response. Conversely, in the recurrent tissues, keratin (KRT1, 10, 12, 20) and hedgehog signaling pathway (PTCH2) genes involved in 'Epidermis Development,', were significantly upregulated. We identified miR-4316, that inhibit tumor proliferation and migration by repressing vascular endothelial growth factors, as being upregulated in non-recurrent SCCA. On the contrary, lncRNA-SOX21-AS1, implicated in the progression of many other cancers, was also found to be more common in our recurrent compared to non-recurrent SCCA.

Our study identified key host factors which may drive the recurrence of SCCA and warrants further studies to understand the mechanism and evaluate their potential use in personalized treatment.Key MessageOur study used RNA sequencing (RNA-seq) to identify pivotal factors in coding and non-coding transcripts which differentiate between patients at risk for recurrent anal cancer after treatment. There were 449 differentially expressed genes (390 mRNA, 12 miRNA, 17 lincRNA and 18 snRNA) between 9 non-recurrent and 3 recurrent squamous cell carcinoma of anus (SCCA) tissues. The enrichment of genes related to allograft rejection was observed in the non-recurrent SCCA tissues, while the enrichment of genes related to epidermis development was positively linked with recurrent SCCA tissues.

Poor predictive ability of urinalysis and microscopic examination to detect urinary tract infection

Results of urinalysis, particularly the leukocyte esterase and nitrite tests, often are used to determine whether treatment is needed or a culture will be performed in cases of suspected urinary tract infection. However, there is disagreement over the quality of urinalysis as a screening test for urinary tract infections. Final urine culture results (n = 225) were obtained from the clinical microbiology laboratory. Stepwise binary logistic regression was used to derive a model using presence of infection as determined by culture as the dependent variable and urinalysis results as independent variables. A second set of data (n = 128) then was obtained to test the model. Statistical significance and the ability to predict infection based on urinalysis results were determined. Results indicated a lack of sensitivity for leukocyte esterase, nitrite, and presence of bacteria in the microscopic examination as indicators of urinary tract infection.

Demonstration of exopolysaccharide production by enterohemorrhagicEscherichia coli

Enterohemorrhagic Escherichia coli O157:H7 produces visibly slimy colonies when grown on Sorbitol/MacConkey or Maloney's agar plates at room temperature, indicative of exopolysaccharide (EPS) production. Eighteen of 27 (67%) wild-type E. coli O157:H7 isolates produced enough EPS to be visually distinguishable. Of five strains that showed no visible EPS production on these media, four (80%) did produce slimy colonies on media containing higher salt concentrations. Measurements of EPS production by colorimetric determination of uronic acid indicated that EPS production was affected by growth temperature, atmosphere, and medium. Wild-type E. coli O157:H7 strain 932 produced the greatest amounts of EPS when grown anaerobically at 37 degrees C, whereas its plasmid-cured derivative 932P produced large quantities of EPS when grown aerobically at room temperature. Electron micrographs revealed thin, flexible fibers extending from the bacterial cell surface. Cells of strain 932P grown aerobically at room temperature were completely encased in a thick EPS matrix. Chemical analysis of purified EPS revealed that it is very similar or identical to colanic acid. E. coli O157:H7 adheres better to INT 407 cells when grown under conditions that favor high EPS production than when grown under conditions that repress EPS production.