Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution

Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications.

Olfactory receptors OR5B21 and OR6C76 are differentially expressed in humans with triple negative breast cancer.

Whole genome profiling data of 226 patients with triple negative breast cancer (1) was stratified based on survival. When comparing the transcriptomes of 87 patients that expired versus 123 patients that survived, two olfactory receptors were among the genes whose expression was most different. We previously reported that genes of the olfactory receptor superfamily were differentially expressed in metastases in the HER2+ Balb-NeuT mouse model of breast cancer (2). The data here indicate that differential expression of OR5B21 and OR6C76 associates with survival outcomes in humans with triple negative breast cancer.

Differential expression of methyltransferase METTL1 associates with death in a cohort of patients with triple negative breast cancer.

Whole genome profiling data of 226 patients with triple negative breast cancer using a published dataset (1) was stratified based on survival. When comparing the transcriptomes of 87 patients that expired versus 123 patients that survived, the methyltransferase like 1 METTL1 was the third most differentially expressed gene in the entire transcriptome. METTL1 mediates 7-methylguanosine modification of microRNAs and tRNAs (2,3,4,5,6). Increased expression of METTL1 is an indication that the disease course will likely result in fatality in patients with triple negative breast cancer and should be treated accordingly.