Isolation and mapping of a putative b subunit of human ATP synthase (ATP-BL) from human leukocytes

An integrated transcriptome and expressed variant analysis of sepsis survival and death

Background

Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality.

Methods

The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (SIRS due to infection), including 78 sepsis survivors and 28 sepsis non-survivors who had previously undergone plasma proteomic and metabolomic profiling. Gene expression differences were identified between sepsis survivors, sepsis non-survivors, and SIRS followed by gene enrichment pathway analysis. Expressed sequence variants were identified followed by testing for association with sepsis outcomes.

Results

The expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflecting immune activation in sepsis. Expression of 1,238 genes differed with sepsis outcome: non-survivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease-rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors. The presence of variants was associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology.

Conclusions

The activation of immune response-related genes seen in sepsis survivors was muted in sepsis non-survivors. The association of sepsis survival with a robust immune response and the presence of missense variants in VPS9D1 warrants replication and further functional studies.

Trial registration

ClinicalTrials.gov NCT00258869. Registered on 23 November 2005.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-014-0111-5) contains supplementary material, which is available to authorized users.

Structural analysis of esp-1 gene (PRSS 21)

The esp-1 gene is originally cloned from human eosinophils and encodes a membrane-type serine protease. This gene is ubiquitously expressed in various tissues but not kidney or muscle, and highly expressed in testis. Among granulocytes, this gene is expressed in eosinophils but not neutrophils, although both are derived from myeloid progenitors. In the present study, we have cloned the esp-1 genome using a BAC library, and determined exon-intron junctions: This gene spans approximately 4.6 kb, and consists of 6 exons and 5 introns. On radiation hybrid and FISH analyses, the esp-1 gene was mapped to 16p13.3. In addition, we have cloned a new splicing variant form of esp-1 from a HeLa cell cDNA library, which contains many esp-1 clones. Both RNase protection and primer extension analyses revealed the transcription initiation site of the esp-1 gene is located at nucleotide position -106, residue G. Dual-luciferase reporter analysis revealed a GC-rich region between nucleotide positions, -106 and -189 containing one AP-1/Sp-1 binding site is responsible for the minimum promoter activity in HeLa cells.