Citations

Blinatumomab is an efficacious immunotherapeutic agent in B cell acute lymphoblastic leukemia (B-ALL). However, the pharmacogenomic basis of leukemia response to blinatumomab is unclear. Using genome-wide CRISPR, we comprehensively identified leukemia intrinsic factors of blinatumomab sensitivity, i.e., the loss of CD58 as a top driver for resistance, in addition to CD19 . Screening 1639 transcription factor genes, we then identified PAX5 as the key activator of CD58. ALL with the PAX5 P80R mutation also expressed the lowest level of CD58 among 20 ALL molecular subtypes in 1988 patients. Genome editing confirmed the effects of this mutation on CD58 expression and blinatumomab sensitivity in B-ALL, with validation in patient leukemic blasts. We described a PAX5-driven enhancer at the CD58 locus, which was disrupted by PAX5 P80R, and the loss of CD58 abolished blinatumomab-induced T cell activation with global changes in transcriptomic/epigenomic program. In conclusion, we identified previously unidentified genetic mechanisms of blinatumomab resistance in B-ALL, suggesting strategies for genomics-guided treatment individualization.

Objectives To investigate the genetic alterations of patients with prostate cancer (PCa) with and without intraductal carcinoma of the prostate (IDC‐P). Patients and Methods We performed targeted sequencing of plasma cell‐free DNA on 161 patients with prostate adenocarcinoma (PAC) with IDC‐P and 84 without IDC‐P. Genomic alterations were compared between these two groups. The association between genetic alterations and patients’ survival outcomes was also explored. Results We identified that 29.8% (48/161) and 21.4% (18/84) of patients with and without IDC‐P harboured genomic alterations in DNA repair pathways, respectively ( P = 0.210). Pathogenic germline DNA repair alterations were frequently detected in IDC‐P carriers compared to IDC‐P non‐carriers (11.8% [19/161] vs 2.4% [two of 84], P = 0.024). Germline BReast CAncer type 2 susceptibility protein ( BRCA2 ) and somatic cyclin‐dependent kinase 12 ( CDK12 ) defects were specifically identified in IDC‐P carriers relative to PAC ( BRCA2 : 8.7% [14/161] vs 0% and CDK12 : 6.8% [11/161] vs 1.2% [one of 84]). Patients with IDC‐P had a distinct androgen receptor (AR) pathway alteration, characterised by an enrichment of nuclear receptor corepressor 2 ( NCOR2 ) mutations compared with patients with pure PAC (21.1% [34/161] vs 6.0% [five of 84], P = 0.004). Increased AR alterations were detected in patients harbouring tumours with an IDC‐P proportion of ≥10% vs those with an IDC‐P proportion of <10% (6.4% [five of 78] vs 18.1% [15/83], P = 0.045). For IDC‐P carriers, tumour protein p53 ( TP53 ) mutation was associated with shorter castration‐resistant‐free survival (median 10.9 vs 28.9 months, P = 0.026), and BRCA2 alteration was related to rapid prostate‐specific antigen progression for those receiving abiraterone treatment (median 9.1 vs 11.9 months, P = 0.036). Conclusion Our findings provide genomic evidence explaining the aggressive phenotype of tumours with IDC‐P, highlighting the potential therapeutic strategies for this patient population.

Abstract TFE3-translocation renal cell carcinoma (TFE3-tRCC) is a rare and heterogeneous subtype of kidney cancer that has no standard treatment for advanced disease. We described comprehensive molecular characteristics of 63 untreated primary TFE3-tRCCs based on whole-exome and RNA sequencing. TFE3-tRCC is highly heterogeneous, both clinicopathologically and genotypically. ASPSCR1-TFE3 fusion, certain fusion isoforms and high somatic copy number alteration burdens were associated with aggressive features and poor outcomes. Apart from tumors with MED15-TFE3 fusion, most TFE3-tRCCs exhibited low PD-L1 expression and low T-cell infiltration. Unsupervised transcriptomic analysis revealed five molecular clusters with distinct angiogenesis, stroma, proliferation and KRAS down signatures, which showed association with fusion patterns and prognosis. Specifically, the high angiogenesis/stroma/proliferation cluster exclusively consisted of tumors with ASPSCR1-TFE3 fusion, which was likely to benefit from combination of immune checkpoint and anti-angiogenesis inhibitors. Our findings reveal the genomic and transcriptomic features of TFE3-tRCC and provide insights into precision medicine for this disease.

AbstractPurpose:Fumarate hydratase–deficient renal cell carcinoma (FH-deficient RCC) is a rare but lethal subtype of RCC. Little is known about the genomic profile of FH-deficient RCC, and the therapeutic options for advanced disease are limited. To this end, we performed a comprehensive genomics study to characterize the genomic and epigenomic features of FH-deficient RCC.Experimental Design:Integrated genomic, epigenomic, and molecular analyses were performed on 25 untreated primary FH-deficient RCCs. Complete clinicopathologic and follow-up data of these patients were recorded.Results:We identified that FH-deficient RCC manifested low somatic mutation burden (median 0.58 mutations per megabase), but with frequent somatic copy-number alterations. The majority of FH-deficient RCCs were characterized by a CpG sites island methylator phenotype, displaying concerted hypermethylation at numerous CpG sites in genes of transcription factors, tumor suppressors, and tumor hallmark pathways. However, a few cases (20%) with low metastatic potential showed relatively low DNA methylation levels, indicating the heterogeneity of methylation pattern in FH-deficient RCC. Moreover, FH-deficient RCC is potentially highly immunogenic, characterized by increased tumor T-cell infiltration but high expression of immune checkpoint molecules in tumors. Clinical data further demonstrated that patients receiving immune checkpoint blockade–based treatment achieved improved progression-free survival over those treated with antiangiogenic monotherapy (median, 13.3 vs. 5.1 months; P = 0.03).Conclusions:These results reveal the genomic features and provide new insight into potential therapeutic strategies for FH-deficient RCC.

BACKGROUND Hospital hyperglycemia is common and associated with potential adverse outcomes. A Hospital-wide Mobile Phone Alert (HMA) system was built to achieve real time glucose monitoring with warnings for glucose excursions. This study investigated the status of glucose control and evaluated the impact of HMA system on inpatient glycemia management. METHODS Inpatients with hyperglycemia hospitalized between 1 January, 2017 and 31 December, 2018 were identified excluding those < 18 years of age. The HMA system was activated on 1 October, 2017. It sent real time cellphone warning messages to the patient’s designated team physician whenever glucose levels > 10 mmol/L or < 3 mmol/L were detected. A serum glucose > 7.8 mmol/L was defined as hospital hyperglycemia (HH), and > 10 mmol/L was defined as significant HH (SHH). Glucose excursions before and after the HMA system was instituted were compared. RESULTS The incidence of HH, SHH and hypoglycemia was 26.1%, 12.8% and 2.5%, respectively. With the HMA system, the monthly glucose related consultation rate for all inpatients increased 65.9%. The rate of HH glucose amount/ total glucose amount improved with the HMA system, being lower than pre HMA system activation for the surgical wards (15.8 ± 4.7% vs 21.1 ± 6.1%，p<0.05). CONCLUSIONS In this study, one third of inpatients were noted to experience hyperglycemia. Real time cellphone warning messages to the patient’s designated team physician can improve consultation utilization for blood glucose excursions. The alert system was found to reduce the incidence of hyperglycemia on surgical wards.

OBJECTIVE Hospital hyperglycemia is common and associated with potential adverse outcomes. A Hospital-wide Mobile Phone Alert (HMA) system was built to achieve real time glucose monitoring with warnings for glucose excursions. This study investigated the status of glucose control and evaluated the impact of HMA system on inpatient glycemia management. METHODS Inpatients with hyperglycemia hospitalized between 1 January, 2017 and 31 December, 2018 were identified excluding those < 18 years of age. The HMA system was activated on 1 October, 2017. It sent real time cellphone warning messages to the patient’s designated team physician whenever glucose levels > 10 mmol/L or < 3 mmol/L were detected. A serum glucose > 7.8 mmol/L was defined as hospital hyperglycemia (HH), and > 10 mmol/L was defined as significant HH (SHH). Glucose excursions before and after the HMA system was instituted were compared. RESULTS The incidence of HH, SHH and hypoglycemia was 26.1%, 12.8% and 2.5%, respectively. With the HMA system, the monthly glucose related consultation rate for all inpatients increased 65.9%. The rate of HH glucose amount/ total glucose amount improved with the HMA system, being lower than pre HMA system activation for the surgical wards (15.8 ± 4.7% vs 21.1 ± 6.1%，p<0.05). CONCLUSIONS In this study, one third of inpatients were noted to experience hyperglycemia. Real time cellphone warning messages to the patient’s designated team physician can improve consultation utilization for blood glucose excursions. The alert system was found to reduce the incidence of hyperglycemia on surgical wards.

Abstract It has been suggested that errors in the repair of DNA double strand breaks (DSB) can result in gross chromosomal rearrangements (GCR), including chromosomal amplifications, deletions, inversions, and translocations. To study repair of DNA DSB in vivo, we established a subclone of the U937 cell line designated F5, in which a single copy of the rare-cutting meganuclease I-SceI recognition site has been integrated into chromosome 7. We transfected an I-SceI expression vector into these cells and analyzed misrepair events. We recovered no GCR, but instead found that most DSBs were repaired by small (<50bp) indels (91.8%). We also noticed some DSBs were repaired by large (<50bp) deletions (6.4%) and rare DSBs were repaired by large (100-500 bp) insertions (1.8%). Surprisingly, the nucleotide sequence of these insertions matched distant regions of the genome. To determine if this templated sequence insertion (TSI) was peculiar to I-SceI induced DNA DSB, we repeated the experiment using TALENs to produce DNA DSB. Again, we found insertions that were derived from distant genomic regions. To determine whether this form of DNA repair was restricted to experimentally induced DNA DSB, we analyzed structural variations identified by whole genome sequence (WGS) of two myeloma cell lines (KP6, MC1286PE1), and identified 15 independent TSIs. These TSIs were verified by Sanger sequencing, and lengths of inserted fragment were 38 to 666 bp (median 189 bp). Six insertions were noted to be identical between the 2 cell lines, suggesting that these TSIs were germline polymorphic events. These TSIs were compared to a catalog of known structural variations identified by WGS of 52 healthy individuals; 13 of 15 TSI junctions were identified, suggesting that these represented polymorphic insertions in the human genome. Two TSIs were potential somatic mutations in the KP6 cell line, including one that had 85bp insertion at the junction of an acquired t(6;12) chromosomal translocation. Six TSIs showed the hallmarks of L1 retrotransposon-mediated insertions, with a 5’-TTTT/A-3’ integration site, a target site duplication (TSD), a polyA tract at the insertion site, and a polyadenylation signal. However, the inserted sequence was neither a LINE nor a SINE, but instead was a transcribed, genic region mapping to a distant genomic region. The presence of these L1 ORF1 hallmarks strongly suggests that these insertions were caused by the L1 integrase and reverse-transcriptase acting on nuclear pre-mRNA. A second class of TSI showed no preference for a 5’-TTTT/A-3’ integration site, no TSD, no poly A tract, but instead showed several bp of microhomology at the insertion junctions. This second class is similar to TSI detected at I-SceI induced DNA DSB, and we predict that these TSI were generated by reverse transcription of pre-mRNA creating a “patch” for a spontaneous DNA DSB that occurred in a germ cell. To determine if TSI at I-SceI induced DNA DSB could be repaired by RNA-templated sequences, we cotransfected murine RNA and an I-SceI expression vector into F5 cells. Approximately 10% of the TSI recovered from these experiments contained mouse sequences, indicating that they were derived from mouse RNA. To further support the contention that TSIs were derived from RNA, we again used I-SceI to induce a DNA DSB, and treated the cells with reverse transcriptase inhibitors. The TSI frequency was reduced by 70%. Finally, a subset of insertions were due to telomere repeat sequences, lending further support for the hypothesis that RNA could serve as a template for the repair of DNA DSB. TSI is novel form of potentially mutagenic DNA DSB repair, which should be considered as an alternative to a balanced chromosomal translocation in the interpretation of reciprocal interchromosomal structural variations identified by short-read deep sequencing. Disclosures: No relevant conflicts of interest to declare.

11546 Background: TRC105, an endoglin-targeting monoclonal antibody with anti-angiogenic and anti-tumor activity, is being evaluated in multiple diseases. Here we report on pharmacodynamic and prognostic biomarkers in patients (pts) treated with both TRC105 and anti-VEGF agents. Methods: Plasma samples were collected from pts on three phase 2 trials combining TRC105 with an anti-VEGF agent: axitinib in metastatic renal cell carcinoma (mRCC), pazopanib in advanced soft tissue sarcoma, and bevacizumab in glioblastoma (GBM). Baseline and on-treatment levels of 22 soluble protein biomarkers were assessed. Results: Soluble endoglin markedly increased after TRC105 treatment in all pts ( p< 0.001) as previously reported. BMP9 (a ligand for endoglin) and TGFβR3 (a type III TGFβ receptor) decreased in sarcoma pts at Cycle 2 Day 1 (C2D1) and generally remained below baseline throughout the course of treatment (BMP9, p= 0.004; TGFβR3, p= 0.003). Although TGFβR3 was decreased at C2D1 in mRCC (p = 0.030), no clear patterns were observed over time. Overall BMP9 levels did not change in response to therapy in either mRCC or GBM. Osteopontin (OPN) levels, a downstream effector of TGFβ signaling, were increased in sarcoma pts [ p= 0.002 at C2D15, p< 0.001 at C4D1 and end of study (EOS)]; however, in mRCC ( p= 0.010) and GBM ( p= 0.003), OPN was only elevated at EOS. Increases in PlGF and VEGFD, and decreases in VEGFR2 were observed across all studies, as previously noted for VEGF inhibitors. In the mRCC trial, 5 of 18 pts exhibited a ≥30% tumor reduction. Lower OPN ( p= 0.026) and higher TGFβR3 ( p= 0.003) levels at baseline correlated with radiographic response to treatment. In the sarcoma trial, 6 of 19 pts responded (CHOI criteria) in which lower baseline levels of ICAM1 ( p= 0.018) and TSP2 ( p= 0.042) correlated with stable disease. Conclusions: In these trials, increases of soluble endoglin in response to TRC105 were observed, independent of the presence of any specific VEGF inhibitor. Differential regulation of BMP9, TGFβR3, and OPN suggests potential disease-specific modulation of key TGFβ signaling molecules in response to dual therapy. Baseline levels of OPN and TGFβR3 showed potential prognostic value in mRCC. Confirmation in larger trials is needed.