Alanine supplementation exploits glutamine dependency induced by SMARCA4/2-loss

SMARCA4 (BRG1) and SMARCA2 (BRM) are the two paralogous ATPases of the SWI/SNF chromatin remodeling complexes frequently inactivated in cancers. Cells deficient in either ATPase have been shown to depend on the remaining counterpart for survival. Contrary to this paralog synthetic lethality, concomitant loss of SMARCA4/2 occurs in a subset of cancers associated with very poor outcomes. Here, we uncover that SMARCA4/2-loss represses expression of the glucose transporter GLUT1, causing reduced glucose uptake and glycolysis accompanied with increased dependency on oxidative phosphorylation (OXPHOS); adapting to this, these SMARCA4/2-deficient cells rely on elevated SLC38A2, an amino acid transporter, to increase glutamine import for fueling OXPHOS. Consequently, SMARCA4/2-deficient cells and tumors are highly sensitive to inhibitors targeting OXPHOS or glutamine metabolism. Furthermore, supplementation of alanine, also imported by SLC38A2, restricts glutamine uptake through competition and selectively induces death in SMARCA4/2-deficient cancer cells. At a clinically relevant dose, alanine supplementation synergizes with OXPHOS inhibition or conventional chemotherapy eliciting marked antitumor activity in patient-derived xenografts. Our findings reveal multiple druggable vulnerabilities of SMARCA4/2-loss exploiting a GLUT1/SLC38A2-mediated metabolic shift. Particularly, unlike dietary deprivation approaches, alanine supplementation can be readily applied to current regimens for better treatment of these aggressive cancers.

Abstract PD5-08: Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers

Understanding how standard-of-care drug treatments affect tumor intrinsic biology and microenvironment is critical for elucidating drug resistance mechanisms and developing better combination therapies as well as new therapies. To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome, transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole exome and whole transcriptome sequencing of a large longitudinal breast cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%) patients achieved pathologic complete response (pCR) while 85 patients (62%) had residual disease with standard chemotherapy regimen. Tumor biopsies were collected for each patient at three time points – pre-treatment, three weeks after the first cycle of anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype. We detected 5,955 protein-altering somatic mutations affecting 4,414 genes in pretreatment samples and 502 acquired mutations in surgery samples affecting 477 genes including 19recurrently mutated genes such as TP53 and NOTCH1. Across all subtypes, 4,346 genes were differentially expressed (DE) following NAC treatment and significantly enriched in pathways such as cell cycle, ER signaling, PI3K/mTOR, immune and metabolism. Expression-based virtual microdissection analysis indicated that NAC treatment induced an increase in the fractions of stromal and adjacent normal tissue compartment, consistent with observed reduction in tumor cellularity. To assess the NAC induced changes in the molecular landscape of these tumors, we compared molecular features including gene expression signatures, mutation prevalence and copy number alteration between three time points while adjusting for confounding effects of molecular subtype and tumor cellularity. We found that NAC induced dynamic changes in gene expression signatures associated with proliferation and immunomodulatory treatment response. We further validated the observed pattern of change in TILs through histopathology and digital imaging analyses. In pretreatment tumors, 116 genes were DE between patients with pCR vs. those with residual disease with significant enrichment in immune/inflammatory pathways. Further, pre-treatment TIL levels were found to be significantly associated with pCR, echoing previous reports in breast cancers that implicated anti-tumor immunity in mediating the efficacy of chemotherapies. Our analyses also revealed associations between NAC response and baseline genomic attributes such as genomic alterations that affect DNA damage repair pathways. Taken together, these results suggest that NAC induced a multitude of changes on the genomic landscape and immune microenvironment of breast cancers, some of which point to combination strategies with immunomodulatory therapies and therapies that target DNA damage repair.

Citation Format: Kan Z, Lal S, Ding Y, Lee JE, Lee S-H, Lee SK, Yu JH, Choi Y-l, Kim SW, Nam SJ, Kim J-Y, Ram S, Powell E, Ching K, Cho SY, Bonato V, Deng S, Park W-Y, Rejto P, Bienkowska J, Park Y-H. Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD5-08.

Abstract P2-07-01: Integrative analyses of immunophenotypes and multi-omics profiles in breast cancers

The advent of immuno-oncology (IO) therapies has made it an imperative to characterize intratumoral immune microenvironment in addition to oncogenic alterations through molecular profiling of the tumor. To elucidate the baseline profiles of tumor infiltrating leukocytes (TILs) in breast cancer (BC) in the context of molecular subtypes and oncogenic alterations, we performed whole-exome sequencing (WES) and RNA-Seq of an Asian BC cohort (SMC) consisting of 178 treatment naïve primary tumors. A subset of 120 tumors was further analyzed by H&E and IHC using a panel of 8 TIL markers (CD45, CD4, CD8, CD163, PD1, PD-L1, IDO1 and FOXP3). Using expression signatures representing distinct immune cell types, we classified an expression compendium of 2,781 tumor samples, including SMC and multiple cancers from TCGA, into three immune subtypes with high, medium and low levels of TILs. Basal and HER2 subtypes show higher levels of TILs than Luminal subtypes, consistent with observed clinical responses to checkpoint blockade in clinical trials. Moreover, Asian BCs were significantly enriched in TIL-high subtype (35.3%) compared to the primarily Caucasian TCGA BC cohort (20.2%) while 50.6% of the highly immunogenic Lung adenocarcinoma was TIL-high. We then applied machine learning methods to detect and quantify TILs from H&E images of 120 SMC and 349 TCGA BC tumors. The expression signature analysis results were concordant with independently derived histology based TIL data. Taken together, our findings suggest that IO therapies may be more effective in HR negative BC subtypes and Asian BCs.

Leukocyte exclusion (LE), an immunophenotype where TILs concentrate at the tumor periphery, has been linked to worse prognosis and resistance to IO therapies. Visual assessment of whole tumor IHC images identified LE patterns in 25% of SMC cases. We observed differential distribution of LE by molecular subtype and evidence for selective exclusion of immune cell subsets. Covariate analyses with clinical and molecular data while controlling for subtype as a confounder identified significant associations with tumor proliferation index, percent tumor purity and TP53 mutations. LE is also significantly associated with expression signatures of chemokine signaling, macrophages, angiogenesis and hypoxia, indicating that marked distinctions exist in both tumor intrinsic and microenvironment characteristics between TIL excluded and TIL infiltrated tumors. To validate these findings, we independently identified LE for 200 cases of TCGA BCs based on patterns of TILs extracted from H&E images and saw significant concordance of covariate relationships identified between TCGA and SMC. Our study provided a rare comprehensive resource for studying tumor associated immunity in breast cancers by generating the integrated multi-omics and IO profiles for a large cohort of primary tumors. Comparative analyses revealed that TIL activities are highly variable across different intrinsic subtypes and geographic origins of BC, with potential implications for IO therapeutic application. Correlative analyses of immunophenotypes with molecular data further yielded insights into LE's role in immune escape and identified hallmark signatures for LE indicative of causal molecular mechanisms.

Citation Format: Kan Z, Powell E, Ram S, Ching K, Ding Y, Vizcarra P, Nichols T, Hardwick J, Lee S-H, Cho SY, Choi Y-L, Yu J-H, Park YH. Integrative analyses of immunophenotypes and multi-omics profiles in breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-01.

Susceptibility to dysphagia after fundoplication revealed by novel automated impedance manometry analysis

BACKGROUND

Conventional measures of esophageal pressures or bolus transport fail to identify patients at risk of dysphagia after laparoscopic fundoplication.

METHODS

Liquid and viscous swallows were evaluated with impedance/manometry in 19 patients with reflux disease before and after surgery. A new method of automated impedance manometry (AIM) analysis correlated esophageal pressure with impedance data and automatically calculated a range of pressure and bolus movement variables. An iterative analysis determined whether any variables were altered in relation to dysphagia. Standard measures of esophago-gastric junction pressure, bolus presence time, and total bolus transit time were also evaluated.

KEY RESULTS

At 5 months postop, 15 patients reported some dysphagia, including 7 with new-onset dysphagia. For viscous boluses, three AIM-derived pressure-flow variables recorded preoperatively varied significantly in relation to postoperative dysphagia. These were: time from nadir esophageal impedance to peak esophageal pressure (TNadImp-PeakP), median intra-bolus pressure (IBP, mmHg), and the rate of bolus pressure rise (IBP slope, mmHgs(-1) ). These variables were combined to form a dysphagia risk index (DRI=IBP×IBP_slope/TNadImp-PeakP). DRI values derived from preoperative measurements were significantly elevated in those with postoperative dysphagia (DRI=58, IQR=21-408 vs no dysphagia DRI=9, IQR=2-19, P<0.02). A DRI >14 was optimally predictive of dysphagia (sensitivity 75% and specificity 93%).

CONCLUSIONS & INFERENCES

Before surgery, a greater and faster compression of a swallowed viscous bolus with less bolus flow time relates to postoperative dysphagia. Thus, susceptibility to postfundoplication dysphagia is related to a pre-existing sub-clinical variation of esophageal function.

Impact of nadir lower oesophageal sphincter pressure on bolus clearance assessed by combined manometry and multi-channel intra-luminal impedance measurement

This study aimed to assess the relationship between nadir lower oesophageal sphincter pressure (LOSP) and wave amplitude (WA) in oesophageal bolus clearance. Concurrent oesophageal manometry and impedance were performed in 146 subjects [41 healthy, 24 non-obstructive dysphagia (NOD) and 81 gastro-oesophageal reflux (GOR)]. Patients with achalasia and diffuse oesophageal spasm were excluded. Swallow responses were categorized by nadir LOSP. For each category of nadir LOSP, WA at the distal 2 recording sites were grouped into bins of 10 mmHg and the proportion of waves in each bin associated with a normal bolus presence time (BPT) was determined. Nadir LOSP, distal BPT, total bolus transit time and the proportion of impaired oesophageal clearance in patients with NOD were greater than those of healthy subjects and patients with GOR. Overall, responses with impaired oesophageal clearance had significantly lower WA (54 +/- 1 vs 81 +/- 1 mmHg; P < 0.0001) and higher nadir LOSP (2.7 +/- 0.4 vs 1.0 +/- 0.1 mmHg, P < 0.001). For each level of nadir LOSP, there was a direct relationship between distal WA and successful bolus clearance of both liquid and viscous boluses from the distal oesophagus. As nadir LOSP increased, the relationship between WA and bolus clearance shifted to the right and higher amplitudes were required to achieve the same effectiveness of clearance. Hypotensive responses with nadir LOSP > or = 3 mmHg were less likely to clear than those with nadir LOSP < 3 mmHg, for both liquid (7/29 vs 162/276; P < 0.001) or viscous boluses (11/46 vs 176/279; P < 0.0001). Nadir LOSP is an important determinant of bolus clearance from the distal oesophagus, particularly in patients with NOD.

Gastric feed intolerance is not increased in critically ill patients with type II diabetes mellitus

OBJECTIVE

To examine the occurrence of feed intolerance in critically ill patients with previously diagnosed type II diabetes mellitus (DM) who received prolonged gastric feeding.

DESIGN AND SETTING

Retrospective study in a level 3 mixed ICU.

PATIENTS

All mechanically ventilated, enterally fed patients (n = 649), with (n = 118) and without type II DM (n = 531) admitted between January 2003 and July 2005.

INTERVENTIONS

Patients with at least 72 h of gastric feeding were identified by review of case notes and ICU charts. The proportion that developed feed intolerance was determined. All patient received insulin therapy.

RESULTS

The proportion of patients requiring gastric feeding for at least 72 h was similar between patients with and without DM (42%, 50/118, vs. 42%, 222/531). Data from patients with DM were also compared with a group of 50 patients matched for age, sex and APACHE II score, selected from the total non-diabetic group. The occurrence of feed intolerance (DM 52% vs. matched non-DM 50% vs. unselected non-diabetic 58%) and the time taken to develop feed intolerance (DM 62.6 +/- 43.8 h vs. matched non-DM 45.3 +/- 54.6 vs. unselected non-diabetic 50.6 +/- 59.5) were similar amongst the three groups. Feed intolerance was associated with a greater use of morphine/midazolam and vasopressor support, a lower feeding rate and a longer ICU length of stay.

CONCLUSIONS

In critically ill patients who require prolonged enteral nutrition, a prior history of DM type II does not appear to be a further risk factor for feed intolerance.

Natural variants of the human papillomavirus type 16 E6 protein differ in their abilities to alter keratinocyte differentiation and to induce p53 degradation

Three naturally occurring variant human papillomavirus type 16 (HPV-16) E6 proteins, which contained amino acid substitutions predominantly near the N terminus, exhibited significant differences in their abilities to abrogate keratinocyte differentiation in response to serum and calcium and to induce the degradation of p53 in vitro. One variant surpassed the reference E6 protein in its ability to abrogate keratinocyte differentiation responses, whereas another showed a reduction in this activity. Interestingly, the biological activities of the HPV-16 E6 proteins and their abilities to induce p53 degradation in vitro were directly correlated. These results demonstrate that naturally occurring variants of HPV-16 differ in biological and biochemical properties which might result in differences in pathogenicity.

A unique, predominant hepatitis C virus variant found in an infant born to a mother with multiple variants

To demonstrate vertical transmission of hepatitis C virus (HCV) from an HCV-infected, non-human immunodeficiency virus type 1-infected mother to her infant and to assess the distribution of viral species in the mother and infant, the hypervariable region of the gene encoding the putative envelope glycoprotein E2 (E2HV) was sequenced in three mothers and one mother-infant pair. The data indicate that (i) quasi-species distributions of HCV E2HV variants were found in all four mothers, (ii) a single predominant HCV E2HV variant was found in the infant of a mother shown to have nine predominant E2HV variants, and (iii) the infant's E2HV variant was highly related to, but not identical with, the nine variants identified in the mother at the time of birth. These findings indicate that HCV is transmitted from mother to infant and raise the possibility that the transmission occurs in utero.