Non-Redundant Mechanisms of Immune Resistance to Radiotherapy Converge on Innate Immunity

PURPOSE/OBJECTIVE(S)

Despite evidence of preclinical synergy between radiotherapy (RT) and immune checkpoint blockade (ICB), randomized trials of RT/ICB have demonstrated limited benefit in solid tumors. We performed single-cell RNA sequencing (scRNA-seq) and CITE-seq (cellular indexing of transcriptomes and epitopes) to address the discordance between preclinical and clinical data. We hypothesized that multiple orthogonal inhibitory immune pathways restrain the local and systemic efficacy of RT beyond T-cell oriented immune checkpoints.

MATERIALS/METHODS

We used the EO771 syngeneic murine model of breast cancer to characterize the immune tumor microenvironment following RT with or without ICB. RT (16 Gy x 1) was delivered using the X-RAD SmART platform with CT image guidance. Neutralizing antibodies (anti-PD-1/Ly6G/Gr-1/CD47) were delivered by intraperitoneal injections. scRNA-seq analysis were performed by Seurat and BBrowser (BioTuring).

RESULTS

We found that adaptive ICB (anti-PD-1) reprogrammed the immune response to RT by promoting an M1-like interferon-primed state (ISG15, CXCL10) in tumor associated macrophages (TAMs) and by increasing the late recruitment of intratumoral neutrophils. Given that neutrophils may drive resistance to RT in other models, we evaluated the effect of intratumoral neutrophil depletion using anti-Ly6G or anti-Gr-1 on the antitumor efficacy of RT/ICB. Both neutrophil depletion strategies led to enhanced tumor control and improved survival in advanced EO771 tumors compared to RT/ICB alone (P<0.001). In parallel to this approach, we found that TAMs upregulated several innate immune checkpoints including SIRPα in response to RT. Disruption of the SIRPα-CD47 interaction by anti-CD47 antibodies similarly enhanced the antitumor efficacy of RT/ICB by improving tumor control and survival (P<0.001). Using scRNA-seq and unbiased clustering, we found that anti-CD47 eliminated an entire cluster of chronically inflamed TAMs, characterized by pro-inflammatory markers (IL1A, NOS2) and chemokines (CCL3, CXCL1/2/3). Anti-CD47 also reduced intratumoral neutrophils by eliminating a cluster of pathologically activated neutrophils, termed myeloid-derived suppressor cells (PMN-MDSCs) that expressed several markers of ferroptosis (TFRC, PTGS2, SLC3A2). Consistent with the potent immunosuppressive capacity of PMN-MDSCs, we found that anti-CD47 increased tumor-infiltrating lymphocytes including central memory TCF7+ T cells and CD19+ B cells. Lastly, by inference and analysis of cell-cell communication (CellChat), we found that anti-CD47 strengthened the interactions between TAMs and CD8+ T cells compared to RT/ICB alone.

CONCLUSION

Our data collectively indicate that resistance to RT/ICB in the EO771 model Is driven by innate immune cells including neutrophils and chronically inflamed TAMs. Targeted disruption of the CD47-SIRPα axis is a promising approach to overcoming immune resistance by reprogramming TAMs and eliminating PMN-MDSCs.

Abstract 6409: Non-redundant mechanisms of immune resistance to radiotherapy converge on innate immunity

Multiple studies have demonstrated synergy between immune checkpoint blockade (ICB) and radiotherapy (RT) in preclinical murine models; however, randomized trials of RT/ICB have been inconsistent in patients with solid tumors. To better understand this discordance, we hypothesized that there are non-redundant inhibitory immune pathways that restrain the efficacy of RT beyond T-cell oriented immune checkpoints. To this end, we performed scRNA-seq and CITE-seq analysis of the EO771 syngeneic murine model of breast cancer to characterize the immune landscape following RT±ICB. We found that ICB reprograms the immune response to RT by shifting tumor-associated macrophages (TAMs) from a lipid-associated phenotype (APOE, FABP5) to an M1-like interferon-stimulated state (CXCL10, ISG15). However, ICB also promoted the late recruitment of intratumoral neutrophils, which drive resistance to RT in other contexts. To evaluate whether neutrophils may be limiting antitumor immunity to RT/ICB, we depleted intratumoral neutrophils using two separate antibodies, anti-Ly6G and anti-Gr-1. Compared to RT/ICB alone, both neutrophil depletion strategies enhanced tumor control and prolonged survival in advanced EO771 tumors (P&lt;0.001). Given that indiscriminate neutrophil depletion is not a viable therapeutic strategy, we tested alternative immune targeting approaches to alter the TAM response to RT/ICB. By scRNA-seq, we found that RT strongly upregulated several innate immune checkpoints on TAMs (e.g., SIRPα, SLAMF3/7, LRP1). Accordingly, we disrupted the SIRPα-CD47 interaction with anti-CD47 antibodies and characterized the impact on response to RT/ICB. Anti-CD47 significantly improved tumor regression and survival when combined with RT/ICB (P&lt;0.001). We then used scRNA-seq and CITE-seq to understand why disruption of SIRPα-CD47 improved antitumor responses to RT/ICB. We found that anti-CD47 depleted an entire cluster of chronically inflamed TAMs, expressing pro-inflammatory markers (IL1A, NOS2) and chemokines (CCL3, CXCL1/2/3). Furthermore, anti-CD47 reduced the recruitment of intratumoral neutrophils and depleted a cluster of pathologically activated neutrophils (PMNs), termed myeloid-derived suppressor cells (PMN-MDSCs), expressing WFDC17, PTGS2, S100A8/9. Lastly, anti-CD47 enhanced the recruitment of tumor-infiltrating lymphocytes including central memory TCF7+ T cells and CD19+ B cells. By inference and analysis of cell-cell communication (CellChat), we found that anti-CD47 strengthened the interactions between myeloid cells and T cells compared to RT/ICB alone. Collectively, our data indicate that innate immune cells, in particular neutrophils and chronically inflamed TAMs, promote resistance to RT/ICB in the EO771 model. These data suggest that inhibition of CD47-SIRPα is a promising therapeutic strategy to overcoming immune resistance through the elimination of PMN-MDSCs.

Citation Format: Anthony T. Nguyen, Tahir B. Dar, Jolene Viramontes, Satchel Stevens, Julie K. Jang, Emily Y. Ko, Diana J. Lu, Eric M. Chung, Samuel C. Zhang, Katelyn M. Atkins, Mitchell Kamrava, Howard M. Sandler, Jlenia Guarnerio, Simon Knott, Zachary S. Zumsteg, David M. Underhill, Stephen L. Shiao. Non-redundant mechanisms of immune resistance to radiotherapy converge on innate immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6409.

Abstract PD10-01: The PEARL trial: Pre-operative pembrolizumab with radiation therapy in early stage triple negative breast cancer

Background: Anti-PD(L)1 in addition to neoadjuvant chemotherapy (NAC) can achieve pathologic complete response (pCR) rates of up to 65% in patients with early stage triple negative breast cancer (TNBC). However, patients with non-pCR can have dismal prognosis. Innovative strategies that render the tumor microenvironment more sensitive to anti-PD(L)1 may confer benefit. Preclinical studies have shown that hypofractionated radiation therapy (RT) delivered to an in-situ breast tumor, when combined with immune checkpoint blockade, stimulates anti-tumor immune responses and induces long-term, tumor-specific memory. Here, we report the first results of a phase II study that established the feasibility and efficacy of this approach in the pre-operative treatment setting for TNBC. Methods: Fifty patients with stage I-III TNBC, defined as ER&lt;10%,PR&lt;10%, HER2-negative, were enrolled between 12/17-4/21. Study treatment consisted of one cycle (C1) of pembro (200 mg iv q 3wks), followed by cycle 2 (C2) of pembro + RT (24Gy) delivered to a breast primary, followed by NAC regimen per MD choice, surgery and adjuvant therapy. Paired tumor biopsies and blood were collected at 3 serial time points: 1) baseline (pre-treatment); 2) after pembro C1; 3) after pembro C2 + RT (prior to initiation of NAC). All patients received breast and axillary surgery and postoperative RT to the chest wall and regional lymph nodes. Dual primary endpoints were: 1) feasibility, defined by the number of patients who did not necessitate a &gt;4-week delay in initiating NAC after pembro C2 + RT; 2) change in tumor infiltrating lymphocyte (TIL) score. Secondary endpoints included pCR, defined as ypT0/TisypN0, in addition to toxicity and cosmesis evaluations. Results: To date, 50 patients are evaluable with a median follow up of 12 months (range 6-12). Median age of cohort is 55y (range 26-76). The majority (92%) were clinical stage II; 2% stage I and 6% stage III. 34% of the cohort had biopsy-proven, node positive disease. All patients received a taxane, 52% carboplatin and 74% anthracycline. 12% did not complete the planned course of NAC due to toxicities. No patients experienced a delay in initiating NAC. 50% received breast-conserving surgery and 50% mastectomy. Grade 1 or 2 toxicities consisted of fatigue (76%), nausea (66%), maculopapular rash (32%), diarrhea (38%), colitis (2%), hypothyroidism (8%) and peripheral neuropathy (40%). Four patients had grade 3 toxicities that were attributable to pembro: hyponatremia(1), colitis (1), adrenal insufficiency(1) and pneumonitis (1). Three patients had grade 4 neutropenia which were not attributable to pembro. The overall rate of pCR was 74% (37/50). Among the 13 patients with non-pCR, 0% were RCB 1, 16% RCB 2 and 10% RCB 3. Among the 17 N+ patients, 13 converted to ypN0, 1 ypN1mic and 3 ypN1a. No patients progressed during treatment. Changes in TIL count, PD-L1 and other biomarkers after pembro +/- RT and their association with treatment response, will be presented at the meeting. Conclusions: The novel combination of pre-operative pembro followed by the addition of RT to pembro prior to NAC is not only feasible, but also achieves pCR rates that are higher-than-expected compared to the pembro arm of KEYNOTE-522. AEs were consistent with known safety profiles of each agent. If confirmed by larger, randomized studies, this combination will be paradigm-changing for the treatment of TNBC.

Citation Format: Heather L McArthur, Stephen Shiao, Scott Karlan, Reva Basho, Farin Amersi, Michele Burnison, Amin Mirhadi, Alice Chung, Cathie T Chung, Catherine Dang, Heather Richardson, Armando E Giuliano, Nimmi Kapoor, Brigid Larkin, Hector Godinez, Samantha A Dunn, Negin Habibi Khameneh, Simon Knott, Philomena McAndrew, Monica Mita, Dorothy J Park, Christina Abaya, Jonathan H Chen, Amy Ly, Veerle Bossuyt, Alice Ho. The PEARL trial: Pre-operative pembrolizumab with radiation therapy in early stage triple negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD10-01.

Astrocytic laminin-211 drives disseminated breast tumor cell dormancy in brain

Although dormancy is thought to play a key role in the metastasis of breast tumor cells to the brain, our knowledge of the molecular mechanisms regulating disseminated tumor cell (DTC) dormancy in this organ is limited. Here using serial intravital imaging of dormant and metastatic triple-negative breast cancer lines, we identify escape from the single-cell or micrometastatic state as the rate-limiting step towards brain metastasis. We show that every DTC occupies a vascular niche, with quiescent DTCs residing on astrocyte endfeet. At these sites, astrocyte-deposited laminin-211 drives DTC quiescence by inducing the dystroglycan receptor to associate with yes-associated protein, thereby sequestering it from the nucleus and preventing its prometastatic functions. These findings identify a brain-specific mechanism of DTC dormancy and highlight the need for a more thorough understanding of tumor dormancy to develop therapeutic approaches that prevent brain metastasis.

Local non-pituitary growth hormone is induced with aging and facilitates epithelial damage

Microenvironmental factors modulating age-related DNA damage are unclear. Non-pituitary growth hormone (npGH) is induced in human colon, non-transformed human colon cells, and fibroblasts, and in 3-dimensional intestinal organoids with age-associated DNA damage. Autocrine/paracrine npGH suppresses p53 and attenuates DNA damage response (DDR) by inducing TRIM29 and reducing ATM phosphorylation, leading to reduced DNA repair and DNA damage accumulation. Organoids cultured up to 4 months exhibit aging markers, p16, and SA-β-galactosidase and decreased telomere length, as well as DNA damage accumulation, with increased npGH, suppressed p53, and attenuated DDR. Suppressing GH in aged organoids increases p53 and decreases DNA damage. WT mice exhibit age-dependent colon DNA damage accumulation, while in aged mice devoid of colon GH signaling, DNA damage remains low, with elevated p53. As age-associated npGH induction enables a pro-proliferative microenvironment, abrogating npGH signaling could be targeted as anti-aging therapy by impeding DNA damage and age-related pathologies.

Chesnokova et al. show that non-pituitary growth hormone (npGH) is induced in aging DNA-damaged colon epithelium and suppresses DNA damage response by attenuating the phosphorylation of DNA repair proteins. npGH induction promotes DNA damage accumulation, resulting in age-associated colon microenvironment changes. Accordingly, disrupted GH signaling in aging mice prevents accumulated DNA damage.

733 Immunological mechanisms of resistance to CDK4/CDK6 inhibitors in breast cancer

Background

Hormone receptor+ (HR+) breast cancer (BC) is the most frequent cause of BC-related deaths. CDK4/6 inhibitors (CDK4/6i) combined with endocrine therapy (ET) emerged as an effective approach for metastatic HR+ BC. However, >60% women with HR+ BC receiving CDK4/6i+ET ultimately relapse, potentially due to activation of poorly characterized immunosuppressive pathways in the tumor microenvironment (TME).1 Thus, strategies breaking resistance to CDK4/6i+ET in women with HR+ BC are urgently awaited. Radiation therapy (RT) mediates immunostimulatory effects that only partially overlap with those of CDK4/6i+ET,2 standing out as a promising therapeutic partner. Consistent with this notion, we recently demonstrated that RT followed by the CDK4/6i palbociclib + ET (RT-P+ET) enables superior tumor control in various immunocompetent mouse models of HR+ BC.3 These findings have inspired the design of a randomized phase II clinical trial testing P+ET vs. RT-P+ET in patients with oligometastatic HR+ BC (CIMER, NCT04563507). In this context, we set out to dissect the immunological mechanisms underlying sensitivity vs. resistance to treatment in HR+ BC exposed to P+ET vs. RT-P+ET.

Methods

To dissect the impact of these treatments on immune contexture in HR+ BC, we performed single-cell RNAseq on CD45+ cells infiltrating MPA/DMBA (M/D)-driven carcinomas established in immunocompetent mice (a unique model of luminal B BC), coupled to bulk RNAseq, bioinformatic analysis on public patient datasets, functional studies on ex vivo immune cells and efficacy studies.

Results

We observed that (1) RT and P+ET alone mediate partial efficacy correlating with accumulation of immunosuppressive TREG and IL17A-producing γδ T cells, respectively, (2) γδ T cell depletion improves the efficacy of P+ET, (3) RT-P+ET mediates superior (but incomplete) tumor control, which is partially offset by CD4+/CD8+ T cell co-depletion and correlates with limited infiltration by γδ T cells and TREGS, but accumulation of PD-L1 expressing myeloid cells and M2-polarized TREM2+ macrophages, which have been ascribed robust immunosuppressive effects in multiple settings4; and (4) that PD-1 blockage does not ameliorate the therapeutic effects of RT-P+ET (not shown), pointing to TREM2+ macrophages as to the main culprits for resistance in this setting.

Conclusions

Our observations suggest that γδ T cells and TREM2+ macrophages support the resistance of HR+ BC to CDK4/6i and RT-CDK4/6i, and hence constitute potential targets to delay disease progression.

References

Pandey et al. Molecular mechanisms of resistance to CDK4/6 inhibitors in breast cancer: a review. Int J Cancer 2019;145(5):1179–1188.

Rodriguez-Ruiz et al. Immunological impact of cell death signaling driven by radiation on the tumor microenvironment. Nat Immunol 2020;21(2):120–134.

Petroni et al. Radiotherapy delivered before CDK4/6 inhibitors mediates superior therapeutic effects in ER + Breast cancer. Clin Cancer Res 2021;27(7):1855–1863.

Xiong et al. A gene expression signature of TREM2 hi macrophages and γδ T cells predicts immunotherapy response. Nat Commun 2020;11(1):5084.

Ethics Approval

Animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of Weill Cornell Medical College (n° 2019–2022).

Abstract PS12-09: Pre-operative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC)

Background: Pembrolizumab (pembro)-mediated checkpoint blockade has shown only modest efficacy in triple negative breast cancer (TNBC). Pathologic complete response (pCR) rates in TNBC are 34-55% with neoadjuvant chemotherapy and 26% with neoadjuvant stereotactic radiation therapy (RT) alone. However, because RT induces immune-mediated cell death that can generate a rich supply of tumor antigens and trigger anti-tumor immunity, the addition of pembro to RT can generate robust anti-tumor immune responses as demonstrated in metastatic TNBC. If administered in the pre-operative setting, immune therapy plus RT could induce long-term tumor-specific memory, and ultimately, improve cure rates. This study aimed to establish the safety of pre-operative pembro plus RT in 20 TNBC patients for whom lumpectomy and adjuvant RT were planned and to explore predictive biomarkers (NCT03366844).

Methods: Women planning breast conserving surgery for operable, stage II/III, TNBC were enrolled in this single-institution pilot study. Study treatment consisted of pre-operative pembro (200mg IV) followed 3 weeks later by pembro (200mg IV) plus RT (24 Gy/3 fractions) to the primary breast tumor followed 3-5 weeks later by standard-of-care (SOC) neoadjuvant chemotherapy. Adjuvant RT was administered per SOC after surgery, but without a boost dose. Research blood and tumor biopsies were obtained at baseline, at week 4 prior to pembro/RT, and at week 6-8 prior to chemotherapy initiation. Co-primary endpoints were: safety/tolerability (defined by the number of patients who do not necessitate a delay in SOC chemotherapy or surgery) and change in tumor infiltrating lymphocyte (TIL) score. Secondary endpoints include safety/toxicity up to 19 weeks after study enrollment and pathologic complete response (pCR) rate.

Results: 20 patients were enrolled and completed all treatment (pembro, RT, chemotherapy and surgery) as of July 2020. The median age is 55y (range 33-70y). The stage distribution is IIA (11), IIB (6), IIIA (2) and IIIC (1) with biopsy proven nodal involvement in 55%. All patients received a taxane containing regimen, 12/20 (60%) received carboplatin and 15/20 (75%) received an anthracycline. Three patients did not complete the planned course of chemotherapy, two of whom had residual disease. None of the patients experienced significant delay (&gt;2 weeks) in receiving SOC treatment. There were no observed grade 3 or 4 toxicities observed during the pembro +/- RT treatment. Grade 4 colitis in 2/20 was reported during SOC chemotherapy and was attributed to pembro. The most frequent grade 1/2 toxicities were nausea (4/20), arthralgia (15/20), fatigue (16/20), maculopapular rash (1/20), diarrhea (1/20) and mucositis (1/20). At the time of surgery, 12/20 (60%) were ypT0N0 and 13/20 (65%) were ypT0/Tis. 15/20 (75%) achieved an RCB 0/1, 4/20 (20%) were RCB 2 and 1/20 (5%) was RCB 3. Of the 11 patients with node-positive disease at diagnosis, 9/11 (82%) became ypN0, 1/11 (9%) became ypN1mic and 1/11 (9%) became ypN1a. No patients progressed during treatment. Change in TILs after pembro or pembro-RT did not correlate with treatment response, however baseline TIL count ≥10% in the initial biopsy was associated with pCR (p = 0.005). Further profiling of the immune cells in the biopsies revealed that RCB 0/1 patients were strongly associated with increased numbers of CD8+ T cells and lower numbers of CD11b+ myeloid cells following the combination of pembro and RT.

Conclusions: Neoadjuvant pembro plus RT prior to SOC chemotherapy is safe/feasible and may increase pCR rates and clearance of nodal metastases beyond chemotherapy alone. A phase 2 study of checkpoint blockade + RT expansion of this trial (n=50) is currently accruing.

Citation Format: Heather McArthur, Stephen Shiao, Scott Karlan, Reva Basho, Farin Amersi, Brittany Arnold, Michele Burnison, Alice Chung, Cathie Chung, Catherine Dang, Armando Giuliano, Nimmi Kapoor, Negin Habibi Khameneh, Simon Knott, Cynthia Martin, Philomena McAndrew, Monica Mita, Dorothy Park, Christina DiLauro Abaya, Alice Ho. Pre-operative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS12-09.

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

A mysterious feature of Crohn's disease (CD) is the extra-intestinal manifestation of "creeping fat" (CrF), defined as expansion of mesenteric adipose tissue around the inflamed and fibrotic intestine. In the current study, we explore whether microbial translocation in CD serves as a central cue for CrF development. We discovered a subset of mucosal-associated gut bacteria that consistently translocated and remained viable in CrF in CD ileal surgical resections, and identified Clostridium innocuum as a signature of this consortium with strain variation between mucosal and adipose isolates, suggesting preference for lipid-rich environments. Single-cell RNA sequencing characterized CrF as both pro-fibrotic and pro-adipogenic with a rich milieu of activated immune cells responding to microbial stimuli, which we confirm in gnotobiotic mice colonized with C. innocuum. Ex vivo validation of expression patterns suggests C. innocuum stimulates tissue remodeling via M2 macrophages, leading to an adipose tissue barrier that serves to prevent systemic dissemination of bacteria.

OR16-06 Age-Associated Local GH Promotes Colon Neoplasia

Colon polyp and cancer frequency increase with age, yet little is known about age-related mechanisms underlying development of these neoplasms. Defective DNA damage response and accumulation of unrepaired DNA damage can trigger genomic instability and cellular transformation.

Patients with acromegaly have a higher prevalence of colon polyps and, arguably, colon adenocarcinoma, while those with GH signaling deficiency do not develop cancer. We showed that APC+/- mice that all develop colon adenomas exhibit a significant decrease in the number and volume of colon tumors with deletion of the GH transcription factor Prop1. Further, DNA damage response triggered GH expression in colon cells, and GH, in turn, altered DNA damage repair, resulting in DNA damage accumulation and cell transformation both in vitro and in vivo. These findings prompted us to hypothesize that accumulated DNA damage in aging colon induces local GH, suppressing DNA damage repair and creating a milieu consistent with genomic instability favoring neoplastic development.

In human colon tissue we now show increased expression of γH2AX, a marker of DNA breaks, associated with increased GH transcription (detected by RNA scope) and translation (assessed by immunohistochemistry) as well as GH induction in both human and murine colon after DNA damaging radiotherapy. In vitro studies support these results, showing GH induction in normal human colon epithelial cells, fibroblasts, and 3D human intestinal organoids after DNA damage. Of note, local GH was secreted in the medium, indicating a paracrine effect. Paracrine/autocrine GH expression in these cellular models resulted in suppression of p53, induction of EMT, and attenuation of DNA damage response, and accumulated unrepaired DNA damage in human colon cells and in human intestinal organoids. In vivo, colon cells infected with lentivirus expressing GH generated more metastases than did cells expressing control vector. Co-culturing of human normal colon fibroblasts expressing GH together with normal human colon cells led to increased motility and accumulation of DNA damage as well as increased proliferation of epithelial cells on a gut-on-a-chip microfluidic device, confirming paracrine GH effects. In an in vitro model of aging, culturing human intestinal organoids for up to 2 months resulted in decreased telomere length and increased GH mRNA and protein expression associated with suppressed DNA damage response evident by decreased phosphorylation of ATM and DNA-PKcs, both kinases involved in DNA repair, and DNA damage accumulation assessed by Comet assay. Suppression of GH in these aging organoids led to increased phospho-p53 and reduced DNA damage. Although somatotroph axis endocrine activity decreases with age, local GH induced in response to age-related DNA damage may trigger a “field change,” creating a milieu favorable for colon neoplastic development.

Abstract P3-09-09: Pre-operative pembrolizumab (pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC)

Background: Pembrolizumab (pembro)-mediated checkpoint blockade has shown modest efficacy in triple negative breast cancer (TNBC). Pathologic complete response (pCR) rates in TNBC are 34-55% with neoadjuvant chemotherapy (Cortazar Lancet 2014, Sharma Clin Cancer Res 2017) and 26% with neoadjuvant stereotactic radiation therapy (RT) alone (Riet Eur J Cancer 2017). However, because RT induces immune-mediated cell death that can generate a rich supply of tumor antigens and trigger anti-tumor immunity, the addition of pembro to RT can generate robust anti-tumor immune responses as demonstrated in metastatic TNBC (McArthur ASCO 2018). If administered in the pre-operative setting, immune therapy plus RT could induce long-term tumor-specific memory, and ultimately, improve cure rates. This study aimed to establish the safety of pre-operative pembro plus RT in 20 TNBC patients for whom lumpectomy and adjuvant RT were planned and to explore predictive biomarkers (NCT03366844). Methods: Women planning breast conserving surgery for operable, stage II/III, TNBC were enrolled in this single-institution pilot study. Study treatment consisted of pre-operative pembro (200mg IV) followed 3 weeks later by pembro (200mg IV) plus RT (24 Gy/3 fractions) to the primary breast tumor followed 3-5 weeks later by standard-of-care (SOC) neoadjuvant chemotherapy. Adjuvant RT was administered per SOC after surgery, but without a boost dose. Research blood and tumor biopsies were obtained at baseline, at week 4 prior to pembro/RT, and at week 6-8 prior to chemotherapy initiation. Co-primary endpoints were: safety/tolerability (defined by the number of patients who do not necessitate a delay in SOCchemotherapy or surgery) and change in tumor infiltrating lymphocyte (TIL) score. Secondary endpoints include safety/toxicity up to 19 weeks after study enrollment and pathologic complete response (pCR) rate. Results: As of 7/8/19, the accrual goal of 20 patients has been met. The median age is 53y (range 33-70y). The stage distribution is IIA (12), IIB (5), IIIA (2) and IIIC (1) with biopsy proven nodal involvement in 40%. To date, 18 patients have completed pembro/RT and 12 have completed chemotherapy and surgery. All patients received a taxane containing regimen, 8/12 (67%) received carboplatin and 10/12 (83%) received an anthracycline. Three patients did not complete the planned course of chemotherapy, two of whom had residual disease. None of the patients experienced significant delay (&gt;2 weeks) in receiving SOC treatment. There were no observed grade 3 or 4 toxicities observed with pembro +/- RT. Grade 4 colitis in 1/18 was reported during SOC chemotherapy and was attributed to pembro. The most frequent grade 1/2 toxicities were nausea (3/18), arthralgia (12/18), fatigue (10/18), maculopapular rash (1/18), diarrhea (1/18) and mucositis (1/18). Of the 12 patients who completed surgery, 8/12 (67%) were ypT0N0, 9/12 (75%) were ypT0/Tis and 10/12 (83%) were ypN0. Of the 5 patients with node-positive disease at diagnosis, 3/5 (60%) became ypN0 and 1/5 (20%) became ypN1mic. Change in TILs after pembro or pembro-RT did not correlate with treatment response, however baseline TIL count ≥10% in the initial biopsy was associated with pCR (p = 0.01). Conclusions: Neoadjuvant pembro plus RT prior to SOC chemotherapy is safe/feasible and may increase pCR rates beyond chemotherapy alone. A randomized phase 2 study of checkpoint blockade +/- RT in a larger cohort is planned.

Citation Format: Heather McArthur, Stephen Shiao, Scott Karlan, Farin Amersi, Brittany Arnold, Reva Basho, Michele Burnison, Alice Chung, Cathie Chung, Catherine Dang, Armando Giuliano, Negin Habibi Khameneh, Simon Knott, Cynthia Martin, Philomena McAndrew, Monica Mita, Dorothy Park, Christina Abaya, Alice Ho. Pre-operative pembrolizumab (pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-09-09.

Abstract OT2-04-04: Neoadjuvant HER2-targeted therapy +/- immunotherapy with pembrolizumab (neoHIP): An open label randomized phase 2 trial

Background: Immune checkpoint inhibition (ICI) is synergistic with HER2-directed therapy in pre-clinical models. Clinically, pembrolizumab (K)-mediated ICI plus HER2-directed therapy with trastuzumab (H) was safe and demonstrated modest activity in H-resistant HER2-positive (HER2+) metastatic breast cancer. Because ICI may confer more robust activity when administered earlier in the course of disease, HER2-directed therapy with ICI administered in the curative-intent, treatment-naive setting may allow for de-escalation of cytotoxic backbones; confer life-long, tumor-specific immunity; and ultimately, improve cure rates. Moreover, the synergy of H and K with paclitaxel (T) may overcome the need for dual HER2-blockade with H plus pertuzumab (P). In this randomized, multicenter, phase II, open-label trial, the efficacy and safety of neoadjuvant THP vs THP-K vs TH-K are being explored (NCT03747120). Methods: 174 patients (pts) ≥18years with previously untreated, clinical stage II-III, HER2+ breast cancer will be randomized 1:1:1 to one of 3 study arms, stratified by clinical nodal status (positive vs. negative) and hormone receptor status (positive vs. negative). In arm A, pts receive THP: T at 80 mg/m2 weekly for 12 weeks, H day 1 at 8 mg/Kg (loading dose) and then 6 mg/Kg every 3 weeks x 3 doses, P day 1 at 840 mg (loading dose) and then 420 mg/Kg every 3 weeks x 3 doses (THP). In arm B, pts receive THP plus K day 1 at 200mg (flat dose) and then every 3 weeks x 3 doses (THP-K). In arm C, pts receive TH-K. Definitive surgery is 3-6 weeks after the last dose of T. After surgery, pts are treated per the treating physician’s discretion including HER2-directed therapy, endocrine therapy and radiotherapy per local clinical standards. The primary endpoint is pathologic complete response (pCR) rate in the breast and axilla (ypT0/Tis ypN0). Secondary end points include pCR rate by ypT0ypN0 and ypT0/Tis, residual cancer burden index, event free survival, breast conserving surgery rate, safety and overall survival. Exploratory correlative studies will characterize potential immune biomarkers predictive of efficacy and/or toxicity.

Citation Format: Heather McArthur, Jorge Leal, David Page, Christina DiLauro Abaya, Reva Basho, Lindsey Ristow, Hannah Coleman, Stephen Shiao, Simon Knott, Monica Mita, Mourad Tighiouart, Alice Chung, Farnaz Dadmanesh, Philomena McAndrew, Scott Karlan, Sunil Verma, Armando Giuliano. Neoadjuvant HER2-targeted therapy +/- immunotherapy with pembrolizumab (neoHIP): An open label randomized phase 2 trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr OT2-04-04.

Natural killer cell activity and prostate cancer risk in veteran men undergoing prostate biopsy

BACKGROUND

A previous pilot study found that men with a positive prostate biopsy had low numbers of circulating natural killer (NK) cells, compared to biopsy negative men.

METHODS

To confirm these data, we analyzed differences in NK cells from 94 men undergoing prostate biopsy to determine whether NK cells could predict for a positive biopsy. NK cells activity (NKA) was measured by an in vitro diagnostic system, with a pre-defined cut-off value for NKA at 200 pg/mL. Logistic regression and receiver operator characteristics (Area Under the Curve (AUC)) analyses were used to test the diagnostic value of NKA.

RESULTS

The NKA test performance showed specificity of 88%, positive predictive value of 84%, sensitivity of 34%, and a negative predictive value of 41%. Among the 94 men analyzed, NKA was not significantly linked with age, race, digital rectal examination (DRE), prostate volume, PSA or biopsy grade group (all P ≥ 0.14). In multivariable logistic regression analysis, the odds ratio (OR) of low NKA (<200 pg/mL) for the detection of PC was 4.89, 95%CI 1.34-17.8, with a ROC area under the curve of 0.79 in all participants and increasing to 0.83 and 0.85 for the detection of PC and high-grade PC, respectively, among men with a normal DRE.

CONCLUSIONS

Men with a low NKA value had five-times higher odds of PC at biopsy. The implementation of this NKA assay in the clinic together with PSA may help to advise patients with the highest risk of PC whether, or not, to undergo a prostate biopsy.

Abstract OT3-04-02: Neoadjuvant Her2-targeted therapy +/- immunotherapy with pembrolizumab (neoHIP): An open label randomized phase II trial

Background: In preclinical models HER2-directed therapy administered with checkpoint blockade is synergistic. Clinically, trastuzumab administered with pembrolizumab-mediated checkpoint blockade in trastuzumab-resistant HER2-positive metastatic breast cancer was safe and demonstrated modest activity. However, because checkpoint blockade can confer improved responses when administered earlier in the course of disease, trastuzumab with pembrolizumab administered in the curative-intent, treatment-naive setting may confer life-long, tumor-specific immunity and ultimately, improve cure rates. Moreover, the potential synergy of trastuzumab and pembrolizumab with paclitaxel may overcome the need for dual HER2-blockade. The neo-HIP study is a randomized, multicenter, phase II, open-label trial to evaluate the efficacy and safety of weekly paclitaxel, trastuzumab plus pertuzumab (THP) vs weekly THP plus pembrolizumab (THP-K) vs a HER2 monotherapy regimen (TH-K) as neoadjuvant treatment in patients with HER2-positive early stage invasive breast cancer.

Methods:Patients ≥18 years old with previously untreated, non-metastatic, stage II-III, HER2-positive (by ASCO/CAP guidelines) breast cancer are eligible. Patients with inflammatory breast cancer or bilateral primary tumors are excluded. Adequate organ function and ECOG PS 0-1 are required. Approximately 174 patients will be randomly assigned to 1 of 3 arms with stratification by clinical nodal status (positive vs. negative) and hormone receptor status (positive vs. negative). In arm A, patients will receive T at 80mg/m2 weekly for 12 weeks, H at 8mg/Kg (1 loading dose) and then 6mg/Kg IV every 3 weeks x 3 doses, P at 840mg (1 loading dose) and then 420mg/Kg IV every 3 weeks x 3 doses (THP). In arm B, patients will receive the same regimen as arm A with the addition of pembrolizumab 200mg IV every 3 weeks x 4 doses (THP-K). In arm C, patients will receive the same regimen as arm B, but without pertuzumab (TH-K). Definitive surgery will be 3-6 weeks after the last treatment dose. After surgery, patients in all arms willbe treated per the treating physician's discretion. After completion of post-operative chemotherapy, patients will receive radiotherapy per local clinical standard and those patients whose tumors are hormone-receptor positive will receive hormone therapy as per local standard-of-care. The purpose of this phase II study is to identify whether Arm B (THP-K) and/or Arm C (TH-K) demonstrate a clinically significant improvement in pCR rate when compared with Arm A (THP). The primary end point is pCR rate in the breast and axilla (ypT0/Tis ypN0). Secondary end points include pCR rate by ypT0ypN0 and ypT0/Tis, residual cancer burden index, event free survival, breast conserving surgery rate, safety and overall survival. Exploratory correlative studies will characterize the immunologic responses to the interventions and explore potential predictors of efficacy and toxicity.

Citation Format: McArthur HL, Leal JHS, DiLauro Abaya C, Basho R, Coleman H, Shiao S, Knott S, Tighiouart M, Dadmanesh F, Giuliano A, Verma S. Neoadjuvant Her2-targeted therapy +/- immunotherapy with pembrolizumab (neoHIP): An open label randomized phase II trial [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 OT3-04-02.

Abstract P2-09-07: Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC)

Background: Radiation therapy (RT) induces immune-mediated cell death and could generate a rich supply of tumor antigens if administered in the pre-operative, curative-intent setting. The addition of PD-1 mediated checkpoint blockade to pre-operative RT could thus, generate robust anti-tumor immune responses, induce long-term tumor-specific memory, and ultimately, improve cure rates. This study aims to establish the safety of pre-operative pembrolizumab (pembro)-mediated immune modulation with a RT “boost” equivalent in patients with operable triple negative breast cancer (TNBC) for whom lumpectomy and adjuvant RT are planned (NCT03366844). Serial research biopsies permit interrogation of conventional biomarkers including tumor infiltrating lymphocytes (TILs) and novel immune correlates as potential predictors of response to pembro alone versus pembro with RT.

Methods: Ten women with operable, primary TNBC &gt;2cm for whom breast-conserving therapy is planned are being enrolled in this single-institution pilot study. Study treatment consists of 1 cycle of pre-operative pembro (200 mg IV) alone, followed 3 weeks later by a RT boost (24 Gy/3 fractions) to the primary breast tumor concurrently with pembro (+/- 5 days). Curative-intent, standard-of-care, neoadjuvant chemotherapy (NAC) or breast-conserving surgery is then undertaken within 8 weeks of study enrollment (i.e. within 5 weeks of pembro #2). Adjuvant RT is administered per standard-of-care after surgery, but without a boost dose. Research blood and fresh tumor biopsies are obtained at baseline and after cycles 1 and 2 of pembro. Co-primary endpoints are: 1) safety/tolerability, as defined by the number of patients who do not necessitate a delay in standard-of-care chemotherapy or surgery and 2) change in TIL score. Secondary endpoints include safety/toxicity up to 19 weeks after study enrollment, pCR rates and disease-free survival. Correlative analysis will include single-cell RNA sequencing of the tumor immune infiltrate and multispectral immunohistochemistry

Results: Seven patients enrolled between 12/19/17 and 7/1/18. As of 7/1/18, 5 patients have completed the experimental pembro/RT phase of the trial and are currently completing standard-of-care NAC; 1 patient is currently being treated in the experimental pembro/RT phase; and 1 patient with a cT2N0 tumor at baseline achieved a pathologic complete response (pCR, ypT0/Tis ypN0) after completing the experimental pembro/RT phase followed by anthracycline- and taxane-based NAC. No grade 3 or 4 toxicities have been observed during pembro/RT in the 6 patients completing the experimental phase to date. Three additional patients will be enrolled

Conclusions: This is the first trial of curative-intent, pre-operative checkpoint blockade with RT in breast cancer and the strategy appears to be well tolerated to date. At the time of presentation, safety, change in TIL score, and pCR rates for all patients completing the experimental and NAC phases of the study will be reported.

Citation Format: McArthur HL, Basho R, Shiao SL, Park D, Mita M, Chung A, Arnold B, Martin C, Dang C, Karlan S, Knott S, Giuliano A, Ho A. Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC) [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 P2-09-07.

Prediction of intramuscular fat content and shear force in Texel lamb loins using combinations of different X-ray computed tomography (CT) scanning techniques

Computed tomography (CT) parameters, including spiral computed tomography scanning (SCTS) parameters, intramuscular fat (IMF) and mechanically measured shear force were derived from two previously published studies. Purebred Texel (n = 377) of both sexes, females (n = 206) and intact males (n = 171) were used to investigate the prediction of IMF and shear force in the loin. Two and three dimensional CT density information was available. Accuracies in the prediction of shear force and IMF ranged from R² 0.02 to R² 0.13 and R² 0.51 to R² 0.71 respectively, using combinations of SCTS and CT scan information. The prediction of mechanical shear force could not be achieved at an acceptable level of accuracy employing SCTS information. However, the prediction of IMF in the loin employing information from SCTS and additional information from standard CT scans was successful, providing evidence that the prediction of IMF and related meat eating quality (MEQ) traits for Texel lambs in vivo can be achieved.

Abstract B13: COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors

Aberrant activation of the mitogen activate kinase (MAPK) pathway is highly prevalent in cancer and therapies targeting the pathway are approved or under active investigation in multiple malignancies. MAPK signaling leads to activation of a transcriptional program that includes general growth promoting genes, negative feedback regulators of the MAPK pathway, and lineage-specific genes. While the mechanisms of upstream signal transduction that leads to MAPK activation have been studied in detail, how MAPK activation is dynamically coupled with downstream nuclear transcriptional response is not fully understood. In gastrointestinal stomal tumor (GIST) and melanoma, two malignancies with aberrant MAPK activation, we find that Pea3 family ETS transcription factors ETV1, ETV4, and ETV5 are critical nuclear effectors of MAPK signaling. We find that the primary mechanism linking MAPK and Pea3 activity is through protein stability via the COP1 E3 ligase. The loss of COP1 leads to decoupling between upstream MAPK signaling and downstream transcription with constitutively stabilized Pea3 protein levels, constitutively high MAPK transcriptome, yet decreased upstream signaling due to Pea3-mediated transcription of negative feedback regulators. This leads to decreased therapeutic sensitivity to MAPK pathway inhibition in vitro and in vivo. These observations indicate that MAPK signaling-dependent regulation of Pea3 ETS protein stability is a crucial pathway that couples downstream transcriptional response to MAPK signaling and can shape the therapeutic sensitivity to MAPK pathway inhibition in cancer.

Citation Format: Yuanyuan Xie, Zhen Cao, Wai Pung Wong, Youxin Guan, Jenny Zhang, Edward Walczak, Devan Murphy, Leili Ran, Inna Sirota, Shangqian Wang, Shipra Shukla, Dong Gao, John Wongvipat, Simon Knott, Kenneth Chang, Cristina Antonescu, Gregory Hannon, Ping Chi, Yu Chen. COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B13.

Regional heritability mapping method helps explain missing heritability of blood lipid traits in isolated populations

Single single-nucleotide polymorphism (SNP) genome-wide association studies (SSGWAS) may fail to identify loci with modest effects on a trait. The recently developed regional heritability mapping (RHM) method can potentially identify such loci. In this study, RHM was compared with the SSGWAS for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG)). Data comprised 2246 adults from isolated populations genotyped using ∼300 000 SNP arrays. The results were compared with large meta-analyses of these traits for validation. Using RHM, two significant regions affecting HDL on chromosomes 15 and 16 and one affecting LDL on chromosome 19 were identified. These regions covered the most significant SNPs associated with HDL and LDL from the meta-analysis. The chromosome 19 region was identified in our data despite the fact that the most significant SNP in the meta-analysis (or any SNP tagging it) was not genotyped in our SNP array. The SSGWAS identified one SNP associated with HDL on chromosome 16 (the top meta-analysis SNP) and one on chromosome 10 (not reported by RHM or in the meta-analysis and hence possibly a false positive association). The results further confirm that RHM can have better power than SSGWAS in detecting causal regions including regions containing crucial ungenotyped variants. This study suggests that RHM can be a useful tool to explain some of the ‘missing heritability' of complex trait variation.

Rapid cycling as a feature of bipolar disorder and comorbid migraine

BACKGROUND

Previous research has suggested the clinical profile of individuals with bipolar disorder (BD) differs according to the presence or absence of comorbid migraine. We aimed to determine the clinical characteristics that differentiate individuals with BD with and without comorbid migraine in a large, representative, clinically well-characterised UK sample.

METHODS

The lifetime clinical characteristics of 1488 individuals with BD (BPI n=1120, BPII n=368) with and without comorbid migraine were compared (n=375 vs. n=1113 respectively).

RESULTS

Individuals with BD and comorbid migraine had a distinctive set of lifetime clinical characteristics. A multivariate model showed that consistent with previous studies those with comorbid migraine were significantly more likely to be female (OR=2.099, p=0.005) and have comorbid panic attacks (OR=1.842, p=0.004). A novel finding was that even after controlling for other differences, the individuals with BD and comorbid migraine were more likely to have a rapid cycling illness course (OR=1.888, p=0.002).

LIMITATIONS

Presence of migraine was assessed using self report measures. Cross-sectional study design limits investigations of bidirectional associations between migraine and bipolar disorder.

CONCLUSIONS

Comorbid migraine in BD may represent a more homogenous subtype of BD with an unstable rapid cycling course. Identifying individuals with BD and comorbid migraine may be of use in a clinical setting and this subgroup could be the focus of future aetiological studies.

Prediction of intramuscular fat levels in Texel lamb loins using X-ray computed tomography scanning

For the consumer, tenderness, juiciness and flavour are often described as the most important factors for meat eating quality, all of which have a close association with intramuscular fat (IMF). X-ray computed tomography (CT) can measure fat, muscle and bone volumes and weights, in vivo in sheep and CT predictions of carcass composition have been used in UK sheep breeding programmes over the last few decades. This study aimed to determine the most accurate combination of CT variables to predict IMF percentage of M. longissimus lumborum in Texel lambs. As expected, predicted carcass fat alone accounted for a moderate amount of the variation (R(2)=0.51) in IMF. Prediction accuracies were significantly improved (Adj R(2)>0.65) using information on fat and muscle densities measured from three CT reference scans, showing that CT can provide an accurate prediction of IMF in the loin of purebred Texel sheep.

Effect of the Texel muscling QTL (TM-QTL) on spine characteristics in purebred Texel lambs

Previous work showed that the Texel muscling QTL (TM-QTL) results in pronounced hypertrophy in the loin muscle, with the largest phenotypic effects observed in lambs inheriting a single copy of the allele from the sire. As the loin runs parallel to the spinal vertebrae, and the development of muscle and bone are closely linked, the primary aim of this study was to investigate if there were any subsequent associations between TM-QTL inheritance and underlying spine characteristics (vertebrae number, VN; spine region length, SPL; average length of individual vertebrae, VL) of the thoracic, lumbar, and thoracolumbar spine regions. Spine characteristics were measured from X-ray computed tomography (CT) scans for 142 purebred Texel lambs which had been previously genotyped. Least-squares means were significantly different between genotype groups for lumbar and thoracic VN and lumbar SPL. Similarly for these traits, contrasts were shown to be significant for particular modes of gene action but overall were inconclusive. In general, the results showed little evidence that spine trait phenotypes were associated with differences in loin muscling associated with the different TM-QTL genotypes.

Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains

Background

Drosophila melanogaster adult males perform an elaborate courtship ritual to entice females to mate. fruitless (fru), a gene that is one of the key regulators of male courtship behavior, encodes multiple male-specific isoforms (Fru^M). These isoforms vary in their carboxy-terminal zinc finger domains, which are predicted to facilitate DNA binding.

Results

By over-expressing individual Fru^M isoforms in fru-expressing neurons in either males or females and assaying the global transcriptional response by RNA-sequencing, we show that three Fru^M isoforms have different regulatory activities that depend on the sex of the fly. We identified several sets of genes regulated downstream of Fru^M isoforms, including many annotated with neuronal functions. By determining the binding sites of individual Fru^M isoforms using SELEX we demonstrate that the distinct zinc finger domain of each Fru^M isoforms confers different DNA binding specificities. A genome-wide search for these binding site sequences finds that the gene sets identified as induced by over-expression of Fru^M isoforms in males are enriched for genes that contain the binding sites. An analysis of the chromosomal distribution of genes downstream of Fru^M shows that those that are induced and repressed in males are highly enriched and depleted on the X chromosome, respectively.

Conclusions

This study elucidates the different regulatory and DNA binding activities of three Fru^M isoforms on a genome-wide scale and identifies genes regulated by these isoforms. These results add to our understanding of sex chromosome biology and further support the hypothesis that in some cell-types genes with male-biased expression are enriched on the X chromosome.

Between- and within-breed variations of spine characteristics in sheep

Implementing the use of spine traits in a commercial breeding program has been seen to improve meat production from the carcass of larger-bodied pigs. The aim of this study was to assess the extent of variation in spine characteristics within and between breeds of sheep and to investigate the association with body length and tissues traits to deliberate if a similar approach could be applicable in the sheep sector. Spine traits (vertebrae number, VN; spine region length, SPL; individual vertebra length, VL) of the thoracic (THOR) lumbar (LUM) and thoracolumbar (T+L) spine regions were measured using x-ray computed tomography (CT) on 254 Texel (TEX), 1100 Scottish Blackface (SBF), 326 Texel cross Mule (TEX × MULE), and 178 Poll Dorset cross Mule (PD × MULE) lambs. Simple descriptive statistics inform that variation in thoracolumbar VN exists within all breeds and crosses; TEX animals showed the largest range of variation in thoracolumbar VN (17 to 21) and the TEX × MULE the smallest (18 to 20). Significant differences were not observed between sexes, but did occur between breeds (P < 0.05), which is indicative of a genetic basis for these traits. Least-squares means identified that TEX had the least thoracolumbar VN (19.24) and SBF possessed the most (19.63); similarly the lowest measures for SPL and VL for each spine region were observed in TEX, but the greatest values for these traits were expressed predominantly in the crosses (TEX × MULE and PD × MULE). Correlation coefficients (r) within each breed or cross support the interpretation of additional vertebrae contributing to a longer length of the spine region in which they occur (P < 0.001; e.g., for PD × MULE lambs), r between traits VNTHOR and SPLTHOR (r = 0.59), VNLUM and SPLLUM (r = 0.94) and VNT+L and SPLT+L (r = 0.65) all reach moderate to very high values. In all breeds and crosses, this relationship is particularly strong for the lumbar region. The few significant (P < 0.05) correlations observed between spine and tissue traits [CT-predicted quantities of carcass fat and muscle (kg) and area of the LM (mm(2))] indicated no substantial relationships, r was small (ranging from -0.25 to 0.19) in each case. To conclude, significant vertebral variation exists within and between sheep breeds and crosses, which can contribute to an increase in body (and carcass) length. Including measurements taken for other primal cuts will further aid in assessing any potential increase in meat production from these longer-bodied sheep.

Optimal use of regression models in genome-wide association studies

The performance of linear regression models in genome-wide association studies is influenced by how marker information is parameterized in the model. Considering the impact of parameterization is especially important when using information from multiple markers to test for association. Properties of the population, such as linkage disequilibrium (LD) and allele frequencies, will also affect the ability of a model to provide statistical support for an underlying quantitative trait locus (QTL). Thus, for a given location in the genome, the relationship between population properties and model parameterization is expected to influence the performance of the model in providing evidence for the position of a QTL. As LD and allele frequencies vary throughout the genome and between populations, understanding the relationship between these properties and model parameterization is of considerable importance in order to make optimal use of available genomic data. Here, we evaluate the performance of regression-based association models using genotype and haplotype information across the full spectrum of allele frequency and LD scenarios. Genetic marker data from 200 broiler chickens were used to simulate genomic conditions by selecting individual markers to act as surrogate QTL (sQTL) and then investigating the ability of surrounding markers to estimate sQTL genotypes and provide statistical support for their location. The LD and allele frequencies of markers and sQTL are shown to have a strong effect on the performance of models relative to one another. Our results provide an indication of the best choice of model parameterization given certain scenarios of marker and QTL LD and allele frequencies. We demonstrate a clear advantage of haplotype-based models, which account for phase uncertainty over other models tested, particularly for QTL with low minor allele frequencies. We show that the greatest advantage of haplotype models over single-marker models occurs when LD between markers and the causal locus is low. Under these situations, haplotype models have a greater accuracy of predicting the location of the QTL than other models tested.

Complex traits analysis of chicken growth using targeted genetical genomics

Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.

Controlling false positives in the mapping of epistatic QTL

This study addresses the poorly explored issue of the control of false positive rate (FPR) in the mapping of pair-wise epistatic quantitative trait loci (QTL). A nested test framework was developed to (1) allow pre-identified QTL to be used directly to detect epistasis in one-dimensional genome scans, (2) to detect novel epistatic QTL pairs in two-dimensional genome scans and (3) to derive genome-wide thresholds through permutation and handle multiple testing. We used large-scale simulations to evaluate the performance of both the one- and two-dimensional approaches in mapping different forms and levels of epistasis and to generate profiles of FPR, power and accuracy to inform epistasis mapping studies. We showed that the nested test framework and genome-wide thresholds were essential to control FPR at the 5% level. The one-dimensional approach was generally more powerful than the two-dimensional approach in detecting QTL-associated epistasis and identified nearly all epistatic pairs detected from the two-dimensional approach. However, only the two-dimensional approach could detect epistatic QTL with weak main effects. Combining the two approaches allowed effective mapping of different forms of epistasis, whereas using the nested test framework kept the FPR under control. This approach provides a good search engine for high-throughput epistasis analyses.

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae

Replication fork stalling at a DNA lesion generates a damage signal that activates the Rad53 kinase, which plays a vital role in survival by stabilizing stalled replication forks. However, evidence that Rad53 directly modulates the activity of replication forks has been lacking, and the nature of fork stabilization has remained unclear. Recently, cells lacking the Psy2-Pph3 phosphatase were shown to be defective in dephosphorylation of Rad53 as well as replication fork restart after DNA damage, suggesting a mechanistic link between Rad53 deactivation and fork restart. To test this possibility we examined the progression of replication forks in methyl-methanesulfonate (MMS)-damaged cells, under different conditions of Rad53 activity. Hyperactivity of Rad53 in pph3Delta cells slows fork progression in MMS, whereas deactivation of Rad53, through expression of dominant-negative Rad53-KD, is sufficient to allow fork restart during recovery. Furthermore, combined deletion of PPH3 and PTC2, a second, unrelated Rad53 phosphatase, results in complete replication fork arrest and lethality in MMS, demonstrating that Rad53 deactivation is a key mechanism controlling fork restart. We propose a model for regulation of replication fork progression through damaged DNA involving a cycle of Rad53 activation and deactivation that coordinates replication restart with DNA repair.

Thermodynamic investigations of ternary liquid alloys

A review of different methods for determining thermodynamic quantities is given. The electromotive force (EMF) method with a liquid and solid electrolyte, the calorimetric and differential scanning calorimetry (DSC) methods, and vapour pressure experiments like the isopiestic and Knudsen effusion methods are discussed.

Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humans

IFN-beta effectively controls clinical exacerbations and magnetic resonance imaging activity in most multiple sclerosis patients. However, its mechanism of action has not been yet fully elucidated. In this study we used DNA microarrays to analyze the longitudinal transcriptional profile of blood cells within a week of IFN-beta administration. Using differential expression and gene ontology analyses we found evidence of a general decrease in the cellular activity of T lymphocytes resembling the endogenous antiviral response of IFNs. In contrast, most of the differentially expressed genes (DEGs) from untreated individuals were involved in cellular physiological processes. We then used mutual information (MI) to build networks of coregulated genes in both treated and untreated individuals. Interestingly, the connectivity distribution (k) of networks generated with high MI values displayed scale-free properties. Conversely, the observed k for networks generated with suboptimal MI values approximated a Poisson distribution, suggesting that MI captures biologically relevant interactions. Gene networks from individuals treated with IFN-beta revealed a tight core of immune- and apoptosis-related genes associated with higher values of MI. In contrast, networks obtained from untreated individuals primarily reflected cellular housekeeping functions. Finally, we trained a neural network to reverse engineer the directionality of the main interactions observed at the biological process level. This is the first study that incorporates network analysis to investigate gene regulation in response to a therapeutic drug in humans. Implications of this method in the creation of personalized models of response to therapy are discussed.

The influence of folic acid depletion on the Nucleotide Excision Repair capacity of human dermal fibroblasts measured by a modified Host Cell Reactivation Assay

Animal and human studies have shown that low levels of folic acid are associated with an impaired DNA Repair Capacity (DRC) and an increased cancer risk. However, the molecular evidence that folic acid enhances the DRC of cultured human cells is still limited because of a paucity of in vitro studies. We investigated the effect of folic acid depletion in vitro on the DRC of human dermal fibroblasts derived from 17 donors of different ages. To assess the cellular Nucleotide Excision DRC, we used a modified Host Cell-Reactivation Assay (HCRA), adapted to the Fluorescence Activated Cell Sorting (FACS)-technology, which is highly sensitive in comparison to luminometer-technology and allows single cell based analysis. We used DsRed as a reporter (irradiated with UVC light) and pEGFP to control the performance of the transformations. Folic acid had a statistically significant effect on the DRC in all of the 17 donors, however, the levels varied considerably between individuals (2.0-19.6%). When the effect of folic acid substituted on the DRC was compared to donor age, we observed that there was less DNA repair in old donors compared to the younger donors, although this was only significant at lower levels.

A neural network based approach for inference and verification of transcriptional regulatory interactions

In this paper, we present a comprehensive neural network based modeling and validation framework for reverse engineering gene regulatory interactions. We employ two approaches, Gene Set Stochastic Sampling and Sensitivity Analysis, to infer these interactions. We first apply these methods to a simulated artificial dataset to ensure their correctness and accuracy. True biological interactions are then modeled by analyzing a rat hippocampus development dataset. Finally, we present a thorough computational methodology to test the validity and robustness of the inferred regulations through novel assemblies of relevant testing datasets.

Effects of following National Committee for Clinical Laboratory Standards and Deutsche Industrie Norm-Medizinische Mikrobiologie guidelines, country of isolate origin, and site of infection on susceptibility of Escherichia coli to amoxicillin-clavulanate (Augmentin)

Amoxicillin-clavulanate (Augmentin), as a combination of two active agents, poses extra challenges over single agents in establishing clinically relevant breakpoints for in vitro susceptibility tests. Hence, reported differences in amoxicillin-clavulanate percent susceptibilities among Escherichia coli isolates may reflect localized resistance problems and/or methodological differences in susceptibility testing and breakpoint criteria. The objectives of the present study were to determine the effects of (i) methodology, e.g., those of the National Committee for Clinical Laboratory Standards (NCCLS) and the Deutsche Industrie Norm-Medizinische Mikrobiologie (DIN), (ii) country of origin (Spain, France, and Germany), and (iii) site of infection (urinary tract, intra-abdominal sepsis, or other site[s]) upon the incidence of susceptibility to amoxicillin-clavulanate in 185 clinical isolates of E. coli. Cefuroxime and cefotaxime were included for comparison. The use of NCCLS methodology resulted in different distribution of amoxicillin-clavulanate MICs than that obtained with the DIN methodology, a difference highlighted by the 10% more strains found to be within the 8- to 32-microg/ml MIC range. This difference reflects the differing amounts of clavulanic acid present. NCCLS and DIN methodologies also produce different MIC distributions for cefotaxime but not for cefuroxime. Implementation of NCCLS and DIN breakpoints produced markedly different incidences of strains that were found to be susceptible, intermediate or resistant to amoxicillin-clavulanate. A total of 86.5% strains were found to be susceptible to amoxicillin-clavulanate by the NCCLS methodology, whereas only 43.8% were found to be susceptible by the DIN methodology. Similarly, 4.3% of the strains were found to be resistant by NCCLS guidelines compared to 21.1% by the DIN guidelines. The use of DIN breakpoints resulted in a fivefold-higher incidence of strains categorized as resistant to cefuroxime. There were no marked differences due to country of origin upon the MIC distributions for amoxicillin-clavulanate, cefuroxime, or cefotaxime, as determined with the NCCLS guidelines. Isolates from urinary tract and intra-abdominal infections were generally more resistant to amoxicillin-clavulanate than were isolates from other sites of infection.

Measuring maternal mortality in developing Pacific island countries: experience with the sisterhood method in the Solomon Islands

AIMS

To estimate the maternal mortality rate in the Solomon Islands, and to assist health planning and implementation of effective interventions.

METHOD

The sisterhood method, an indirect technique for deriving population-based estimates of maternal mortality was used in interviews with 2580 randomly chosen women reporting on the fertility and mortality experience of their sisters.

RESULTS

The maternal mortality ratio in this study was 549 per 100,000 (95% CI 431, 684). This equates to one maternal death in every 180 pregnancies.

CONCLUSION

The sisterhood method was found to be easy to administer, inexpensive and quick, and is recommended as a measurement tool to other developing countries.

Disposition and pharmacology of propofol glucuronide administered intravenously to animals

1. Propofol glucuronide (PG) is the major human metabolite of the i.v. anaesthetic propofol, 2,6-diisopropylphenol. 2. Bolus i.v. doses of 14C-PG (1 mg/kg) to rat and dog were eliminated in urine (40 and 66% respectively) and faeces (48 and 19%); 25 and 48% of the dose were excreted unchanged in urine. 3. In dog, PG was distributed from plasma (t 1/2 4 min) into a volume equivalent to extracellular water and eliminated with t 1/2 80 min. Total body clearance was 1.8 ml/min per kg, and renal clearance about 20% GFR. In rat, plasma 14C concentrations were about one-tenth those in dog, thus PG levels were not quantified. 4. Propofol was not detected in the plasma showing that PG is hydrolytically stable. Enterohepatic circulation of PG occurred in rat and to a lesser extent in dog. Metabolites, mainly side-chain hydroxylation products, were evident in both species from 4 h after dosing. 5. Bolus i.v. doses of PG (200 mg/kg) showed no hypnotic activity in mice.

Species differences in blood profiles, metabolism and excretion of 14C-propofol after intravenous dosing to rat, dog and rabbit

1. Bolus i.v. doses of 14C-propofol (7-10 mg/kg) to rat, dog and rabbit, or an infusion dose (0.47 mg/kg per min for 6 h) to dog were eliminated primarily in urine (60-95% dose); faecal elimination (13-31%) occurred for rat and dog, but was minimal (less than 2%) for rabbit. 2. After bolus administration, blood 14C concentrations were maximal (8-30 micrograms equiv./ml) at 2-15 min; these declined rapidly during the 0-2 h period and thereafter more slowly. Propofol concentrations were maximal (4-16 micrograms/ml) at 2 min and the profiles were best fitted by a tri-exponential (rat and dog) or bi-exponential (rabbit) equation. Duration of sleep ranged from 5 to 8 min. 3. Infusion of 14C-propofol in dog gave a blood 14C concentration of 117 micrograms equiv./ml at the end of the 6 h infusion period; this declined at a similar rate to that after the bolus dose. Propofol concentration on termination of infusion was 13 micrograms/ml; thereafter, propofol concentrations declined less rapidly than after the bolus dose. Waking occurred about 44 min post-infusion. 4. Propofol was cleared by conjugation of the parent molecule or its quinol metabolite; hydroxylation of an isopropyl group also occurred in rat and rabbit. Biliary excretion leading to enterohepatic recirculation, and in turn increased sulphate conjugation, occurred in rat and dog, but not rabbit, resulting in a marked interspecies variation in drug clearance and metabolite profiles.

Distribution in female rats of an anaesthetic intravenous dose of 14C-propofol

1. Bolus i.v. doses of 14C-propofol (9 mg/kg) were administered to female rats for measurement of tissue levels of total 14C and propofol from 2 min to 24 h post-dose; whole-body autoradiography was studied at 6 min, 2 h and 24 h post-dose, and also involved 15-day pregnant rats. 2. The blood propofol concentration-time profile was fitted by a tri-exponential function corresponding to a three-compartment open model. Data show rapid distribution during the mixing period into highly perfused tissues and muscle, comprising the central compartment, and slower uptake into less well-perfused skin and adipose tissues comprising the deeper compartments. 3. The initial decline in blood propofol concentration was associated with redistribution (t1/2 4 min), the second decline (15-240 min post-dose) was associated with metabolism (t1/2 33 min) and the third decline reflected slow depletion of drug from deep tissue compartments (t1/2 6.4 h). 4. Blood and brain propofol concentrations on waking (at 7 min post-dose) were 4 micrograms/ml and 9 micrograms/g respectively; the model shows that, at this time, 30% of the dose was lost from the central compartment by redistribution and a similar amount by metabolism. 5. Tissue profiles of total 14C and propofol diverged for highly perfused tissues (other than brain) because of slow clearance of metabolites, accentuated by enterohepatic recirculation.

The disposition of tert-butyl-D-serine in the rat

1. Following intravenous administration of 14C-tert-butyl-D-serine to rats, radioactivity was eliminated rapidly via the kidneys. 2. One metabolite was detected in urine and was identified as the N-acetyl derivative of tert-butyl-serine. 3. Elimination was more rapid in female than male rats.

Isometric contractions of motor units in a fast twitch muscle of the cat

1. Isosmetric contractions of cat flexor digitorum longus whole muscles and of functionally isolated motor units have been measured under conditions similar to those used by Buller & Lewis (1965a).2. Motor unit twitch time to peak was inversely related to axonal conduction velocity. The logarithm of tetanic tension was directly related to conduction velocity. These relationships suggest that each motoneurone has an influence on the muscle fibres which it innervates.3. The ratio of twitch to tetanic tension was directly related to the time to peak of the motor unit. This fact might be explained by variation between motor units of the duration of ;active state'.4. The muscle length at which tension was maximal varied between motor units and the optima were found over the range of muscle lengths which could occur in the body. Slow motor units had longer optimal lengths.5. The sample of motor units was considered to be unbiased because the distribution of axon conduction velocities was compatible with reported motor fibre diameter spectra of the muscle nerve. The mean motor unit tetanic tension gave a reasonable estimate of the number of alpha-motor axons in the muscle nerve. Twitch tensions gave a value that was 40% higher.6. Motor unit and whole muscle data were in good agreement for length-tetanus tension curves, for times to peak and for twitch-tetanus ratios at long muscle lengths.