Abstract P6-10-05: Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition

Background: Heterozygous hotspot mutations in the RNA splicing factor SF3B1, occur in 3% of unselected breast cancers and are associated with oestrogen receptor (ER+) breast cancer (BC) where they are enriched in metastatic disease and are associated with a poor clinical outcome. SF3B1 mutations drive distinct signatures of alternative splicing through cryptic 3’ splice site selection leading to global transcriptomic and proteomic changes. The functional consequences of the mis-splicing events and resultant genetic vulnerabilities are poorly understood and precision medicine approaches that exploit these characteristics are not clinically available (Table 1).

Methods: To understand the role of SF3B1 mutations in ER+ BC, we generated a series of SF3B1 mutant (SF3B1MUT) isogenic cell lines which were characterised using RNA-sequencing and high content mass-spectrometry proteomic profiling. SF3B1 interactome analysis was also performed using immunoprecipitation of SF3B1 followed by mass-spectrometry. The molecular consequences of aberrant splicing were investigated using a targeted screening approach of 280 genes predicted to be alternatively spliced in SF3B1MUT BC, while high-throughput drug screens were used to identify novel therapeutic options for patients with SF3B1MUT breast cancer using isogenic cells. Hits were validated in vitro and in vivo using cell line and patient derived xenografts.

Results: Transcriptomic and proteomic profiling of SF3B1MUT cells identified global alternative 3’ splice site selection and subsequent proteomic changes induced by the mutations. Investigation of the SF3B1K700E interactome identified an enrichment of SF3B1K700E binding with ER, aberrant splicing of ER target genes, global rewiring of ER chromatin binding and resistance to endocrine therapy. Silencing of the aberrantly spliced candidate genes PPIH, TRIM37, HIGD1A, BRD9, and PHKG2 significantly enhanced the growth of the SF3B1 mutant cells, suggestive of a dose dependent tumour suppressive effect.

Through synthetic-lethal drug screens we found that SF3B1MUT cells are selectively sensitive to PARP inhibitors. SF3B1MUT cells display a defective response to PARPi induced replication stress. Mechanistically, this occurs via defective ATR signalling in SF3B1MUT cells, which upon PARPi exposure leads to increased replication origin firing and loss of pChk1 (S317) induction. The resultant replication stress leads to failure to resolve DNA replication intermediates via the endonuclease MUS81 and cell cycle stalling at the G2/M checkpoint. These defects can be further targeted by ATM, CDK7 or FACT inhibition, when used in combination with PARPi treatment. This SF3B1MUT selective PARPi sensitivity is preserved across multiple cell lines and patient derived tumour models. In vivo, PARPi produce profound anti-tumour effects in multiple SF3B1MUT cancer models and eliminate distant metastases.

Conclusions: Our integrative analysis reveals mechanistic insight into the role of SF3B1 mutations in endocrine therapy response in ER+ breast cancers, where altered SF3B1 induces ER-transcriptional re-programming. We further identified a robust synthetic-lethal relationship of mutant SF3B1 with PARP inhibition that is caused by a defective response to PARPi induced replication stress. Furthermore, we identified several potential selective combination strategies together with PARPi that are selective for SF3B1MUT cells. Together, these data provide the pre-clinical and mechanistic rationale for assessing already-approved PARPi in a biomarker-defined subset of advanced ER+ BC.

Table 1. Identified potential therapies for SF3B1 mutant cancers from this study and the literature

Citation Format: Phil Bland, Harry Saville, Abigail Read, Patty Wai, Gareth Muirhead, Lucinda Curnow, Jadwiga Nieminuszczy, Nivedita Ravindran, Marie John, Somaieh Hedayat, Holly Barker, James Wright, Lu Yu, Ioanna Mavrommati, Barrie Peck, Mark Allen, Patrycja Gazinska, Helen Pemberton, Aditi Gulati, Sarah Nash, Farzana Noor, Naomi Guppy, Ioannis Roxanis, Samantha Barlow, Helen Kalirai, Sarah Coupland, Ronan Broderick, Samar Alsafadi, Alexandre Houy, Marc-Henri Stern, Stephen Pettit, Jyoti Choudhary, Syed Haider, Wojciech Niedzwiedz, Christopher Lord, Rachael Natrajan. Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-10-05.

Management of a spontaneously conceived live unilateral twin ectopic pregnancy in Australia: A case report

Introduction

Unilateral twin ectopic pregnancies are exceedingly rare, occurring in one in every 250,000 pregnancies. While clear guidelines exist regarding the management of singleton ectopic pregnancies, no such recommendations exist for multi-gestational ectopic pregnancies.

Case presentation

A 36-year-old woman, gravida 3 para 1, presented to the emergency department at 6 weeks and 4 days of gestation with a live twin ectopic pregnancy diagnosed on a dating ultrasound scan. Given the high likelihood of rupture, she underwent a laparoscopic salpingectomy and was discharged home the following day. The patient was followed-up with weekly serum β-hCG tests, to ensure there was no remaining pregnancy.

Discussion

While the morbidity and mortality associated with singleton ectopic pregnancies has gradually declined, the risk of rupture is higher in twin ectopic pregnancies and rupture is estimated to occur in 30–50% of cases. Surgical intervention remains the mainstay of treatment for these pregnancies.

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Unilateral live twin ectopic pregnancies are extremely rare.

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Five of 21 previously reported cases of unilateral live ectopic pregnancy were asymptomatic on diagnosis.

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No international guidelines specifically address multiple ectopic pregnancies.

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There are no reported cases of medical management of live unilateral ectopic pregnancy.

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Surgical intervention appears the most appropriate course of management.

Comet 81P/Wild 2 Under a Microscope

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.

Rapid protection of gnotobiotic pigs against experimental salmonellosis following induction of polymorphonuclear leukocytes by avirulent Salmonella enterica

Oral inoculation of 5-day-old gnotobiotic pigs with Salmonella enterica serovar Typhimurium strain F98 resulted in severe enteritis and invasive disease. Preinoculation 24 h earlier with an avirulent mutant of Salmonella enterica serovar Infantis (1326/28) completely prevented disease for up to 14 days (when the experiment was terminated). S. enterica serovar Infantis colonized the alimentary tract well, with high bacterial counts in the intestinal lumen but with almost no invasion into the tissues. Unprotected pigs had high S. enterica serovar Typhimurium counts in the intestines, blood, and major nonintestinal organs. Recovery of this strain from the blood and major organs in S. enterica serovar Infantis-protected pigs was substantially reduced despite the fact that intestinal counts were also very high. Protection against disease thus did not involve a colonization exclusion phenomenon. Significant (P < 0.05) infiltration of monocytes/macrophages was observed in the submucosal regions of the intestines of both S. enterica serovar Infantis-protected S. enterica serovar Typhimurium-challenged pigs and unprotected S. enterica serovar Typhimurium-challenged pigs. However, only polymorphonuclear neutrophils (PMNs) were observed throughout the villus, where significant (P < 0.05) numbers infiltrated the lamina propria and the subnuclear and supranuclear regions of the epithelia, indicating that PMN induction and positioning following S. enterica serovar Infantis inoculation was consistent with rapid protection against the challenge strain. Similarly, in vitro experiments using a human fetal intestinal epithelial cell line (INT 407) demonstrated that, although significantly (P < 0.05) fewer S. enterica serovar Infantis than S. enterica serovar Typhimurium organisms invaded the monolayers, S. enterica serovar Infantis induced an NF-kappaB response and significantly (P < 0.05) raised interleukin 8 levels and transmigration of porcine PMN. The results of this study suggest that attenuated Salmonella strains can protect the immature intestine against clinical salmonellosis by PMN induction. They also demonstrate that PMN induction is not necessarily associated with clinical symptoms and/or intestinal pathology.

The prevalence of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Bacteroides forsythus in humans 1 year after 4 randomized treatment modalities

The relationship between probing attachment changes in treated periodontal pockets and the prevalence of selected periodontal pathogens was assessed in 10 patients with adult periodontitis 1 year following randomized therapy. All patients had at least 1 tooth in each quadrant with an inflamed pocket of probing depth > or =5 mm and clinical attachment loss and harbored at least one of the following 3 major periodontal pathogens: Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, or Bacteroides forsythus. The number of target organisms per site was determined preoperatively; at 1 week; and at 1, 3, 6, and 12 months postoperatively utilizing DNA probes. The following clinical parameters were measured and recorded preoperatively and at 1, 3, 6, and 12 months post-treatment: gingival fluid flow, gingival index, plaque index, probing depth, probing attachment level, gingival recession, and bleeding on probing. One quadrant in each patient was randomly assigned to 1 of the following 4 treatments: 1) scaling and root planing; 2) pocket reduction through osseous surgery and apically-positioned flap; 3) modified Widman flap; and 4) modified Widman flap and topical application of saturated citric acid at pH 1 for 3 minutes. All 4 treatments were rendered in one appointment using local anesthesia. No postoperative antibiotics were used, but patients rinsed with 0.12% chlorhexidine for the first 3 months postoperatively and received a prophylaxis every 3 months. This investigation revealed: 1) 30.0% of the sites were infected by at least 1 species at 3, 6, and 12 months postoperatively. 2) Failing sites were infected by a high number of both Pg and Bf These sites had a mean of 24.2+/-9.0 x 10(3) Pg and 93.1+/-42.0 X 10(3) Bf while stable sites had a mean of 6.8+/-0.5 x 10(3) Pg and 7.2+/-1.2 x 10(3) Bf (P = 0.06 and P = 0.05, respectively). 3) The infected sites lost significantly more mean clinical attachment at 12 months (1.5+/-0.5 mm compared to a loss of 0.2+/-0.3 mm for uninfected sites, P = 0.017). 4) The infected sites had a significantly greater BOP (67+/-14% versus 25+/-8% for uninfected sites at 12 months, P = 0.012). 5) The choice of treatment modality did not affect the prevalence of the target species at 1 year post-treatment. These results suggest that prevalence of microbial pathogens negatively affects the 1 year outcome of periodontal surgical and nonsurgical therapy.

The survival rate of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Bacteroides forsythus following 4 randomized treatment modalities

The overall goal of this clinical study was to determine the short-term anti-infective effects of four randomized treatment modalities on Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Bacteroides forsythus (Bf) and determine the effects of bacterial survival on treatment outcomes in patients with adult periodontitis. Twelve adult patients requiring therapy for moderate periodontitis were selected for this study. All patients had at least one tooth in each quadrant that had an inflamed pocket of probing depth > or =5 mm with probing attachment loss that harbored at least one of the following three periodontal pathogens: Aa, Pg, or Bf. The number of target organisms per site was determined pre-operatively, at 1 week, and 1 month and 3 months postoperatively utilizing DNA probes. One quadrant in each patient was randomly assigned to each one of the following four treatment groups: 1) scaling and root planing (SRP group); 2) pocket reduction through osseous surgery and apically-positioned flap (OS group); 3) modified Widman flap (MWF group); and 4) modified Widman flap and topical application of saturated citric acid at pH 1 for 3 minutes (CA group). The 4 treatment modalities were performed in one appointment. No postoperative antibiotics were used. Patients were instructed to supplement their daily oral hygiene with chlorohexidine oral rinse during the study. The results of this investigation indicated that: 1) none of the treatment modalities was effective in eliminating the target species; 2) the incidence of infected sites for all groups was 100% preoperatively; 62.5%, 33.3%, and 31.3% at 1 week, and 1 and 3 months postoperatively, respectively; 3) these infected sites lost 1.1 +/- 0.4 mm of probing attachment compared to gain of 0.0 +/- 0.3 mm for uninfected sites; 4) the infected sites had higher plaque and bleeding on probing 0.9 +/- 0.3, 73 +/- 12%, respectively, compared to 0.3 +/- 0.1 and 30 +/- 8% for the uninfected sites; and 5) no statistically significant differences were detected among the infected sites in regard to gingival index (1.0 +/- 0.2 vs. 0.8 +/- 0.1) or probing depth (3.5 +/- 0.4 vs. 3.0 +/- 0.1 mm). These results indicate that bacterial survival negatively affects the short-term clinical outcomes of non-surgical and surgical periodontal therapy.

Retrospective correction of surface coil MR images using an automatic segmentation and modeling approach

The use of surface coils in magnetic resonance imaging offers significant improvements in the signal-to-noise ratio over volume coils for many applications. However, the inhomogeneous reception profile of surface coils hampers their usefulness by introducing significant nonuniformities or intensity variations which can vary by greater than six-fold across the sample. In this study, we evaluated an automatic technique for retrospective correction of intensity variations observed in a high-resolution surface coil MR image of the rat brain obtained using an adiabatic magnetic resonance imaging sequence. The images are shown to have a coefficient of variation less than 12% following application of this correction algorithm. This image intensity correction technique can be applied retrospectively to all data sets and corrects both sample/patient dependent effects (e.g. attenuation of overlying tissue) or sample independent effects (e.g. coil geometry or position). This approach should also prove valuable in improving regions of interest analysis, volume histograms and thresholding techniques.

Cytotoxic reactivity of gut lamina propria CD4+ alpha beta T cells in SCID mice with colitis

Polyclonal, mucosa-seeking memory/effector CD4+ T cells containing a large fraction of blasts activated in situ accumulate in the gut lamina propria of severe-combined immunodeficient (SCID) mice developing colitis after CD4+ T cell transplantation. CD4+ T cells isolated from different repopulated lymphoid tissues of transplanted SCID mice proliferate in vitro in the presence of interleukin (IL)-2 + IL-7. CD3 ligation enhances this cytokine-supported proliferation in CD4+ T cells from the spleen and the mesenteric lymph node of transplanted SCID mice; CD3 ligation suppresses the cytokine-supported proliferation in CD4+ T cells from the gut lamina propria in a cell density- and dose-dependent manner. Almost all CD4+ T cells from repopulated lymphoid tissues of transplanted SCID mice express CD95 (Fas) on the cell surface, and a large fraction of CD4+ T cells from the gut lamina propria of transplanted SCID mice express the Fas ligand on the surface. Gut lamina propria CD4+ T cells show Fas-dependent cytotoxicity. A large fraction of gut lamina propria CD4+ T cells that infiltrate the inflamed colon in transplanted SCID mice are activated in situ and many CD4+ T cells are apoptotic. Hence, a large fraction of colitis-inducing CD4+ T cells undergo activation-induced cell death in situ and can damage other cells through Fas-dependent cytotoxicity.

Identification of a molecule uniquely expressed on a gamma/delta TCR+ subset within bovine intestinal intraepithelial lymphocytes

An antigen has been identified, recognized by a novel monoclonal antibody CC45, which is expressed by a subpopulation of bovine gamma/delta T-cell receptor-positive (gamma/delta TCR+) T cells restricted in their distribution to the intestinal epithelium. This subset of intestinal intraepithelial lymphocytes (iIEL) which represented 8-29% of gamma/delta TCR+ T cells in the gut epithelium expressed CD45, CD3 and L-selectin; most of these cells were CD2- and CD8-. Electron microscopic studies of CC45+ cells revealed that they were large mononuclear leucocytes containing numerous mitochondria and smooth vesicles; a proportion of these contained membrane-bound dense granules. Immunoprecipitation of 125I-labelled iIEL analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis under reducing and non-reducing conditions revealed polypeptides of 60,000 and 200,000 molecular weights, respectively indicating that the antigen, which appears distinct from molecules described in other species, is expressed on the cell surface as a complex.

An analysis of selectivity bias in the Medicare AAPCC (adjusted average per capita cost)

Using econometric models of endogenous sample selection, we examine possible payment bias to Medicare Tax Equity and Fiscal Responsibility Act of 1982 (TEFRA) risk health maintenance organizations (HMOs) in the Twin Cities in 1988. We do not find statistically significant evidence of favorable HMO selection. In fact, the sign of the selection term indicates adverse selection into HMOs. This finding is interesting, in view of the fact that three of the five risk HMOs in the study have since converted to non-risk contracts.

Comparison of the requirement of porcine peripheral blood monocytes and intestinal lamina propria macrophages as accessory cells in primary allogeneic mixed leukocyte responses and oxidative mitogenesis

Differences and/or similarities of the accessory cell activity of circulating peripheral blood monocytes (PBM) and intestinal lamina propria macrophages (LPM) in the pig have never been evaluated. Therefore this study was designed to compare the accessory cell activity of these cells in the induction of primary allogeneic mixed leukocyte responses (MLR) and polyclonal mitogenesis. Splenic adherent cells (SPAC) were used as control accessory cells. It was observed that PBM, LPM and SPAC induced significant T cell proliferation in response to allo-antigens. Significantly higher responses were elicited by SPAC, followed by PBM whereas, LPM induced low responses when cultures were established a T cell: accessory cell ratio of 1:1. PBM was the only accessory cell which induced significant responses at a cell ratio of 10:1. Whereas LPM and SPAC were able to induce significant oxidative mitogenesis, PBM were poor stimulators of this response. The observed difference between PBM, SPAC and LPM is attributed partly to differences in number of major histocompatibility complex (MHC) class II positive cells and the intensity of expression of the glycoproteins.

The accessory cell activity of porcine intestinal macrophages in the induction of T cell responses

Although intestinal macrophages stimulated significant T cell responses to MHC class II antigens and polyclonalmitogens, they were weak stimulators of ovalbumin-driven responses. These cells showed numerous and large endocytic vacuoles, lysosomes and phagolysosomes which may be indicative of active phagocytosis during the isolation process. The poor antigen presenting activity of the cells in protein antigen-elicited may be an in vitro artifact attributed to acquired inefficiency in antigen uptake and/or processing.

Liver-tumor boundary detection: human observer vs computer edge detection

As a preliminary step in computing tumor volume, we developed a computer edge detection program to define the liver-tumor interface in computed tomography (CT) images. Computer program performance was tested using CT images from a lucite liver/tumor phantom; from normal livers containing computer-generated pseudotumors of known size, object contrast, and liver-tumor edge gradients; and from 12 abdominal livers containing 19 focal tumors, eight with well-defined and 11 with ill-defined borders. Calculated sizes of the tumor phantom and pseudo-tumors were compared with measured volumes and predetermined cross-sectional areas, respectively. In the absence of a truth standard for the size of the focal hepatic tumors, computer-calculated cross-sectional areas of the tumors were compared with the measurements made by an experienced interpreter of CT images using the trackball cursor at the CT console. The console measurements were made five times on separate days during a one-week period. The variability in the measured areas of these tumors averaged 7.1% for the well-defined tumors and 14.0% for the poorly defined tumors (P = 0.05). The edge-linking algorithm systematically overestimated the volumes of individual slices of the hemispherical tumors in the lucite phantom. Nevertheless, because of algorithm failure in the slices containing the poles of the hemispheres, errors in total tumor volumes were -2.1% for the 5.1 cm radius tumor, +1.2% for the 2.7 cm radius tumor, and +15% for the 1.8 cm radius tumor. The edge-linking algorithm was reasonably successful in calculating areas of pseudotumors with object contrast of 3.0% or greater and steep edge gradients.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of transmitted motion in fetal lung: quantitative analysis

A simple two-dimensional analytic model is evaluated for transmitted cardiac motion in fetal lung. The model treats the latter as being an incompressible viscoelastic medium. The mean radial deformation in an elastic medium is demonstrated to depend on a length parameter l approximately square root of mu/rho omega 2, where mu, rho, and omega correspond to elastic shear modulus, mass density, and frequency of cardiac motion, respectively. Digitized M-mode images are demonstrated as a feasible method to measure such deformations in vivo. Data for two patients are presented to illustrate the technique.

Adaptive histogram equalization in digital radiography of destructive skeletal lesions

Adaptive histogram equalization, an image-processing technique that distributes pixel values of an image uniformly throughout the gray scale, was applied to 28 plain radiographs of bone lesions, after they had been digitized. The non-equalized and equalized digital images were compared by two skeletal radiologists with respect to lesion margins, internal matrix, soft-tissue mass, cortical breakthrough, and periosteal reaction. Receiver operating characteristic (ROC) curves were constructed on the basis of the responses. Equalized images were superior to nonequalized images in determination of cortical breakthrough and presence or absence of periosteal reaction. ROC analysis showed no significant difference in determination of margins, matrix, or soft-tissue masses.

Ultrastructure of Babesia major vermicules from the tick Haemaphysalis punctata as demonstrated by negative staining

The ultrastructure of Babesia major vermicules was studied in samples derived from the haemolymph of Haemaphysalis punctata adults and negatively stained with phosphotungstic acid. Most of the organelles observed were typical of those found in apicomplexan parasites. These were the apical complex with the polar ring and the ribs, micronemes and subpellicular microtubules. The number of ribs was 27 or 28. The outer membrane of the pellicle was composed of a large number of fibrils running along the length of the parasite. The inner membrane had large numbers of irregularly scattered holes. A cytoplasmic organelle similar to the granular body described in Theileria annulata ookinetes was seen for the first time in a B. major vermicule.

The ultrastructure of penetrating stages of Babesia major infecting the ovary of Haemaphysalis punctata

The ultrastructure of penetrating stages of Babesia major merozoites responsible for causing trans-ovarian infection of the tick Haemaphysalis punctata was studied. These merozoites were different from forms of other Babesia species previously described in the tick in that they were highly pleomorphic. Most of the organelles found in these forms were similar to those found in other stages: however, the apical complex was found to be very active. Micronemes were found to be predominant in the cytoplasm of these merozoites and a cytoplasmic projection anterior to the polar ring and bounded by concentric rings was visible. A polar ring with radiating ribs, and microtubules was present. It is thought that the apical complex of these merozoites plays an important role in assisting the parasite to infect the ovary of the tick.

Ultrastructure of Babesia major in the tick Haemaphysalis punctata

Haemaphysalis punctata ticks were infected with Babesia major by allowing them to feed on an infected splenectomised calf. Heavily infected ticks were dissected and the guts and the ovaries were processed to study the ultrastructure of B major in these organs. The morphology of the parasites in the gut and the ovary was identical. It was shown that the parasite contained a reduced form of an apical complex consisting of characteristic organelles such as the polar ring, rhoptries, micronemes and microtubules. A primitive conoid was situated at the anterior end of the parasite and consisted of delicate helical rings. The occurrence of these organelles confirmed the inclusion of this parasite in the subphylum Apicomplexa.

Structural changes in the bovine nematode Haemonchus placei, that may be associated with host immune response

The structure of H. placei adult worms, obtained from calves at 4, 7, 10 or 11–13 weeks after primary infection, has been studied. A reorganization of rough endoplasmic reticuhim in the cytoplasm of the gut cells was seen at 10 weeks and this was followed by marked vacuolation of many of these cells, associated with an increase in lipid production. Increases of lipid were also found in the hypodermis, lateral cords and occasionally muscle cells of worms examined at 11–13 weeks after infection.

It is suggested that these changes are the result of the host immune response, because they resemble changes which occur in the rat nematode Nippostrongylus brasiliensis and which are known to be caused by host immunity.