Abstract 4277: Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing

Background:

Tumour proliferation rate is a key phenotypic feature of cancer, with higher rates linked to poorer clinical outcomes. Thus far, proliferation rates have been measured using pathological or experimental techniques on bulk tumour samples. However, while tumours are heterogeneous compositions of distinct clones with varying levels of fitness, measuring the proliferation of individual clones has not been possible to date. We hypothesise that enabling the identification of the most proliferative clones would reveal genomic hallmarks of aggressive clones, or the prediction of their potential phenotype, e.g., metastatic potential.

Methods:

We have developed SPRINTER (Single-cell Proliferation Rate Inference in Neoplasms Through Evolutionary Routes), a novel computational method to measure proliferation rates in individual tumour clones using single-cell whole-genome DNA sequencing. To assess the accuracy and power of SPRINTER, we have also developed an experimental approach to DNA sequence >18,000 single cells, accurately separated in different DNA-replication phases. We have sequenced and applied SPRINTER to >10,000 non-small cell lung cancer cells from longitudinal and metastatic tumour samples within the TRACERx study and PEACE autopsy programme. We have further analysed published data from >10,000 breast cancer cells.

Results:

We demonstrate that SPRINTER can accurately identify subpopulations of cells with different proliferation rates using relatively small numbers of cells, in contrast to previous preliminary approaches. While our estimates are concordant with previous bulk experimental studies (5-40%), we importantly have identified clonal heterogeneity in proliferation rates. Using bulk analysis, we have identified patterns of dissemination of tumour clones in non-small cell lung cancer. Integrating this with single-cell data, our results indicate that more widely disseminating tumour clones have higher proliferation rates, suggesting a link between proliferation and dissemination potential. We additionally find that clones are more proliferative in the metastatic versus the primary setting. Furthermore, we have identified high proliferation clones that may have a selective advantage in a breast tumour, and have inferred that they likely arose recently in cancer evolution.

Conclusions:

We have developed a novel method that enables accurate identification of proliferation rates of individual tumour clones using single-cell DNA sequencing data, allowing the investigation of genomic hallmarks in highly proliferative clones that might lead to higher fitness.

Citation Format: Olivia Lucas, Sophie Ward, Rija Zaidi, Mark Hill, Emilia Lim, Haoran Zhai, Abigail Bunkum, Sonya Hessey, Michelle Dietzen, Andrew Rowan, Cristina Naceur-Lombardelli, Nnenna Kanu, Mariam Jamal-Hanjani, Charles Swanton, Simone Zaccaria. Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing. [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 4277.

Intratumoral CD8+ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer

CD8⁺ tumor-infiltrating lymphocytes with a tissue-resident memory T (T_RM) cell phenotype are associated with favorable prognosis in patients with triple-negative breast cancer (TNBC). However, the relative contribution of CD8⁺ T_RM cells to anti-tumor immunity and immune checkpoint blockade efficacy in breast cancer remains unknown. Here, we show that intratumoral CD8⁺ T cells in murine mammary tumors transcriptionally resemble those from TNBC patients. Phenotypic and transcriptional studies established two intratumoral sub-populations: one more enriched in markers of terminal exhaustion (T_EX-like) and the other with a bona fide resident phenotype (T_RM-like). Treatment with anti-PD-1 and anti-CTLA-4 therapy resulted in expansion of these intratumoral populations, with the T_RM-like subset displaying significantly enhanced cytotoxic capacity. T_RM-like CD8⁺ T cells could also provide local immune protection against tumor rechallenge and a T_RM gene signature extracted from tumor-free tissue was significantly associated with improved clinical outcomes in TNBC patients treated with checkpoint inhibitors.

Abstract 3620: Investigating the role of altered replication timing during tumor evolution in lung and breast cancer

Introduction: Faithful DNA replication is a key requirement for normal cell division which initiates from replication origins distributed throughout the genome. Not all origins initiate replication at the same time, generating a conserved temporal order of DNA replication (the replication timing program) which is cell and tissue type specific. The extent to which replication timing alters during malignant transformation and the resultant impact on the genomic landscape in cancer remains unclear. Here, we explored the landscape of altered replication timing in lung and breast cancer and the interplay between altered replication timing and genomic cancer evolution.

Methods: To characterize replication timing profiles, the Repli-Seq protocol was applied to 4 lung adenocarcinoma, 3 lung squamous cell carcinoma, and 4 breast cancer cell lines, as well as the cell-of-origin of each cancer type. Replication timing was measured as the log2-transformed ratio between early and late replicated reads in 50kb windows. To identify altered replication timing regions the log2-ratio of each cancer cell line was compared to its matched normal. Publicly available WGS and RNA-seq data from patients were used to investigate the relationship between replication timing and genomic alterations.

Results: We identified a systematic shift in replication timing from normal to cancer cell lines in 6%-17% of the genome, half of which were classified as late-to-early and half early-to-late replicated. We identified an increase in mutation load in early-to-late replicated regions in comparison to non-altered early replicated regions, whereas the opposite was true for late-to-early replicated regions. We observed a more prevalent shift in the mutational landscape in breast compared to lung cancer, suggesting that most mutations in breast cancer were accumulated after the alteration in replication timing. In addition, we identified known and novel mutational processes active in differently replicated parts of the genome. Furthermore, we observed an enrichment of APOBEC3-associated mutation clusters (omikli events) in early and late-to-early replicated regions. Recurrently gained copy number segments showed an enrichment in not-altered early replicated regions. Also, late-to-early replicated genes exhibited an increase in expression in cancer relative to normal, whereas early-to-late replicated genes exhibited a decrease in expression. Cancer type-specific cancer genes were enriched in late-to-early replicated regions that became up-regulated in cancer, whereas essential genes tended not to change their replication timing during malignant transformation.

Conclusion: We identified significant alterations in the replication timing program during malignant transformation which influence the genomic and transcriptomic landscape during tumor evolution.

Citation Format: Michelle Dietzen, Haoran Zhai, Olivia Lucas, Sophia Ward, Yanping Guo, Wei Ting-Lu, Oriol Pich, Simone Zaccaria, Charles Swanton, Nicholas McGranahan, Nnennaya Kanu. Investigating the role of altered replication timing during tumor evolution in lung and breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3620.

A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks

In mollusk aquaculture, a large number of Vibrio species are considered major pathogens. Conventional methods based on DNA amplification and sequencing used to accurately identify Vibrio species are unsuitable for monitoring programs because they are time-consuming and expensive. The aim of this study was, therefore, to develop the MALDI-TOF MS method in order to establish a rapid identification technique for a large panel of Vibrio species. We created the EnviBase containing 120 main spectra projections (MSP) of the Vibrio species that are potentially responsible for mollusk diseases, comprising 25 species: V. aestuarianus, V. cortegadensis, V. tapetis and species belonging to the Coralliilyticus, Harveyi, Mediterranei, and Orientalis clades. Each MSP was constructed by the merger of raw spectra obtained from three different media and generated by three collaborating laboratories to increase the diversity of the conditions and thus obtain a good technique robustness. Perfect discrimination was obtained with all of the MSP created for the Vibrio species and even for very closely related species as V. europaeus and V. bivalvicida. The new EnviBase library was validated through a blind test on 100 Vibrio strains performed by our three collaborators who used the direct transfer and protein extraction methods. The majority of the Vibrio strains were successfully identified with the newly created EnviBase by the three laboratories for both protocol methods. This study documents the first development of a freely accessible database exclusively devoted to Vibrio found in marine environments, taking into account the high diversity of this genus. KEY POINTS: • Development of a MALDI-TOF MS database to quickly affiliate Vibrio species. • Increase of the reactivity when faced with Vibrio associated with mollusk diseases. • Validation of MALDI-TOF MS as routine diagnostic tool.

Dominance Hierarchies in Marine Invertebrates

AbstractDominance hierarchies have been well studied in myriad terrestrial animals, but surprisingly little is known about hierarchies in marine invertebrates; examples are limited to a few species of decapod crustaceans and cephalopods. Is the marine environment less conducive to the establishment of dominance hierarchy structures, or does this just underline the lack of detailed behavioral information about most marine invertebrates? In this review, we highlight the published information about marine invertebrate dominance hierarchies, which involve ranks established through fights or displays. We focus on the method of hierarchy formation, examine the ecological implications of this population structure, and compare the habitat and behavioral characteristics of species that exhibit this behavior. Because dominance hierarchies can influence habitat use, population distributions, energetics, mating, resource exploitation, and population genetic structure, it is crucial to understand how this trait evolves and which species are likely to exhibit it. A better understanding of marine invertebrate hierarchies could change the way we think about population dynamics of some species and could have important implications for fisheries, conservation, or even modeling of social and economic inequality.

Management of Late Relapses After Chemotherapy in Testicular Cancer: Optimal Outcomes with Dose-intense Salvage Chemotherapy and Surgery

BACKGROUND

Late relapse (LR) in testicular cancer is defined as disease recurrence more than 2yr after primary treatment. Optimal management for this rare group is unknown.

OBJECTIVE

To identify prognostic factors relevant to outcomes in a large LR series following primary treatment with platinum-based chemotherapy.

DESIGN, SETTING, AND PARTICIPANTS

We performed a retrospective analysis of all patients treated for advanced testicular cancer within the Anglian Germ Cell Cancer Network between 1995 and 2016. We identified 53 cases of LR following initial treatment for metastatic disease with platinum-based chemotherapy, and collected data on patient and tumour characteristics, treatments, and outcomes.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Progression-free survival (PFS) and overall survival (OS) were calculated for all patients. Survival curves were plotted according to the Kaplan-Meier method and univariate analysis of descriptive variables was performed using the log-rank method.

RESULTS AND LIMITATIONS

Across the cohort, PFS at 36 mo was 41% and OS was 61%. Multiple factors were correlated with PFS. Use of dose-intense or high-dose chemotherapy was associated with better PFS compared to conventional-dose chemotherapy (PFS 48 vs 9.8 mo; p=0.0036). Resection of residual disease post-relapse chemotherapy was associated with better PFS (hazard ratio 3.46; p=0.0076). There was a nonsignificant trend towards worse PFS in very late (>7 yr) relapses. The study is limited by its retrospective nature and selection bias cannot be excluded.

CONCLUSIONS

This study provides new insight into prognostic factors in LR. It confirms that surgery is critical to optimal outcomes, and suggests that dose-intense or high-dose chemotherapy in multisite nonresectable disease should be considered wherever feasible.

PATIENT SUMMARY

We studied patients with testicular cancer that recurred at least 2yr after initial treatment with chemotherapy. We found that patients who are able to have surgery to remove cancer and who have more intensive chemotherapy may be more likely to live longer.

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses

The human skin microbiota is quantitatively dominated by Gram-positive bacteria, detected by both culture and metagenomics. However, metagenomics revealed a huge variety of Gram-negative taxa generally considered from environmental origin. For species affiliation of bacteria in skin microbiota, clones of 16S rRNA gene and colonies growing on diverse culture media were analyzed. Species-level identification was achieved for 81% of both clones and colonies. Fifty species distributed in 26 genera were identified by culture, mostly belonging to Actinobacteria and Firmicutes, while 45 species-level operational taxonomic units distributed in 30 genera were detected by sequencing, with a high diversity of Proteobacteria. This mixed approach allowed the detection of 100% of the genera forming the known core skin Gram-negative microbiota and 43% of the known diversity of Gram-negative genera in human skin. The orphan genera represented 50% of the current skin pan-microbiota. Improved culture conditions allowed the isolation of Roseomonas mucosa, Aurantimonas altamirensis and Agrobacterium tumefaciens strains from healthy skin. For proteobacterial species previously described in the environment, we proposed the existence of skin-specific ecotypes, which might play a role in the fine-tuning of skin homeostasis and opportunistic infections but also act as a shuttle between environmental and human microbial communities. Therefore, skin-associated proteobacteria deserve to be considered in the One-Health concept connecting human health to the health of animals and the environment.

Effect of PREDICT on chemotherapy/trastuzumab recommendations in HER2-positive patients with early-stage breast cancer

PREDICT is an online prognostication tool for early-stage breast cancer, which incorporates human epidermal growth factor 2 (HER2) status and stratifies absolute treatment benefits for hormone therapy, chemotherapy and trastuzumab. The present study compared historical multidisciplinary team (MDT) decisions regarding adjuvant treatment with PREDICT estimates, to determine whether certain patients are being over- or undertreated, particularly when stratified by age and oestrogen-receptor (ER) status. HER2-positive early-stage breast cancer cases over a five-year period at the Cambridge Breast Unit (Addenbrooke’s Hospital, Cambridge, UK) were retrospectively reviewed. Patients receiving neo-adjuvant therapy were excluded. Adjuvant chemotherapy/trastuzumab recommendations based on PREDICT (<3%, no benefit; 3–5%, discuss treatment; and >5%, recommend treatment) were compared with actual MDT decisions. In total, 109 eligible patients were identified. The average age at diagnosis was 59.6 years, with 21 patients older than 70 years (19%). Four patients were predicted to gain an absolute benefit of >5% from chemotherapy/ trastuzumab, but were not offered treatment (all >70 years). Amongst the 19 patients aged >70 years predicted to benefit >3%, six were not offered treatment (32%). In the patients aged <69 years, there was evidence of overtreatment with adjuvant chemotherapy/trastuzumab in 8 out of 12 cases with <3% benefit using PREDICT. For all 20 patients with ER-negative tumours, the MDT and PREDICT decisions correlated, whilst for ER-positive cases, more than half (8 out of 14) were offered treatment despite a <3% predicted benefit. PREDICT can aid decision-making in HER2-positive early-stage breast cancer by identifying older patients at risk of undertreatment with chemotherapy/trastuzumab, and by reducing the overtreatment of patients with little predicted benefit, particularly in ER-positive disease.

[Occipitalization of the atlas. Radiological diagnosis and clinical significance]

INTRODUCTION

Occipitalization of the atlas is the most common malformation of the craniovertebral junction. It can be diagnosed on lateral teleradiography and its finding imposes screening for associated atlantoaxial instability. In case of instability, brisk movements of the cervical spine during surgery may result in compression and distortion of the spinal chord and vertebro-basilar vascular system.

OBSERVATION

An 18 year-old female patient was referred to our department for facial dysmorphosis and extraction of the third molars. A lateral teleradiography revealed an occipitalization of the atlas and the fusion of the second and third cervical vertebral body. Further pre-operative investigations allowed ruling out any joint instability or associated craniovertebral junction malformations.

DISCUSSION

Occipitalization of the atlas is not usually well-known by maxillofacial surgeons. It may be diagnosed with a lateral teleradiography. Its diagnosis imposes screening for other spinal malformations (spinal fusion, hemivertebra, spina bifida occulta). The major risk is compression and distortion of the spinal chord and vertebro-basilar vascular system, during surgery or anesthesia.

[Buttocks sciatic pain]

Confusion between radicular and nerve trunk syndrome is not rare. With sciatic pain, any nerve trunk pain or an atypical nerve course should suggest nerve trunk pain of the sciatic nerve in the buttocks. The usual reflex with sciatic pain is vertebral-radicular conflict. The absence of spinal symptoms and the beginning of pain in the buttocks and not in the lumbar region should reorient the etiologic search. Once a tumor of the nerve trunk has been ruled out (rarely responsible for pain other than that caused by tumor pressure), a myofascial syndrome should be explored searching for clinical, electrophysiological, and radiological evidence of compression of the sciatic trunk by the piriform muscle but also the obturator internus muscle. Hamstring syndrome may be confused with this syndrome. Treatment is first and foremost physical therapy. Failures can be treated with classical CT-guided infiltrations with botulinum toxin. Surgery should only be entertained when all these solutions have failed.

[Somatic perineal pain other than pudendal neuralgia]

In addition to the well-established syndrome of pudendal compression, and given the rich nerve trunk innervation of the perineum, pain originating in other nerve trunks can occur and must be remembered. Nerves originating high in the thoracolumbar area (ilioinguinal nerve, iliohypogastric nerve, genitor femoral nerve) can be the seat of traumatic lesions occurring during surgical approaches through the abdominal wall or can undergo compressions when crossing the fascia of the large abdominal muscles. Misleading perineal irradiations do not resemble pudendal neuralgia and should suggest pain in these trunks whose cutaneous territories are not solely perineal and whose clinical expression as pain is does not occur in the seated position. Similarly, painful minor intervertebral dysfunction of the thoracolumbar junction is not simply in the mind and should be considered, searched for, and treated. Related more to pudendal neuralgia, pain in the inferior cluneal nerve, triggered by the seated position, should be considered when the pain reaches the lateral anal region, the scrotum, or the labia majora but not involving the glans penis or the clitoris. Specific treatments (physical therapy, infiltrations, surgery) have proven effective.

Role of endothelium in the modulation of isoflurane-induced vasodilatation in rat thoracic aorta

The mechanisms by which endothelium attenuates vasodilation caused by isoflurane are not well understood. We examined the role of endothelium-derived substances, nitric oxide (NO), endothelium-derived hyperpolarizing factors (EDHF), prostanoids and endothelins in the response to isoflurane in rat thoracic aorta. Increasing cumulative concentrations of isoflurane were administered to aortic rings suspended in Hepes solution and preconstricted with either phenylephrine 10(-6) mol litre-1 or KCl 40 mmol litre-1 (which inhibit EDHF). Rings were intact, denuded or incubated with an inhibitor of nitric oxide synthesis (N omega-nitro-L-arginine (LNNA 5 x 10(-5) mol litre-1), an inhibitor of prostanoid synthesis (indomethacin 10(-5) mol litre-1) or a blocker of the vascular receptors to endothelins (cyclo (-D-trp-D-Asp-Pro-D-Val-Leu (BQ 123 10(-5) mol litre-1)- Endothelium attenuated isoflurane-induced vasodilation in KCl-constricted rings at concentrations of 4% (mean 95 (SEM 4)% vs 72 (4)%; P = 0.0005) and 5% (100 (4)% vs 80 (4)%; P = 0.0008) and in phenylephrine constricted rings at concentrations of 4% (54 (8)% vs 35 (3)%; P = 0.04) and 5% (78 (10)% vs 49 (5)%; P = 0.03). Relaxation was significantly greater in rings treated with LNNA than in intact rings at concentrations of 4% (85 (4)% vs 72 (4)%; P = 0.0005) and 5% (90 (4)% vs 80 (4)%; P = 0.0008). Indomethacin and BQ 123 did not alter isoflurane-induced vasodilation. We conclude that endothelium attenuated the vasodilator effect of isoflurane by a mechanism which was abolished by inhibition of nitric oxide. We hypothesize that isoflurane inhibits the release of nitric oxide, leading to a relative vasoconstriction counter-balancing its vasodilator effect. In contrast, EDHF, prostanoids and endothelins were not involved in the attenuation of isoflurane-induced vasodilatation.

[Cerebral abscess disclosing tetralogy of Fallot with situs inversus in adulthood]

The authors report the case of tetralogy of Fallot (TOF) associated with situs inversus, the first description of this rare association in a previously asymptomatic adult. A 32 years old chauffeur was admitted to hospital with pyrexia and convulsions due to a left temporo-parietal cerebral abscess which had a favourable outcome. The chest X-ray and Doppler echocardiographic study showed a TOF with a high infundibular stenosis and dextrocardia. Abdominal ultrasonography confirmed a complete situs inversus. The good tolerance was attributed to the equilibrated character of the TOF. The orientation of the heart and the cono-truncal septation occur at different times during embryogenesis. However, there are genetic arguments in favour of the non-fortuitous nature of this association.

Alpha-, beta-MHC mRNA quantification in adult cardiomyocytes by in situhybridization: effect of thyroid hormone

Cardiac myocytes isolated from adult rats and cultured for up to 5 days in a defined serum- and 3,5,3'-triiodothyronine-(T3) free medium were processed for in situ hybridization using [35S]cRNA probes specific for alpha- or beta-myosin heavy chain (MHC) mRNAs. A computer-assisted image analysis system was used to quantitate the hybridization signals within individual myocytes (100 cells/experimental point). The method was validated by comparison with dot-blot quantitation. The mean alpha-MHC mRNA density per cell decreased by 50% (P < 0.01) after 2 days in culture and remained stable thereafter, whereas the relative amount of beta-MHC mRNA did not increase until day 5. Addition of 10(-12) M T3 to the culture medium for 2 or 3 days was sufficient to maintain alpha-MHC mRNA levels similar to the day 0 values, whereas 10(-9) M T3 was necessary to completely inhibit beta-MHC mRNA expression. The independent analysis of myocytes exhibiting different morphological phenotypes with time in culture demonstrated that rounded myocytes contain relatively more alpha-MHC mRNA and were as sensitive to T3 as their rod-shaped counterparts. Their beta-MHC RNA content was similar to that found in rod-shaped cells and was still depressed by T3. In conclusion, we show that 1) physiological doses of T3 are sufficient to maintain in vitro a MHC phenotype close to that observed in vivo in adult, 2) the dose responsiveness of adult myocytes to T3 differs from that reported in neonatal myocytes, and 3) the alpha-MHC mRNA content and the T3 sensitivity of spheroidal myocytes imply that there is no alteration in their state of maturation.