Comparing nodal versus bony metastatic spread using tumour phylogenies

Lymph nodes: at the intersection of cancer treatment and progression

Metastasis to lymph nodes (LNs) is a common feature of disease progression in most solid organ malignancies. Consequently, LN biopsy and lymphadenectomy are common clinical practices, not only because of their diagnostic utility but also as a means of deterring further metastatic spread. LN metastases have the potential to seed additional tissues and can induce metastatic tolerance, a process by which tumor-specific immune tolerance in LNs promotes further disease progression. Nonetheless, phylogenetic studies have revealed that distant metastases are not necessarily derived from nodal metastases. Furthermore, immunotherapy efficacy is increasingly being attributed to initiation of systemic immune responses within LNs. We argue that lymphadenectomy and nodal irradiation should be approached with caution, particularly in patients receiving immunotherapy.

Common iliac node positive prostate cancer treated with curative radiotherapy: N1 or M1a?

PURPOSE

Common iliac (CI) nodes are staged as (oligo)metastatic M1a for prostate cancer. It is unclear if outcomes of pelvic node-positive (cN1) differ from CI node-positive (CI-M1a) prostate cancer after curative treatment. Present study compares outcomes in these patients treated with radical whole pelvic radiotherapy and long-term ADT.

MATERIALS AND METHODS

Patients with node positive adenocarcinoma prostate were identified, either CI-M1a or cN1, from a prospectively maintained database. Over 75% of these patients were staged with Ga68PSMA-PETCT at diagnosis. All patients received long-term ADT and moderately or extremely hypofractionated radiotherapy to the prostate and pelvis including the CI region. At biochemical failure (BCF), restaging was done with Ga68PSMA-PETCT to establish the patterns of failure. CI-M1a cohort was classified as proximal or distal CI nodal location and studied for outcomes.

RESULTS

Of the 130 patients analyzed, 87 had cN1 and 43 had CI-M1a stage. Median duration of ADT before RT was 7 months and total duration was atleast 24 months. Majority (65%) had Gleason grade group IV-V while 75% had ≥T3 disease. After a median FU of 61 months, BCF in the 2 groups were similar, cN1, 21/87 (24.1%); CI-M1a, 11/43 (25.6%), p=0.86. At BCF, restaging Ga68-PSMA-PET-CT located distant metastases in 20 (63%) of the 32 patients (57% in cN1, and 73% in CI-M1a, p=0.47). Five-year biochemical failure-free survival (cN1; 77.4% and CI-M1a; 70.4%, p=0.43), distant metastasis-free survival (cN1; 86.9% and CI-M1a; 79.4%, p=0.23) and overall survival (cN1 92.6% and CI-M1a 90.1%, p=0.80) were similar in the two groups. Outcomes within CI-M1a were similar for proximal versus distal CI nodal location, 5-year BFFS 73.6% vs 58.6% (p=0.81).

CONCLUSION

Oligometastatic CI-M1a and cN1 prostate cancer patients showed similar outcomes when treated with curative whole pelvic radiotherapy and long-term ADT. The treatment for these 'oligometastatic' patients should be prospectively evaluated and optimized accordingly.

Lymph node colonization induces tumor-immune tolerance to promote distant metastasis

For many solid malignancies, lymph node (LN) involvement represents a harbinger of distant metastatic disease and, therefore, an important prognostic factor. Beyond its utility as a biomarker, whether and how LN metastasis plays an active role in shaping distant metastasis remains an open question. Here, we develop a syngeneic melanoma mouse model of LN metastasis to investigate how tumors spread to LNs and whether LN colonization influences metastasis to distant tissues. We show that an epigenetically instilled tumor-intrinsic interferon response program confers enhanced LN metastatic potential by enabling the evasion of NK cells and promoting LN colonization. LN metastases resist T cell-mediated cytotoxicity, induce antigen-specific regulatory T cells, and generate tumor-specific immune tolerance that subsequently facilitates distant tumor colonization. These effects extend to human cancers and other murine cancer models, implicating a conserved systemic mechanism by which malignancies spread to distant organs.

Allele-specific multi-sample copy number segmentation in ASCAT

MOTIVATION

Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other.

RESULTS

Here, we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT.

AVAILABILITY AND IMPLEMENTATION

asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.

Is there a utility of adding skeletal imaging to 68-Ga-prostate-specific membrane antigen-PET/computed tomography in initial staging of patients with high-risk prostate cancer?

PURPOSE

Both bone-scan and cross-sectional imaging are indicated in the staging of high-risk prostate cancer (PCa). However, 68Ga-prostate-specific membrane antigen (PSMA)-PET/computed tomography (CT) has proven to be an excellent tracer for detection of skeletal metastases. The aim of this study was to assess if adding skeletal imaging (with 18F-Fluoride-PET/CT) to 68-Ga-PSMA-PET/CT had any impact on high-risk PCa staging.

METHOD

Fifty treatment-naive, histopathologically proven, high-risk (European Association of Urology) PCa patients underwent both 68-Ga-PSMA-PET/CT and 18F-Fluoride-PET/CT for staging.

RESULTS

Fluoride-PET/CT detected significantly a higher number of skeletal metastases/patient than PSMA-PET/CT (median 4.5/patient vs 3.0; Wilcoxan-signed-rank-test, P = 0.060) and there was a significantly higher proportion of only Fluoride-avid than only PSMA-avid lesions (McNemar-test P < 0.001). No significant advantage was seen in patient-wise metrics. Most lesions missed by PSMA-PET/CT were in flat bones (25/33). serum prostate specific antigen (S.PSA) showed positive correlation with both, the number of lesions [r(PSMA)-0.555 (P = 0.006) and r(Fluoride)-0.622 (P = 0.001)] as well as tumor to background ratio (TBR) [[r-0.706 (P < 0.001) and 0.516 (P = 0.010)]. Median TBR was significantly higher in PSMA-PET/CT (22.77 vs 16.30; P < 0.001). All three patients with only Fluoride-avid lesions (also not identified in bone-scan) showed biochemical response with additional therapy.

CONCLUSION

Though, Fluoride-PET/CT detected a higher absolute number of lesions than PSMA-PET/CT, no significant advantage was seen in patient-wise metrics. Fluoride-PET/CT added second-line management in only 3/50 patients, which could have been reduced to 1/50, with more sensitive evaluation of flat bones in PSMA-PET-CT. Therefore, additional skeletal imaging is not needed with 68-Ga-PSMA-PET/CT in initial staging of high-risk PCa.

Genomic and phenotypic heterogeneity in prostate cancer

From a clinical, morphological and molecular perspective, prostate cancer is a heterogeneous disease. Primary prostate cancers are often multifocal, having topographically and morphologically distinct tumour foci. Sequencing studies have revealed that individual tumour foci can arise as clonally distinct lesions with no shared driver gene alterations. This finding demonstrates that multiple genomically and phenotypically distinct primary prostate cancers can be present in an individual patient. Lethal metastatic prostate cancer seems to arise from a single clone in the primary tumour but can exhibit subclonal heterogeneity at the genomic, epigenetic and phenotypic levels. Collectively, this complex heterogeneous constellation of molecular alterations poses obstacles for the diagnosis and treatment of prostate cancer. However, advances in our understanding of intra-tumoural heterogeneity and the development of novel technologies will allow us to navigate these challenges, refine approaches for translational research and ultimately improve patient care.

Rationale for Involved Field Stereotactic Body Radiation Therapy-Enhanced Intermittent Androgen Deprivation Therapy in Hormone-Sensitive Nodal Oligo-Recurrent Prostate Cancer Following Prostate Stereotactic Body Radiation Therapy

Lymph node recurrent prostate cancer is a common clinical scenario that is likely to increase significantly with the widespread adoption of novel positron emission tomography (PET) agents. Despite increasing evidence that localized therapy is disease modifying, most men with lymph node recurrent prostate cancer receive only systemic therapy with androgen deprivation therapy (ADT). For men who receive localized therapy the intent is often to delay receipt of systemic therapy. Little evidence exists on the optimal combination of local and systemic therapy in this patient population. In this hypothesis generating review, we will outline the rationale and propose a framework for combining involved field SBRT with risk adapted intermittent ADT for hormone sensitive nodal recurrent prostate cancer. In patients with a limited number of nodal metastases, involved field stereotactic body radiation therapy (SBRT) may have a role in eliminating castrate-resistant clones and possibly prolonging the response to intermittent ADT. We hypothesize that in a small percentage of patients, such a treatment approach may lead to long term remission or cure.

CHD1 loss negatively influences metastasis-free survival in R0-resected prostate cancer patients and promotes spontaneous metastasis in vivo

The outcome of prostate cancer (PCa) patients is highly variable and depends on whether or not distant metastases occur. Multiple chromosomal deletions have been linked to early tumor marker PSA recurrence (biochemical relapse, BCR) after radical prostatectomy (RP), but their potential role for distant metastasis formation is largely unknown. Here, we specifically analyzed whether deletion of the tumor suppressor CHD1 (5q21) influences the post-surgical risk of distant metastasis and whether CHD1 loss directly contributes to metastasis formation in vivo. By considering >6800 patients we found that the CHD1 deletion negatively influences metastasis-free survival in R0 patients (HR: 2.32; 95% CI: 1.61, 3.33; p < 0.001) independent of preoperative PSA, pT stage, pN status, Gleason Score, and BCR. Moreover, CHD1 deletion predicts shortened BCR-free survival in pT2 patients and cancer-specific survival in all patients. In vivo, CHD1 loss increases spontaneous pulmonary metastasis formation in two distinct PCa models coupled with a higher number of multicellular colonies as compared to single-cell metastases. Transcriptome analyses revealed down-regulation of the PCa-specific metastasis suppressor and TGFβ signaling regulator PMEPA1 after CHD1 depletion in both tested PCa models. CHD1 loss increases the risk of postoperative metastasis in R0-resected PCa patients and promotes spontaneous metastasis formation in vivo.

Patterns of Lymph Node Failure in Patients With Recurrent Prostate Cancer Postradical Prostatectomy and Implications for Salvage Therapies

PURPOSE

There is increasing use of radical prostatectomy to treat patients with high-risk prostate cancer. This has contributed toward a pathologic stage migration, and a greater number of patients are subsequently being diagnosed with biochemical failure. There is increasing use of advanced imaging techniques in the setting of biochemical failure, including positron emission tomography-computed tomography (PET-CT).

METHODS AND MATERIALS

This critical literature review highlights the evidence for PET-CT in postprostatectomy biochemical failure and identifies sites of pelvic lymph node relapse in the setting of biochemical failure and the potential implications that the locations of these relapses may have for salvage therapies. Potential future directions are then considered.

RESULTS

The optimal PET-CT tracer remains uncertain but there is increasing use of prostate-specific membrane antigen PET-CT for investigating sites of nodal metastasis at low prostate-specific antigen levels, and this is leading to a blurring of the biochemical and radiologic recurrence phases. The optimal therapeutic approach remains undefined, with current trials investigating postoperative radiation therapy to the whole pelvis in addition to the prostatic fossa, the use of PET-CT in the setting of biochemical recurrence to guide delivery of salvage radiation therapy, and, for patients with node-only relapsed prostate cancer, the addition of whole pelvis radiation therapy to metastasis-directed therapies such as stereotactic ablative radiotherapy.

CONCLUSIONS

The most appropriate target volume for salvage radiation therapy remains uncertain, and the findings of studies using PET-CT to map nodal recurrences suggest that there could be a role for extending whole pelvis radiation therapy volumes to increase coverage of superior nodal regions. The emerging fields of radiomics and radiogenomics could provide important prognostic information and aid decision making for patients with relapsed prostate cancer.

Copy number evolution with weighted aberrations in cancer

MOTIVATION

Copy number aberrations (CNAs), which delete or amplify large contiguous segments of the genome, are a common type of somatic mutation in cancer. Copy number profiles, representing the number of copies of each region of a genome, are readily obtained from whole-genome sequencing or microarrays. However, modeling copy number evolution is a substantial challenge, because different CNAs may overlap with one another on the genome. A recent popular model for copy number evolution is the copy number distance (CND), defined as the length of a shortest sequence of deletions and amplifications of contiguous segments that transforms one profile into the other. In the CND, all events contribute equally; however, it is well known that rates of CNAs vary by length, genomic position and type (amplification versus deletion).

RESULTS

We introduce a weighted CND that allows events to have varying weights, or probabilities, based on their length, position and type. We derive an efficient algorithm to compute the weighted CND as well as the associated transformation. This algorithm is based on the observation that the constraint matrix of the underlying optimization problem is totally unimodular. We show that the weighted CND improves phylogenetic reconstruction on simulated data where CNAs occur with varying probabilities, aids in the derivation of phylogenies from ultra-low-coverage single-cell DNA sequencing data and helps estimate CNA rates in a large pan-cancer dataset.

AVAILABILITY AND IMPLEMENTATION

Code is available at https://github.com/raphael-group/WCND.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone

The latency associated with bone metastasis emergence in castrate-resistant prostate cancer is attributed to dormancy, a state in which cancer cells persist prior to overt lesion formation. Using single-cell transcriptomics and ex vivo profiling, we have uncovered the critical role of tumor-intrinsic immune signaling in the retention of cancer cell dormancy. We demonstrate that loss of tumor-intrinsic type I IFN occurs in proliferating prostate cancer cells in bone. This loss suppresses tumor immunogenicity and therapeutic response and promotes bone cell activation to drive cancer progression. Restoration of tumor-intrinsic IFN signaling by HDAC inhibition increased tumor cell visibility, promoted long-term antitumor immunity, and blocked cancer growth in bone. Key findings were validated in patients, including loss of tumor-intrinsic IFN signaling and immunogenicity in bone metastases compared to primary tumors. Data herein provide a rationale as to why current immunotherapeutics fail in bone-metastatic prostate cancer, and provide a new therapeutic strategy to overcome the inefficacy of immune-based therapies in solid cancers.

Role of Para-aortic Radiotherapy in the Management of Prostate Cancer

Recent studies assessing the patterns of failure following locoregional definitive therapy suggest that recurrences do happen in the adjacent most proximal drainage sites, not infrequently occurring within the common iliac and para-aortic regions. This pattern of recurrence and identification at initial presentation is being increasingly recognised using novel imaging techniques and there is limited evidence on how to manage these patients. We are awaiting definitive evidence regarding the clinical benefit of whole pelvic radiotherapy, and currently there is no consensus as to the optimal superior border. There is some acknowledgement that the superior border should encompass the common iliac nodal region. However, whether it should be extended even more proximally is currently unknown. Prospective randomised trials are required to determine if there is a role for extending the radiotherapy field in patients with or at high risk of para-aortic metastases.

Frequent clonal relations between metastases and non-index prostate cancer lesions

Primary prostate cancer lesions are clonally heterogeneous and often arise independently. In contrast, metastases were reported to share a monoclonal background. Because prostate cancer mortality is the consequence of distant metastases, prevention of metastatic outgrowth by primary tumor ablation is the main focus of treatment for localized disease. Focal therapy is targeted ablation of the primary index lesion, but it is unclear whether remaining primary lesions metastasize at a later stage. In this study, we compared copy number aberration profiles of primary prostate cancer lesions with matching pelvic lymph node metastases of 30 patients to establish clonality between a lymph node metastasis and multiple primary lesions within the same patient. Interestingly, in 23.3% of the cases, the regional metastasis was not clonally linked to the index primary lesion. These findings suggest that focal ablation of only the index lesion is potentially an undertreatment of a significant proportion of prostate cancer patients.

Decomposing the subclonal structure of tumors with two-way mixture models on copy number aberrations

Multistage tumorigenesis is a dynamic process characterized by the accumulation of mutations. Thus, a tumor mass is composed of genetically divergent cell subclones. With the advancement of next-generation sequencing (NGS), mathematical models have been recently developed to decompose tumor subclonal architecture from a collective genome sequencing data. Most of the methods focused on single-nucleotide variants (SNVs). However, somatic copy number aberrations (CNAs) also play critical roles in carcinogenesis. Therefore, further modeling subclonal CNAs composition would hold the promise to improve the analysis of tumor heterogeneity and cancer evolution. To address this issue, we developed a two-way mixture Poisson model, named CloneDeMix for the deconvolution of read-depth information. It can infer the subclonal copy number, mutational cellular prevalence (MCP), subclone composition, and the order in which mutations occurred in the evolutionary hierarchy. The performance of CloneDeMix was systematically assessed in simulations. As a result, the accuracy of CNA inference was nearly 93% and the MCP was also accurately restored. Furthermore, we also demonstrated its applicability using head and neck cancer samples from TCGA. Our results inform about the extent of subclonal CNA diversity, and a group of candidate genes that probably initiate lymph node metastasis during tumor evolution was also discovered. Most importantly, these driver genes are located at 11q13.3 which is highly susceptible to copy number change in head and neck cancer genomes. This study successfully estimates subclonal CNAs and exhibit the evolutionary relationships of mutation events. By doing so, we can track tumor heterogeneity and identify crucial mutations during evolution process. Hence, it facilitates not only understanding the cancer development but finding potential therapeutic targets. Briefly, this framework has implications for improved modeling of tumor evolution and the importance of inclusion of subclonal CNAs.

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples

Cancer is an evolutionary process driven by somatic mutations. This process can be represented as a phylogenetic tree. Constructing such a phylogenetic tree from genome sequencing data is a challenging task due to the many types of mutations in cancer and the fact that nearly all cancer sequencing is of a bulk tumor, measuring a superposition of somatic mutations present in different cells. We study the problem of reconstructing tumor phylogenies from copy-number aberrations (CNAs) measured in bulk-sequencing data. We introduce the Copy-Number Tree Mixture Deconvolution (CNTMD) problem, which aims to find the phylogenetic tree with the fewest number of CNAs that explain the copy-number data from multiple samples of a tumor. We design an algorithm for solving the CNTMD problem and apply the algorithm to both simulated and real data. On simulated data, we find that our algorithm outperforms existing approaches that either perform deconvolution/factorization of mixed tumor samples or build phylogenetic trees assuming homogeneous tumor samples. On real data, we analyze multiple samples from a prostate cancer patient, identifying clones within these samples and a phylogenetic tree that relates these clones and their differing proportions across samples. This phylogenetic tree provides a higher resolution view of copy-number evolution of this cancer than published analyses.