Filmer Family NET report update 6/9/2023
PI: Prof. Martyn Caplin ‘MC’ (RFH/UCL) PI: Prof. Krista Rombouts ‘KR’ (UCL/RF ILDH)
Academic supervision: Dr Daniel Krell ‘DK’ (RFH) Dr Dalvinder Mandair ‘DM’ (RFH)
Collaborator: Dr TuVinh Luong ‘TL' (RFH- NET Histopathology)
Clinical Research Fellow: Dr Saiji Nageshwaran (RFH/PhD UCL Division of Medicine: official enrolment date 1/7/2023)
Primary project proposal: A comprehensive evaluation of the genetic and epigenetic landscape of World Health Organisation (WHO) Grade 3 Gastroenteropancreatic Neuroendocrine Carcinoma (GEP-NEC) ‘GETGEPNEC’
Lay version: a laboratory-based study analysing the genetic make-up of a rare form of aggressive type of neuroendocrine cancer arising from the organs of the digestive system in order to identify targets for treatment.
Establishing a database:
1. Identification of 799 histopathologically confirmed cases of neuroendocrine carcinoma (all visceral sites) FFPE tissue samples in storage RFH Histopathology laboratory (10 years to 31/12/2022) (TL and SN)
2. Data cleaning and coding: retrospective case note review to identify pure GEP-NEC histology, pseudoanoymised demographic data, site of origin, performance status at diagnosis, lines of interventions (surgery/systemic anti-cancer therapy/directed therapies), time to treatment failure, progression free survival, overall survival). Open Source code: https://github.com/Drsaijin87/Data-Capture-Form-GEPNEC-V1.git (SN)
3. To date: 48 cases identified for potential interrogation (access restricted)
Lay version: reviewing 799 medical reports from surgeries and biopsies to identify patients with this type of tumour, collecting relevant information related to these patients (e.g age, sex, ethnicity, organs affected, type of treatment, time on that treatment, effectiveness of treatment, survival e.t.c) and creating a programme to collect this information for a machine to analyse alongside the findings of laboratory work that will be done on their tumour tissue
Project progress:
1. Protocol refinement: addition of spatial transcriptomics and proteomics with newly acquired (ILDH), FFPE compatible, high throughput sequencing technologies GeoMx Digital Spatial Profiler (DSP) and CosMx Spatial Molecular Imager (SMI). Expected delivery 10/2023.
2. Sponsor acquisition (UCL- Joint Research Office) Research Ethical Approval and Integrated Research Application System (IRAS number 329209) submission (in progress) (SN, KR, MC, DK, DM). Approval expected: 13/9/2023
3. Wet laboratory work in preparation for work on tumour tissue (SN overseen by KR)
1. Tissue culture with LX2 cell line (Hepatic Stellate Cells) – overexpression and silencing of genes in cell culture, refining technique/ homogenising and optimising extraction FFPE protocols
2. DNA and RNA extraction with Promega and Qiagen kits
3. Nanodrop, QuBit use and interpretation
4. Assistance with SI NET mesenteric fibrosis lab project (overlapping methods)- handling of fresh tumour tissue: resection, isolation of cancer associated fibroblasts, Cytospin technique, liquid nitrogen storage
Lay version: new, state of the art, machines have been acquired that will improve the rigor of the genetic analyses and will be used to complement established methods we have been working on. In parallel, the study is being examined for its scientific and ethical integrity by UCL Joint Research Office (study sponsor) the Health Research Authority before consenting patients can commence. Whilst these processes take place, SN has been building his repertoire of laboratory techniques required for work with cancer tissue, (under KR’s supervision) to allow expedient processing of tumour tissue once approvals are granted.
Literature review:
Extensive systematic literature review of GEPNEC- SN, MC, KR, TL, DK, DM) and further review articles in preparation:
1. Molecular and Therapeutic Targets in Grade 3 Neuroendocrine Tumours and Carcinomas and then (SN, DK, KR, MC)
2. Current understanding and potential for manipulation of the microbiome to affect neuroendocrine tumour biology and therapy. (SN, DM, DK, KR, MC, AS)
Provisional submission date 1/10/2023 (Clinical Cancer Research or Nature Reviews Clinical Oncology or Frontiers)
Lay version: the entire existing body of research articles related to this study (to 31/12/22) have been reviewed and compiled to establish what is known and not known in this area (restricted to humans and written in English) and has been used to generate the study objectives. This will form the first chapter of SN’s PhD Thesis and will be published in a scientific journal.
Project evolution: prospective recruitment to RFH-UCL Biobank with assessment of intratumoral and gut microbiome (GEMGEPNEN)
Collaborators: Prof Andrew Smith ‘AS’ and Dr Silke Rath ‘SR' (Microbial diseases, UCL Eastman Dental Institute, RFH Campus).
11/3/2023: initial meeting to discuss feasibility of incorporating microbiome and metabolic assessment in newly diagnosed NET patients in the following groups, forming the rationale for review article 2 and increasing understanding of its role in the pathobiology of NET, with potential for therapeutic manipulation:
A.
Small intestinal NET with Desmoplasia. Stable SSTA. No right hemicolectomy.
Small intestinal NET NO desmoplasia. Stable SSTA. No right hemicolectomy
B.
New diagnosis NET, Naïve to therapy. i. Non-functional Pancreas and ii. non-functional SI NET PRE-SSTA. Then 12 weeks POST SSTA.
C.
High grade NET G3 or NEC G3, any type could include (G2 Pancreas?). PRE and POST chemotherapy 1, 3, 6 months.
D.
Small intestinal NET. Stable SSTA. PRE AND POST Right hemicolectomy 1, 3 and 6 months
E.i
Pancreatic NET. Stable SSTA. PRE and POST PRRT 1, 3, 6 and 12 months
E.ii
Small Intestinal NET. Stable SSTA. PRE and POST PRRT 1, 3, 6 and 12 months
Current status: pending ethical and R&D approval from UCL-RFH biobank- expected 9/2023 (see separate IRAS form and protocol attached) (DM, MC, AS, KR, SN, RS, DK)
Projections to January 1st 2024
1) Readout from comprehensive multi-omic (genetic, epigenetic, spatial transcriptomic and proteomic analyses of first 10-20 recruited patient’s tumour tissue (GETGEPNEC study)
2) Readout from comprehensive multi-omic and microbiome analyses of first 10-20 consecutively and prospectively recruited NEN patients fresh tumour tissue, whole blood, saliva and faeces (GEMGEPNEN study)
3) Submission of early findings, where possible, as abstracts to European Neuroendocrine Tumour Society’s 21st Annual Conference by 22/11/2023, European Society of Medical Oncology Gastrointestinal Cancer Congress by 12/2023
4) Peer-reviewed publication of three articles in accepting scientific journals
Lay version: collaboration with Infectious Disease experts, to look at the role of the gut microbiome (a community of microorganisms living in our digestive system that have been shown to be important for immune health) within neuroendocrine tumours (as a whole). This is a new way of improving the effectiveness of immunotherapies in cancer and will provide insights in NETs, where it has not been investigated thoroughly. We will analyse the types and prevalence of different micro-organisms in participants faeces, saliva and blood at different time points in the standard treatment.