The spectrum of TP53 mutations in Rwandan patients with gastric cancer

BACKGROUND

Gastric cancer is the sixth most frequently diagnosed cancer and third in causing cancer-related death globally. The most frequently mutated gene in human cancers is TP53, which plays a pivotal role in cancer initiation and progression. In Africa, particularly in Rwanda, data on TP53 mutations are lacking. Therefore, this study intended to obtain TP53 mutation status in Rwandan patients with gastric cancer.

RESULTS

Formalin-fixed paraffin-embedded tissue blocks of 95 Rwandan patients with histopathologically proven gastric carcinoma were obtained from the University Teaching Hospital of Kigali. After DNA extraction, all coding regions of the TP53 gene and the exon-intron boundary region of TP53 were sequenced using the Sanger sequencing. Mutated TP53 were observed in 24 (25.3%) of the 95 cases, and a total of 29 mutations were identified. These TP53 mutations were distributed between exon 4 and 8 and most of them were missense mutations (19/29; 65.5%). Immunohistochemical analysis for TP53 revealed that most of the TP53 missense mutations were associated with TP53 protein accumulation. Among the 29 mutations, one was novel (c.459_477delCGGCACCCGCGTCCGCGCC). This 19-bp deletion mutation in exon 5 caused the production of truncated TP53 protein (p.G154Wfs*10). Regarding the spectrum of TP53 mutations, G:C > A:T at CpG sites was the most prevalent (10/29; 34.5%) and G:C > T:A was the second most prevalent (7/29; 24.1%). Interestingly, when the mutation spectrum of TP53 was compared to three previous TP53 mutational studies on non-Rwandan patients with gastric cancer, G:C > T:A mutations were significantly more frequent in this study than in our previous study (p = 0.013), the TCGA database (p = 0.017), and a previous study on patients from Hong Kong (p = 0.006). Even after correcting for false discovery, statistical significance was observed.

CONCLUSIONS

Our results suggested that TP53 G:C > T:A transversion mutation in Rwandan patients with gastric cancer is more frequent than in non-Rwandan patients with gastric cancer, indicating at an alternative etiological and carcinogenic progression of gastric cancer in Rwanda.

Clinicopathological Characteristics and Mutational Landscape of APC, HOXB13, and KRAS among Rwandan Patients with Colorectal Cancer

Cancer research in Rwanda is estimated to be less than 1% of the total African cancer research output with limited research on colorectal cancer (CRC). Rwandan patients with CRC are young, with more females being affected than males, and most patients present with advanced disease. Considering the paucity of oncological genetic studies in this population, we investigated the mutational status of CRC tissues, focusing on the Adenomatous polyposis coli (APC), Kirsten rat sarcoma (KRAS), and Homeobox B13 (HOXB13) genes. Our aim was to determine whether there were any differences between Rwandan patients and other populations. To do so, we performed Sanger sequencing of the DNA extracted from formalin-fixed paraffin-embedded adenocarcinoma samples from 54 patients (mean age: 60 years). Most tumors were located in the rectum (83.3%), and 92.6% of the tumors were low-grade. Most patients (70.4%) reported never smoking, and 61.1% of patients had consumed alcohol. We identified 27 variants of APC, including 3 novel mutations (c.4310_4319delAAACACCTCC, c.4463_4470delinsA, and c.4506_4507delT). All three novel mutations are classified as deleterious by MutationTaster2021. We found four synonymous variants (c.330C>A, c.366C>T, c.513T>C, and c.735G>A) of HOXB13. For KRAS, we found six variants (Asp173, Gly13Asp, Gly12Ala, Gly12Asp, Gly12Val, and Gln61His), the last four of which are pathogenic. In conclusion, here we contribute new genetic variation data and provide clinicopathological information pertinent to CRC in Rwanda.

Abstract 2609: Non-CpG sites preference in G:C>A:T transition of TP53 in gastric cancer of Eastern Europe (Poland, Romania and Hungary) compared to East Asian countries (China and Japan) : gastric cancer in the world, mutation spectrum revisited

Aim: Mutation spectrum of TP53 in gastric cancer (GC) has been investigated world-widely, but a comparison of mutation spectrum among GCs from various regions in the world are still sparsely documented. In order to identify the difference of TP53 mutation spectrum in GCs in Eastern Europe and in East Asia, we sequenced TP53 in GCs from Eastern Europe, Lujiang (China), and Yokohama, Kanagawa (Japan) and identified the feature of TP53 mutations of GC in these regions.

Subjects and Method: In total, 689 tissue samples of GC were analyzed: 288 samples from East European populations (25 from Hungary, 71 from Poland and 192 from Romania), 268 from Yokohama, Kanagawa, Japan and 133 from Lujiang, Anhui province, China. DNA was extracted from FFPE tissue of Chinese, East European cases; and from frozen tissue of Japanese GCs. PCR products were direct-sequenced by Sanger method, and in ambiguous cases, PCR product was cloned and up to 8 clones were sequenced. We used No. NC_000017.11(hg38) as the reference sequence of TP53. Mutation patterns were categorized into nine groups: six base substitutions, insertion, deletion and deletion-insertion. Within G:C>A:T mutations the mutations in CpG and non-CpG sites were divided. Furthermore, 40 cases of Rwanda GC were compared in the world for mutation spectrum. The Cancer Genome Atlas data (TCGA, ver.R20, July, 2019) having somatic mutation list of GCs from Whites, Asians, and other ethnicities were used as a reference for our data.

Results: The most frequent base substitutions were G:C>A:T transition in all the areas investigated. The G:C>A:T transition in non-CpG sites were prominent in East European GCs, compared with Asian ones. Mutation pattern from TCGA data revealed the same trend between GCs from White (TCGA category) vs Asian countries. Chinese and Japanese GCs showed higher ratio of G:C>A:T transition in CpG sites and A:T>G:C mutation was more prevalent in Asian countries.

Conclusion: The divergence in mutation spectrum of GC in different areas in the world may reflect various pathogeneses and etiologies of GC, region to region. Diversified mutation spectrum in GC in Eastern Europe may suggest GC in Europe has different carcinogenic pathway of those from Asia. Whether the Rwanda pattern belong to Asian or East European would be interesting.

Citation Format: Hiroko Natsume, Kinga Szczepaniak, Hidetaka Yamada, Yuji Iwashita, Marta Gędek, Jelena Šuto, Rika Kasajima, Felix Manirakiza, Augustin Nzitakera, Rei Ishikawa, Eric Rutaganda, François Ngabonziza, Benoit Seminega, Placide Kamali, Vincent Dusabejambo, Belson Rugwizangoga, Nobuhito Nobuhito, Yaping Wang, Yohei Miyagi, Simona Gurzu, Haruhiko Sugimura. Non-CpG sites preference in G:C>A:T transition of TP53 in gastric cancer of Eastern Europe (Poland, Romania and Hungary) compared to East Asian countries (China and Japan) : gastric cancer in the world, mutation spectrum revisited [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 2609.

Compartmental mathematical modelling of dynamic transmission of COVID-19 in Rwanda

OBJECTIVES

Mathematical modelling is of interest to study the dynamics of coronavirus disease 2019 (COVID-19), and models such as SEIR (Susceptible-Exposed-Infected-Recovered) have been considered. This article describes the development of a compartmental transmission network model - Susceptible-Exposed-Quarantine-Infectious-Infectious, undetected-Infectious, home-based care-Hospitalized-Vaccinated-Recovered-Dead - to simulate the dynamics of COVID-19 in order to account for specific measures put into place by the Government of Rwanda to prevent further spread of the disease.

METHODS

The compartments of this model are connected by parameters, some of which are known from the literature, and others are estimated from available data using the least squares method. For the stability of the model, equilibrium points were determined and the basic reproduction number R 0 was studied; R ₀ is an indicator for contagiousness.

RESULTS

The model showed that secondary infections are generated from the exposed group, the asymptomatic group, the infected (symptomatic) group, the infected (undetected) group, the infected (home-based care) group and the hospitalized group. The formulated model was reliable and fit the data. Furthermore, the estimated R 0 of 2.16 shows that COVID-19 will persist without the application of control measures.

CONCLUSIONS

This article presents results regarding predicted spread of COVID-19 in Rwanda.

Analysis of COVID-19 mathematical model for predicting the impact of control measures in Rwanda

This paper shows the impact of control measures on the predictive COVID-19 mathematical model in Rwanda through sensitivity analysis of the basic reproduction number R 0 . We have introduced different levels of the control measures in the model, precisely, 90%, 80%, 60%, 40%, 20%, 0% and studied their effects on the variation of the model variables. The results from numerical simulations reveal that the more the adherence to the control measures at the percentage of 90%, 80%, 60%, 40%, 20%, 0%, the more the number of COVID-19 cases, hospitalized and deaths reduces which indicates the reduction of the spread of the pandemic in Rwanda. Moreover, It was shown that the transition rate from the infectious compartment is very sensitive to R 0 as the increase/decrease in its value increases/decreases the value of R 0 and this leads to the high spread or the containment of the pandemic respectively.

Abstract 41: International Collaborative Rwanda Endoscopy Week Conferences Demonstrate Feasibility and identify H. pylori Testing as an Important Target for Capacity-Building Interventions

Purpose: Gastrointestinal (GI) endoscopy is a growing field in Rwanda, a country of 12.6 million with significant GI morbidity and mortality. Endoscopy alongside Helicobacter pylori identification and eradication aids in GI cancer prevention and diagnosis in this population. Our collaborative training-focused endoscopy conference provides preliminary data to focus future training and capacity building programs in Rwanda to improve oncologic outcomes.

Methods: Since 2017, ‘Rwanda Endoscopy Week' (REW) is held annually at multiple hospitals throughout Rwanda. It consists of several days of didactic training in endoscopy, oncology and research, followed by a week of endoscopy procedures performed jointly by visiting and hosting endoscopists, and ending with a summary of results of didactic and endoscopic activity.

Results: Four (4) hospitals performed 244 training endoscopies in 2017 and 448 cases in 2018. In 2019 this expanded to 668 endoscopies performed at 7 hospitals, including academic, district, and private hospitals. The case distribution remained similar over 3 years at 86.0% (1170/1360) upper endoscopies, 13.2% (180/1360) colonoscopies, and 0.7% (10/1360) endoscopic retrograde cholangiopancreatographies. Thirty-nine (5.8%, 39/668) patients had a tumor finding suspicious for gastric (4.0%, 27/668), colorectal (1.5%,10/668), ampullary (0.1%, 1/668), or gallbladder (0.1%, 1/668) malignancy. 54% of patients receiving endoscopy were tested for H. Pylori (367/669); 38% of those tested had inconclusive results (141/367) and 20% were positive (74). There were 2 non-serious bleeding events.

Conclusions: Participation by Rwandan urban, district, public and private hospitals in a cooperative international GI training conference has experienced a nearly three-fold increase in patients and identified malignant pathology while maintaining safe endoscopic care over a three-year period. H. pylori, ubiquitous in this population, is an important risk factor for gastric cancer and gastric diseases. Necessary next steps include increased training and capacity-building interventions to improve the quality of the testing and surveillance of those treated.

Citation Format: Nikitha Gangasani, Eric Rutaganda, Felcien Shikama, Steve Bensen, Vincent Dusabejambo, Mary Chamberlin. International Collaborative Rwanda Endoscopy Week Conferences Demonstrate Feasibility and identify H. pylori Testing as an Important Target for Capacity-Building Interventions [abstract]. In: Proceedings of the 9th Annual Symposium on Global Cancer Research; Global Cancer Research and Control: Looking Back and Charting a Path Forward; 2021 Mar 10-11. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2021;30(7 Suppl):Abstract nr 41.

Proximal deep vein thrombosis among hospitalised medical and obstetric patients in Rwandan university teaching hospitals: prevalence and associated risk factors: a cross-sectional study

OBJECTIVES

To determine the prevalence of proximal deep vein thrombosis (DVT) by ultrasound scanning, as well as associated clinical features and known risk factors, among medical and obstetrics-gynaecology inpatients in two Rwandan tertiary hospitals.

DESIGN

Cross-sectional study.

SETTINGS

Rwanda teaching hospitals: Kigali and Butare University Teaching Hospitals.

PARTICIPANTS

901 adult patients admitted to the Departments of Internal Medicine and Obstetrics-Gynecology (O&G) who were at least 21 years of age and willing to provide a consent.

OUTCOMES

Prevalence of proximal DVT, clinical features and known risk factors associated with DVT.

METHODS

Between August 2015 and August 2016, participants were screened for DVT by compressive ultrasound of femoral and popliteal veins, conducted as a monthly cross-sectional survey of all consenting eligible inpatients. Patients completed a self-report survey on DVT risk factors. Prevalence of proximal DVT by compression ultrasonography was the primary endpoint, with univariate and multivariate regression analyses performed to assess associated clinical features and risk factors.

RESULTS

Proximal DVT was found in 5.5% of the study population, with similar rates in medical and O&G inpatients. The mean age was 41±16 SD (range, 21-91), 70% were female and 7% were pregnant. Univariate analysis showed active malignancy, immobilisation, prolonged recent travel and history of DVT to be significant risk factors for proximal DVT (all p values <0.05); while only active malignancy was an independent risk factor on multivariate regression (OR 5.2; 95% CI 2.0 to 13). Leg pain or tenderness, increased calf circumference, unilateral limb swelling or pitting oedema were predictive clinical features of DVT on both univariate analysis and multivariate regression (all p values <0.05).

CONCLUSION

Proximal DVT prevalence is high among hospitalised medical and O&G patients in two tertiary hospitals in Rwanda. For reducing morbidity and mortality, research to develop Africa-specific clinical prediction tools for DVT and interventions to increase thromboprophylaxis use in the region are urgently needed.

Feasibility Study of Molecular Profiling of Gastric Cancer Specimens From Rwanda

Abstract 51

Background:

Gastric cancer is associated with high mortality in Rwanda. Geographic or genetic differences may lead to variations in somatic mutations and novel therapies. Overseas collaboration to determine gastric cancer molecular profiles is paramount. We undertook this work to determine the feasibility of collaboration between researchers in Rwanda and the United States by creating a research platform for gastric and other cancers in Rwanda.

Methods:

Patients consented for biopsy. Cases that were confirmed as gastric adenocarcinoma were included. Formalin-fixed paraffin-embedded tissue blocks or eight unstained sections (4 μm) were transported to the United States. DNA extraction and library preparation was performed by using 50 ng gDNA. Samples were normalized, pooled, and sequenced by using the Pillar NGS SLIMamp Lung Hot Spot Panel (Pillar Biosciences, Natick, MA). FASTq files were uploaded to Pillar Biosciences to perform sequence alignment, annotation, and variant classification.

Results:

Fifty-seven samples were received and 35 were excluded because of low DNA yield or quality (18 and 17, respectively). Mutations were detected in nine (41%) of 22 samples. One sample contained three mutations, other cases had one to two mutations identified. In total, 12 mutations were identified: TP53 (four), SMAD4 (two), ERBB4 (two; S341L and D228N), PTEN (two; K267RfsTer9 and C136Y), FBXW7 (one), and KRAS (one).

Conclusion:

Overseas collaboration for the molecular profiling of gastric cancer samples is feasible. Quality improved with larger biopsies or tissue blocks. Frequency of mutations is lower than expected. ERBB4 mutations identified are not known to be pathogenic. PTEN mutations are considered pathogenic—a potential target for therapy in larger trials. A larger fusion panel may be more effective in identifying potential targets. Funding: Pillar Biosciences provided reagents for sequencing.

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

Mary D. Chamberlin Research Funding: Pillar Biosciences Belson Rugwizangoga No relationship to disclose Francine B. DeAbreu No relationship to disclose Eric Rutaganda No relationship to disclose Vincent Dusabejambo No relationship to disclose Oswald Habyarimana No relationship to disclose Steve Bensen No relationship to disclose Gregory J. Tsongalis Honoraria: Roche, ChromaCode, Foundation Medicine, Physician Choice Labs Consulting or Advisory Role: Baystate Health System, Jackson Laboratory for Genomic Medicine (Inst) Research Funding: Qiagen, Illumina, QuanDx, Leica Biosystems, Abbott Molecular, Affymetrix