Adaptive immune receptor features related to breast cancer tissue in Kenyan patients: high immunoglobulin gene expression and high levels of gamma-delta T-cells.

BACKGROUND: Characterization of the breast cancer (BC) immune response may provide information for a point of intervention, such as application of immunotherapeutic treatments. In this study, we sought to recover and characterize the adaptive immune receptor (IR) recombination reads from genomics files representing Kenyan patients, to better understand the immune response specifically related to those patients. METHODS: We used a previously applied algorithm and software to obtain productive IR recombination reads from cancer and adjacent normal tissue samples representing 22 Kenyan BC patients. RESULTS: From both the RNAseq and exome files, there were significantly more T-cell receptor (TCR) recombination reads recovered from tumor samples compared to marginal tissue samples. Also, the immunoglobulin (IG) genes were expressed at a much higher level than the TCR genes (p-value = 0.0183) in the tumor samples. And, the tumor IG CDR3s consistently represented more positively charged amino acid R-groups, in comparison to the marginal tissue, IG CDR3s. CONCLUSION: For Kenyan patients, a high level of IG expression, representing specific CDR3 chemistries, was associated with BC. These results lay the foundation for studies that could support specific immunotherapeutic interventions for Kenyan BC patients.

Cancer referrals at African Inland Church Kijabe Hospital, Kiambu County (2014-2020) and the impact of COVID-19.

In Kenya, cancer is the third leading cause of death. The African Inland Church Kijabe Hospital (AICKH) is a level 4 missionary hospital. The hospital serves the Kenyan population in many areas, including cancer care, and some of these services were affected during the coronavirus disease 2019 (COVID-19) pandemic. We aimed to leverage a recently established hospital-based cancer registry of patients treated at AICKH between 2014 and 2020 to describe the cancer cases and patient referral patterns seen at AICKH during the COVID-19 pandemic in 2020. A cross-sectional retrospective survey was conducted through medical records abstraction in the surgery, breast clinic, palliative care and pathology departments. A total of 3279 cases were included in the study, with females accounting for 58.1% of the cases. The top-three cancers overall were breast (23.0%), oesophagus (20.5%) and prostate (8.6%). There was a minimal increase in the number of cancer cases in 2020 (1.7%) compared with 2019, with an increase of 19.3% in 2019 compared with 2018. In conclusion, AICKH is one of the few hospitals in Kenya where a large number of cancer patients seek healthcare, and referral of cancer cases changed in 2020, which may be due to the COVID-19 pandemic. Future efforts can leverage this registry to determine the impacts of cancer diagnosis and treatment on survival outcomes.

A sample-to-answer COVID-19 diagnostic device based on immiscible filtration and CRISPR-Cas12a-assisted detection.

In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic and disparities of vaccination coverage in low-and middle-income countries, it is vital to adopt a widespread testing and screening programme, combined with contact tracing, to monitor and effectively control the infection dispersion in areas where medical resources are limited. This work presents a lab-on-a-chip device, namely 'IFAST-LAMP-CRISPR', as an affordable, rapid and high-precision molecular diagnostic means for detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The herein proposed 'sample-to-answer' platform integrates RNA extraction, amplification and molecular detection with lateral flow readout in one device. The microscale dimensions of the device containing immiscible liquids, coupled with the use of silica paramagnetic beads and guanidine hydrochloride, streamline sample preparation (including RNA extraction, concentration and purification) in 15 min with minimal hands-on steps. The pre-amplification in combination with CRISPR-Cas12a detection assays targeting the nucleoprotein (N) gene achieved visual identification of ≥ 470 copies mL-1 genomic SARS-CoV-2 samples in 45 min. On-chip assays showed the ability to isolate and detect SARS-CoV-2 RNA from 100 genome copies mL-1 of replication-deficient viral particles in 1 h. This simple, affordable and integrated platform demonstrated a visual, faster, and yet specificity- and sensitivity-comparable alternative to the costly gold-standard reverse transcription-polymerase chain reaction (RT-PCR) assay, requiring only a simple heating source. Initial testing illustrates the platform viability both on nasopharyngeal swab and saliva samples collected using the easily accessible Swan-brand cigarette filter, providing a complete workflow for COVID-19 diagnostics in low-resource settings.

Leveraging technology for health services continuity in times of COVID-19 pandemic: Patient follow-up, and mitigation of worse patient outcomes.

BACKGROUND: Since the outbreak of the COVID-19 pandemic in Wuhan, China, which has now spread globally, the health systems continue to face challenges in the provision of health care, there is a risk of exposure for both the physicians and the patients. While there is significant progress in the adoption of technology in health care. This study sought to examine the adverse effects of the measures put in place by the government to curb the spread of COVID-19 and come up with an intervention to prevent worse outcomes for chronic conditions. METHODS: Booking registers for four specialty clinics in Machakos Level 5 Hospital were reviewed to identify patients who missed clinic appointments for follow-up. An automated data collection tool (ODK-collect) was used for data collection. COVID-19 Machakos App was developed to facilitate follow-up and referral of patients to the nearest facilities, capturing and posting of information in real-time to a central database. The mobile App also facilitated the tracking of patients and aided doctors to give feedback on whether the patients reported to the referred facilities. The doctors were also able to capture doctors' notes on the patients' status while ensuring the confidentiality and privacy of the patients. An interactive dashboard was developed to generate analytics reports and summaries to monitor clinic attendance and trends in the provision of health care during the pandemic period. RESULTS: Register data showed 977 (81.5%) out of a total of 1199 patients had missed their scheduled appointments. Among the 977, 746 (76%) were residents of Machakos County and qualified for follow-up. Missed appointments varied by clinic: Cancer Clinic 12 (1.6) %), Diabetes Clinic 212 (28.4%), Hypertension 293 (39.3%), and Paediatrics Clinic 229 (30.7%). Contact was made and follow-up was attempted for 746 patients, of which 453 patients (60.7%) were successful. The follow-up distribution of the 453 patients varied by the clinic as follows: Cancer Clinic 10, Diabetes Clinic 146, Hypertension 185, and Paediatrics Clinic 112. During the follow-up process, 331 patients from diabetes and hypertension clinics were requested to choose a preferred or nearby facility to be referred to. 191 (58%) patients chose Machakos Level 5 Hospital as their preferred facility and 137 (41%) patients chose to be referred to level 3 or 4 hospitals within the County. Three deaths were reported from the medical (Hypertension) clinic. Through the developed App, a total, 82 (60%) patients out of the 137 were reviewed at the referral facilities jointly with a specialist at Machakos Level 5 Hospital. For the duration of the study, some patients reported worse conditions by the time of review after missing scheduled appointments. CONCLUSIONS: This intervention demonstrated that mobile phone technology could be leveraged to provide specialty treatment services remotely to mitigate against worse patient outcomes. The study reveals that there is a dire need to integrate technological interventions in the provision of health care services to ensure continuity.